Starting phenix.real_space_refine
on Fri Dec  8 06:19:15 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/12_2023/7n76_24221.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/12_2023/7n76_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 {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/12_2023/7n76_24221.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/12_2023/7n76_24221.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/12_2023/7n76_24221.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n76_24221/12_2023/7n76_24221.pdb"
  }
  resolution = 2.9
  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=   0.001 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
    Residue "A PHE  103": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  832": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7399
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1039, 7399
          Classifications: {'peptide': 1036, 'water': 3}
          Incomplete info: {'truncation_to_alanine': 176}
          Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963, None: 3}
            Not linked:
              pdbres="PRO A1168 "
              pdbres="HOH A1201 "
            Not linked:
              pdbres="HOH A1201 "
              pdbres="HOH A1202 "
            Not linked:
              pdbres="HOH A1202 "
              pdbres="HOH A1203 "
          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: {'GLN:plan1': 10, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 6, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 21}
          Unresolved non-hydrogen planarities: 347
  Time building chain proxies: 4.45, per 1000 atoms: 0.60
  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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.71
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.13
  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: 2.95

  Time building geometry restraints manager: 2.98 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:
       99.83 -   106.67: 278
      106.67 -   113.51: 4289
      113.51 -   120.35: 2727
      120.35 -   127.19: 2929
      127.19 -   134.03: 81
  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 2.440
  nonbonded pdb=" OE2 GLU A 172 "
            pdb=" NE2 GLN A 175 "
     model   vdw
     2.159 2.520
  nonbonded pdb=" NH1 ARG A 816 "
            pdb=" O   PRO A1167 "
     model   vdw
     2.239 2.520
  nonbonded pdb=" O   ASP A 325 "
            pdb=" OG1 THR A 391 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" O   PHE A 958 "
            pdb=" ND2 ASN A 962 "
     model   vdw
     2.311 2.520
  ... (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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          5.870
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     24.030
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  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:11.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.550
-------------------------------------------------------------------------------
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= 0.339
  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 : 5.80
  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 (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:  0.22 (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
   TRP   0.022   0.002   TRP A 100 
   HIS   0.014   0.001   HIS A 364 
   PHE   0.024   0.002   PHE A 958 
   TYR   0.052   0.002   TYR A 935 
   ARG   0.012   0.001   ARG A 281 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.865 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 1.1859
  time to fit residues: 64.8304
Evaluate side-chains
  36 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.834 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1017
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.4980
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:   50.0000
   chunk 41 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7536  Z= 0.191
  Angle     :  0.562   8.990  10304  Z= 0.279
  Chirality :  0.042   0.151   1269
  Planarity :  0.005   0.055   1316
  Dihedral  :  4.181  17.138   1099
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1024
  helix:  1.46 (0.23), residues: 503
  sheet:  0.33 (0.42), residues: 151
  loop :  0.02 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A1166 
   HIS   0.002   0.000   HIS A 408 
   PHE   0.023   0.002   PHE A 958 
   TYR   0.026   0.001   TYR A 935 
   ARG   0.011   0.000   ARG A 984 

*********************** 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 fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.796 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 44
  average time/residue: 0.9089
  time to fit residues: 43.8624
Evaluate side-chains
  40 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.832 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 0.0672
  time to fit residues: 1.2484
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:   40.0000
   chunk 29 optimal weight:    0.9980
   chunk 77 optimal weight:    0.1980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 93 optimal weight:    0.0170
   chunk 101 optimal weight:    0.0370
   chunk 83 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7536  Z= 0.144
  Angle     :  0.503   8.680  10304  Z= 0.247
  Chirality :  0.040   0.137   1269
  Planarity :  0.004   0.050   1316
  Dihedral  :  3.806  16.313   1099
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  6.89 %
    Favored  : 91.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.27), residues: 1024
  helix:  1.85 (0.23), residues: 505
  sheet:  0.43 (0.42), residues: 153
  loop :  0.22 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 170 
   HIS   0.002   0.000   HIS A 408 
   PHE   0.018   0.001   PHE A 958 
   TYR   0.018   0.001   TYR A 935 
   ARG   0.006   0.000   ARG A 984 

*********************** 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
  51 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.878 
Fit side-chains
  outliers start: 11
  outliers final: 4
  residues processed: 46
  average time/residue: 0.7957
  time to fit residues: 40.8419
Evaluate side-chains
  42 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.779 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 0.0634
  time to fit residues: 1.1254
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0050
   chunk 62 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 99 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7536  Z= 0.155
  Angle     :  0.492   7.667  10304  Z= 0.241
  Chirality :  0.040   0.135   1269
  Planarity :  0.004   0.049   1316
  Dihedral  :  3.677  15.894   1099
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  7.45 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.27), residues: 1024
  helix:  2.09 (0.23), residues: 505
  sheet:  0.43 (0.41), residues: 159
  loop :  0.50 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 170 
   HIS   0.001   0.000   HIS A 408 
   PHE   0.016   0.001   PHE A 958 
   TYR   0.012   0.001   TYR A 935 
   ARG   0.003   0.000   ARG A 984 

*********************** 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
  52 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.850 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 46
  average time/residue: 0.8520
  time to fit residues: 43.3904
Evaluate side-chains
  40 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.864 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 0.0722
  time to fit residues: 1.2876
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 74 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:   40.0000
   chunk 89 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A1122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065   7536  Z= 0.548
  Angle     :  0.649   9.160  10304  Z= 0.320
  Chirality :  0.046   0.185   1269
  Planarity :  0.005   0.050   1316
  Dihedral  :  4.139  16.456   1099
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  9.00 %
    Favored  : 88.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.27), residues: 1024
  helix:  1.83 (0.23), residues: 503
  sheet:  0.32 (0.41), residues: 156
  loop :  0.40 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 170 
   HIS   0.006   0.001   HIS A 364 
   PHE   0.020   0.002   PHE A1154 
   TYR   0.019   0.002   TYR A  40 
   ARG   0.004   0.001   ARG A 207 

*********************** 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
  55 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.831 
Fit side-chains
  outliers start: 18
  outliers final: 8
  residues processed: 44
  average time/residue: 0.8400
  time to fit residues: 41.1065
Evaluate side-chains
  44 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.834 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 5
  residues processed: 3
  average time/residue: 0.7344
  time to fit residues: 3.4701
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 58 optimal weight:   50.0000
   chunk 24 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7536  Z= 0.280
  Angle     :  0.552  10.594  10304  Z= 0.269
  Chirality :  0.042   0.150   1269
  Planarity :  0.004   0.048   1316
  Dihedral  :  3.930  16.645   1099
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.55 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.27), residues: 1024
  helix:  2.08 (0.23), residues: 503
  sheet:  0.39 (0.41), residues: 157
  loop :  0.50 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A1166 
   HIS   0.002   0.001   HIS A 364 
   PHE   0.014   0.002   PHE A 940 
   TYR   0.012   0.001   TYR A 935 
   ARG   0.003   0.000   ARG A 281 

*********************** 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
  52 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.883 
Fit side-chains
  outliers start: 15
  outliers final: 7
  residues processed: 47
  average time/residue: 0.8044
  time to fit residues: 42.0996
Evaluate side-chains
  43 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.858 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 5
  residues processed: 2
  average time/residue: 0.6351
  time to fit residues: 2.5323
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0170
   overall best weight:    1.5824

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7536  Z= 0.288
  Angle     :  0.548   9.797  10304  Z= 0.267
  Chirality :  0.042   0.160   1269
  Planarity :  0.004   0.048   1316
  Dihedral  :  3.882  19.297   1099
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.27), residues: 1024
  helix:  2.16 (0.23), residues: 503
  sheet:  0.41 (0.41), residues: 157
  loop :  0.56 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A1166 
   HIS   0.002   0.001   HIS A 364 
   PHE   0.015   0.002   PHE A 940 
   TYR   0.012   0.001   TYR A  40 
   ARG   0.002   0.000   ARG A 207 

*********************** 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
  50 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.785 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 46
  average time/residue: 0.8647
  time to fit residues: 43.8065
Evaluate side-chains
  45 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.662 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 7
  residues processed: 1
  average time/residue: 0.0578
  time to fit residues: 1.0166
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 59 optimal weight:   40.0000
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0570
   chunk 67 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 78 optimal weight:    0.6980
   chunk 90 optimal weight:    0.4980
   chunk 95 optimal weight:    0.5980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   7536  Z= 0.149
  Angle     :  0.516   9.807  10304  Z= 0.248
  Chirality :  0.041   0.169   1269
  Planarity :  0.004   0.047   1316
  Dihedral  :  3.651  16.998   1099
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.67 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.27), residues: 1024
  helix:  2.35 (0.23), residues: 504
  sheet:  0.45 (0.41), residues: 157
  loop :  0.62 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A 170 
   HIS   0.001   0.000   HIS A 408 
   PHE   0.012   0.001   PHE A 940 
   TYR   0.012   0.001   TYR A 935 
   ARG   0.002   0.000   ARG A1153 

*********************** 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 fitting.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.864 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 49
  average time/residue: 0.7519
  time to fit residues: 41.2189
Evaluate side-chains
  43 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.859 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 6
  residues processed: 0
  time to fit residues: 1.1328
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   chunk 55 optimal weight:    8.9990
   chunk 40 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7536  Z= 0.174
  Angle     :  0.523   9.281  10304  Z= 0.251
  Chirality :  0.041   0.202   1269
  Planarity :  0.004   0.047   1316
  Dihedral  :  3.595  16.173   1099
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.38 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.27), residues: 1024
  helix:  2.45 (0.23), residues: 505
  sheet:  0.47 (0.41), residues: 157
  loop :  0.63 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 170 
   HIS   0.001   0.000   HIS A 408 
   PHE   0.013   0.001   PHE A 940 
   TYR   0.010   0.001   TYR A 935 
   ARG   0.002   0.000   ARG A1153 

*********************** 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
  48 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.856 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 46
  average time/residue: 0.8292
  time to fit residues: 42.5256
Evaluate side-chains
  43 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.910 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 6
  residues processed: 0
  time to fit residues: 1.1639
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 59 optimal weight:   50.0000
   chunk 46 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    0.7980
   chunk 94 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:   50.0000
   chunk 64 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2363

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= 0.216
  Angle     :  0.551  10.391  10304  Z= 0.261
  Chirality :  0.042   0.182   1269
  Planarity :  0.004   0.047   1316
  Dihedral  :  3.633  16.987   1099
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 13.08 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.27), residues: 1024
  helix:  2.45 (0.23), residues: 504
  sheet:  0.52 (0.42), residues: 156
  loop :  0.66 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A1166 
   HIS   0.001   0.001   HIS A 364 
   PHE   0.014   0.001   PHE A 940 
   TYR   0.010   0.001   TYR A 161 
   ARG   0.004   0.000   ARG A1153 

********************** 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 fitting.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.914 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 46
  average time/residue: 0.8735
  time to fit residues: 44.5159
Evaluate side-chains
  45 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.788 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 6
  residues processed: 1
  average time/residue: 0.0783
  time to fit residues: 1.4075
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 71 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.5180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.095289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.068192 restraints weight = 19300.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.81
r_work: 0.3054 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2520

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= 0.152
  Angle     :  0.524  12.986  10304  Z= 0.249
  Chirality :  0.041   0.193   1269
  Planarity :  0.004   0.046   1316
  Dihedral  :  3.513  15.992   1099
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 13.50 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.27), residues: 1024
  helix:  2.53 (0.23), residues: 505
  sheet:  0.51 (0.42), residues: 156
  loop :  0.66 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A 170 
   HIS   0.001   0.000   HIS A 408 
   PHE   0.012   0.001   PHE A 940 
   TYR   0.011   0.001   TYR A 935 
   ARG   0.002   0.000   ARG A1153 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1974.05 seconds
wall clock time: 36 minutes 35.19 seconds (2195.19 seconds total)