Starting phenix.real_space_refine
on Mon Mar 11 10:16:42 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/03_2024/7n73_24218_trim.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/03_2024/7n73_24218.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/7n73_24218/03_2024/7n73_24218.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/03_2024/7n73_24218.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/03_2024/7n73_24218_trim.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/03_2024/7n73_24218_trim.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=   0.024
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       2      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    5088      2.51       5
     N    1322      2.21       5
     O    1398      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7866
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1045, 7866
          Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1, 'Y01': 2}
          Classifications: {'peptide': 1036, 'undetermined': 6, 'water': 3}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963, None: 9}
            Not linked:
              pdbres="PRO A1168 "
              pdbres="ADP A1201 "
            Not linked:
              pdbres="ADP A1201 "
              pdbres="ALF A1202 "
            Not linked:
              pdbres="ALF A1202 "
              pdbres=" MG A1203 "
            Not linked:
              pdbres=" MG A1203 "
              pdbres=" MG A1204 "
            Not linked:
              pdbres=" MG A1204 "
              pdbres="Y01 A1205 "
            ... (remaining 4 not shown)
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 259
          Unresolved non-hydrogen angles: 329
          Unresolved non-hydrogen dihedrals: 227
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 177
  Time building chain proxies: 5.09, per 1000 atoms: 0.65
  Number of scatterers: 7866
  At special positions: 0
  Unit cell: (92.312, 99.655, 125.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      49     16.00
     P       2     15.00
     Al      1     13.00
     Mg      2     11.99
     F       4      9.00
     O    1398      8.00
     N    1322      7.00
     C    5088      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.55
  Conformation dependent library (CDL) restraints added in 1.7 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 8 sheets defined
      51.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  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: 3.988A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    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 196
    Processing helix  chain 'A' and resid 200 through 212
      removed outlier: 3.778A  pdb=" N   ALA A 209 " --> pdb=" O   MET A 205 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ILE A 210 " --> pdb=" O   VAL A 206 " (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
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 364 through 366
      No H-bonds generated for 'chain 'A' and resid 364 through 366'
    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
      removed outlier: 3.848A  pdb=" N   LEU A 430 " --> pdb=" O   ALA A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 463
      removed outlier: 3.722A  pdb=" N   ILE A 454 " --> pdb=" O   ASN A 450 " (cutoff:3.500A)
      removed outlier: 3.650A  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 494 through 500
      removed outlier: 3.981A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY A 500 " --> pdb=" O   ILE A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 566 through 577
      removed outlier: 3.608A  pdb=" N   THR A 576 " --> pdb=" O   MET A 572 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY A 577 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 659
    Processing helix  chain 'A' and resid 667 through 677
    Processing helix  chain 'A' and resid 695 through 700
    Processing helix  chain 'A' and resid 703 through 709
      removed outlier: 3.581A  pdb=" N   GLY A 709 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 737
    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
      removed outlier: 3.665A  pdb=" N   GLN A 842 " --> pdb=" O   LYS A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 863
    Processing helix  chain 'A' and resid 874 through 876
      No H-bonds generated for 'chain 'A' and resid 874 through 876'
    Processing helix  chain 'A' and resid 877 through 884
    Processing helix  chain 'A' and resid 909 through 948
    Processing helix  chain 'A' and resid 954 through 964
      removed outlier: 3.761A  pdb=" N   LEU A 959 " --> pdb=" O   ASP A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 974
      removed outlier: 4.361A  pdb=" N   SER A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1020
      removed outlier: 3.647A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1061
      removed outlier: 3.875A  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
      removed outlier: 3.629A  pdb=" N   PHE A1127 " --> pdb=" O   PHE A1123 " (cutoff:3.500A)
      Proline residue:  A1138  - end of helix
    Processing helix  chain 'A' and resid 1152 through 1164
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90
    Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109
      removed outlier: 5.753A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE A 169 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR A 178 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 292
    Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 315
      removed outlier: 4.522A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   LEU A 387 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   ASP A 325 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350
      removed outlier: 6.852A  pdb=" N   GLU A 332 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ALA A 378 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   MET A 334 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490
      removed outlier: 5.824A  pdb=" N   GLY A 887 " --> pdb=" O   PHE A 901 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   SER A 903 " --> pdb=" O   GLY A 887 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER A 889 " --> pdb=" O   SER A 903 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   VAL A 505 " --> pdb=" O   VAL A 742 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   VAL A 744 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   PHE A 507 " --> pdb=" O   VAL A 744 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ALA A 741 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   PHE A 846 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   MET A 743 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   THR A 844 " --> pdb=" O   ARG A 816 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   LEU A 818 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   PHE A 846 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU A 820 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 525
      removed outlier: 3.532A  pdb=" N   GLY A 522 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   LEU A 713 " --> pdb=" O   SER A 687 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   SER A 687 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 631 " --> pdb=" O   PHE A 625 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   PHE A 625 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ALA A 637 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   VAL A 619 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   SER A 588 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 558

    443 hydrogen bonds defined for protein.
    1275 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.12

  Time building geometry restraints manager: 3.77 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: 2157
        1.33 -     1.45: 1155
        1.45 -     1.57: 4636
        1.57 -     1.69: 11
        1.69 -     1.81: 77
  Bond restraints: 8036
  Sorted by residual:
  bond pdb=" F2  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.808 -0.123 2.00e-02 2.50e+03 3.80e+01
  bond pdb=" F3  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.792 -0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" F4  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.686  1.788 -0.102 2.00e-02 2.50e+03 2.62e+01
  bond pdb=" F1  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.684  1.779 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" CAV Y01 A1205 "
       pdb=" CBC Y01 A1205 "
    ideal  model  delta    sigma   weight residual
    1.523  1.605 -0.082 2.00e-02 2.50e+03 1.70e+01
  ... (remaining 8031 not shown)

  Histogram of bond angle deviations from ideal:
       89.25 -   107.31: 412
      107.31 -   125.38: 10446
      125.38 -   143.45: 131
      143.45 -   161.52: 0
      161.52 -   179.59: 2
  Bond angle restraints: 10991
  Sorted by residual:
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F2  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     108.68  178.71  -70.03 3.00e+00 1.11e-01 5.45e+02
  angle pdb=" F3  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.63  179.59  -69.96 3.00e+00 1.11e-01 5.44e+02
  angle pdb=" F2  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     110.21   89.87   20.34 3.00e+00 1.11e-01 4.60e+01
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.02   89.25   19.77 3.00e+00 1.11e-01 4.34e+01
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F3  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.69   90.35   19.34 3.00e+00 1.11e-01 4.15e+01
  ... (remaining 10986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.30: 4679
       22.30 -    44.60: 223
       44.60 -    66.89: 20
       66.89 -    89.19: 4
       89.19 -   111.49: 2
  Dihedral angle restraints: 4928
    sinusoidal: 1934
      harmonic: 2994
  Sorted by residual:
  dihedral pdb=" C5' ADP A1201 "
           pdb=" O5' ADP A1201 "
           pdb=" PA  ADP A1201 "
           pdb=" O2A ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -171.49  111.49     1      2.00e+01 2.50e-03 3.28e+01
  dihedral pdb=" O2A ADP A1201 "
           pdb=" O3A ADP A1201 "
           pdb=" PA  ADP A1201 "
           pdb=" PB  ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   50.14 -110.14     1      2.00e+01 2.50e-03 3.23e+01
  dihedral pdb=" O1B ADP A1201 "
           pdb=" O3A ADP A1201 "
           pdb=" PB  ADP A1201 "
           pdb=" PA  ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -125.53   65.53     1      2.00e+01 2.50e-03 1.41e+01
  ... (remaining 4925 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.231: 1328
       0.231 -    0.462: 6
       0.462 -    0.692: 0
       0.692 -    0.923: 0
       0.923 -    1.154: 1
  Chirality restraints: 1335
  Sorted by residual:
  chirality pdb=" CB  VAL A 617 "
            pdb=" CA  VAL A 617 "
            pdb=" CG1 VAL A 617 "
            pdb=" CG2 VAL A 617 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.48   -1.15 2.00e-01 2.50e+01 3.33e+01
  chirality pdb=" CBG Y01 A1205 "
            pdb=" CAQ Y01 A1205 "
            pdb=" CBD Y01 A1205 "
            pdb=" CBI Y01 A1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.73    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CBG Y01 A1206 "
            pdb=" CAQ Y01 A1206 "
            pdb=" CBD Y01 A1206 "
            pdb=" CBI Y01 A1206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.71    0.38 2.00e-01 2.50e+01 3.61e+00
  ... (remaining 1332 not shown)

  Planarity restraints: 1373
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 174 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" CD  GLN A 174 "    0.055 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 174 "   -0.021 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 174 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 451 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.17e+00
        pdb=" CD  GLU A 451 "   -0.052 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 451 "    0.019 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 451 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 590 "   -0.018 2.00e-02 2.50e+03   1.68e-02 4.96e+00
        pdb=" CG  PHE A 590 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 590 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 590 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 590 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 590 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 590 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1370 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 48
        2.46 -     3.07: 5596
        3.07 -     3.68: 12005
        3.68 -     4.29: 17650
        4.29 -     4.90: 30591
  Nonbonded interactions: 65890
  Sorted by model distance:
  nonbonded pdb=" O   THR A 510 "
            pdb="MG    MG A1203 "
     model   vdw
     1.850 2.170
  nonbonded pdb=" NZ  LYS A1062 "
            pdb=" OD2 ASP A1134 "
     model   vdw
     2.043 2.520
  nonbonded pdb=" O   LEU A 672 "
            pdb=" OG1 THR A 676 "
     model   vdw
     2.062 2.440
  nonbonded pdb=" O   VAL A 462 "
            pdb=" O   HOH A1301 "
     model   vdw
     2.066 2.440
  nonbonded pdb=" OG1 THR A 745 "
            pdb=" F1  ALF A1202 "
     model   vdw
     2.070 2.390
  ... (remaining 65885 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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          5.990
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     27.780
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  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:12.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
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      :  0.006   0.123   8036  Z= 0.400
  Angle     :  1.268  70.028  10991  Z= 0.490
  Chirality :  0.064   1.154   1335
  Planarity :  0.004   0.032   1373
  Dihedral  : 13.003 111.491   2994
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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:  1.31 (0.27), residues: 1024
  helix:  1.63 (0.24), residues: 500
  sheet: -0.24 (0.42), residues: 158
  loop :  0.51 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 246 
 HIS   0.017   0.002   HIS A 385 
 PHE   0.038   0.001   PHE A 590 
 TYR   0.023   0.001   TYR A 443 
 ARG   0.008   0.001   ARG A1159 

*********************** 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
  59 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A  415 LYS cc_start: 0.7833 (tttt) cc_final: 0.7505 (tttt)
REVERT: A  421 MET cc_start: 0.7532 (tpp) cc_final: 0.7115 (tmt)
REVERT: A 1151 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7917 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 1.2199
  time to fit residues: 77.3995
Evaluate side-chains
  38 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.7780

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.0981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8036  Z= 0.213
  Angle     :  0.859  29.365  10991  Z= 0.347
  Chirality :  0.041   0.143   1335
  Planarity :  0.004   0.036   1373
  Dihedral  :  7.398  97.288   1262
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  5.19 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.69 (0.27), residues: 1024
  helix:  2.05 (0.23), residues: 500
  sheet: -0.04 (0.42), residues: 157
  loop :  0.48 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.014   0.001   PHE A 590 
 TYR   0.010   0.001   TYR A 931 
 ARG   0.007   0.000   ARG A1159 

*********************** 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
  53 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
REVERT: A  415 LYS cc_start: 0.7836 (tttt) cc_final: 0.7405 (tttt)
REVERT: A  421 MET cc_start: 0.7536 (tpp) cc_final: 0.7285 (tmt)
REVERT: A 1144 LEU cc_start: 0.9049 (tt) cc_final: 0.8774 (tp)
REVERT: A 1151 LYS cc_start: 0.8153 (ptpp) cc_final: 0.7928 (ptpp)
  outliers start: 9
  outliers final: 6
  residues processed: 51
  average time/residue: 1.1957
  time to fit residues: 66.7246
Evaluate side-chains
  44 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  333 CYS
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue 1001 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 94 optimal weight:    0.7980
   chunk 102 optimal weight:    0.5980
   chunk 84 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1003 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: 0.8283
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8036  Z= 0.195
  Angle     :  0.835  30.111  10991  Z= 0.332
  Chirality :  0.040   0.148   1335
  Planarity :  0.004   0.038   1373
  Dihedral  :  6.789  91.786   1262
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  7.12 %
    Favored  : 91.31 %
  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:  1.90 (0.27), residues: 1024
  helix:  2.23 (0.23), residues: 501
  sheet:  0.14 (0.42), residues: 154
  loop :  0.53 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.012   0.001   PHE A 940 
 TYR   0.010   0.001   TYR A 931 
 ARG   0.002   0.000   ARG A1159 

*********************** 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
  57 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7999 (pp)
REVERT: A  415 LYS cc_start: 0.7738 (tttt) cc_final: 0.7321 (tttt)
REVERT: A  421 MET cc_start: 0.7551 (tpp) cc_final: 0.7310 (tmt)
REVERT: A  632 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8397 (ptm)
REVERT: A 1151 LYS cc_start: 0.8146 (ptpp) cc_final: 0.7925 (ptpp)
  outliers start: 13
  outliers final: 3
  residues processed: 51
  average time/residue: 1.1464
  time to fit residues: 63.3586
Evaluate side-chains
  48 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  632 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.0170
   chunk 71 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 94 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.6018

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8036  Z= 0.172
  Angle     :  0.824  29.971  10991  Z= 0.324
  Chirality :  0.040   0.140   1335
  Planarity :  0.004   0.037   1373
  Dihedral  :  6.490  92.587   1262
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  9.41 %
    Favored  : 89.51 %
  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:  2.02 (0.27), residues: 1024
  helix:  2.37 (0.23), residues: 502
  sheet:  0.14 (0.42), residues: 154
  loop :  0.55 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.004   0.001   HIS A 554 
 PHE   0.010   0.001   PHE A 940 
 TYR   0.009   0.001   TYR A 161 
 ARG   0.002   0.000   ARG A 196 

*********************** 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
  56 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7989 (pp)
REVERT: A  415 LYS cc_start: 0.7783 (tttt) cc_final: 0.7315 (tttt)
REVERT: A  421 MET cc_start: 0.7552 (tpp) cc_final: 0.7158 (tmt)
REVERT: A 1144 LEU cc_start: 0.8837 (tp) cc_final: 0.8376 (tt)
REVERT: A 1151 LYS cc_start: 0.8149 (ptpp) cc_final: 0.7944 (ptpp)
  outliers start: 9
  outliers final: 3
  residues processed: 52
  average time/residue: 1.0984
  time to fit residues: 61.8639
Evaluate side-chains
  46 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0470
   chunk 69 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.1882

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

Flipped N/Q/H residues before XYZ refinement:
** A 225 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: 0.8296
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8036  Z= 0.252
  Angle     :  0.843  30.253  10991  Z= 0.335
  Chirality :  0.041   0.158   1335
  Planarity :  0.004   0.038   1373
  Dihedral  :  6.412  95.977   1262
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.74 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.02 (0.27), residues: 1024
  helix:  2.32 (0.23), residues: 502
  sheet:  0.13 (0.42), residues: 154
  loop :  0.63 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.012   0.001   PHE A 590 
 TYR   0.011   0.001   TYR A 161 
 ARG   0.002   0.000   ARG A 366 

*********************** 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
  54 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: A  415 LYS cc_start: 0.7782 (tttt) cc_final: 0.7342 (tttm)
REVERT: A  421 MET cc_start: 0.7608 (tpp) cc_final: 0.7199 (tmt)
REVERT: A 1144 LEU cc_start: 0.8850 (tp) cc_final: 0.8394 (tt)
REVERT: A 1151 LYS cc_start: 0.8149 (ptpp) cc_final: 0.7942 (ptpp)
  outliers start: 10
  outliers final: 6
  residues processed: 50
  average time/residue: 0.9839
  time to fit residues: 53.7996
Evaluate side-chains
  50 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  632 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0010
   chunk 24 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 8 optimal weight:    0.2980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 225 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: 0.8265
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8036  Z= 0.162
  Angle     :  0.825  29.843  10991  Z= 0.322
  Chirality :  0.040   0.145   1335
  Planarity :  0.004   0.036   1373
  Dihedral  :  6.193  94.905   1262
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 11.94 %
    Favored  : 87.21 %
  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:  2.11 (0.27), residues: 1024
  helix:  2.43 (0.23), residues: 502
  sheet:  0.15 (0.42), residues: 154
  loop :  0.63 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.004   0.001   HIS A 554 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 366 

*********************** 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: 7
    poor density    : 45
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8525 (mp)
REVERT: A  415 LYS cc_start: 0.7770 (tttt) cc_final: 0.7281 (tttm)
REVERT: A  421 MET cc_start: 0.7596 (tpp) cc_final: 0.7201 (tmt)
REVERT: A 1144 LEU cc_start: 0.8830 (tp) cc_final: 0.8378 (tt)
REVERT: A 1151 LYS cc_start: 0.8184 (ptpp) cc_final: 0.7977 (ptpp)
  outliers start: 7
  outliers final: 4
  residues processed: 51
  average time/residue: 1.0933
  time to fit residues: 60.5778
Evaluate side-chains
  47 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   chunk 56 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.8180

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8036  Z= 0.199
  Angle     :  0.830  29.861  10991  Z= 0.327
  Chirality :  0.040   0.138   1335
  Planarity :  0.004   0.038   1373
  Dihedral  :  6.131  95.266   1262
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.58 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.15 (0.27), residues: 1024
  helix:  2.44 (0.23), residues: 501
  sheet:  0.19 (0.42), residues: 154
  loop :  0.69 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.005   0.001   HIS A 554 
 PHE   0.010   0.001   PHE A 590 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 366 

*********************** 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
  57 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8146 (pp)
REVERT: A   90 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8540 (mp)
REVERT: A  415 LYS cc_start: 0.7756 (tttt) cc_final: 0.7274 (tttt)
REVERT: A 1144 LEU cc_start: 0.8836 (tp) cc_final: 0.8385 (tt)
REVERT: A 1151 LYS cc_start: 0.8185 (ptpp) cc_final: 0.7982 (ptpp)
  outliers start: 14
  outliers final: 6
  residues processed: 53
  average time/residue: 0.9916
  time to fit residues: 57.4480
Evaluate side-chains
  50 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 78 optimal weight:    0.5980
   chunk 91 optimal weight:    0.6980
   chunk 96 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 93 optimal weight:    0.3980
   overall best weight:    0.5780

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8036  Z= 0.164
  Angle     :  0.824  29.805  10991  Z= 0.323
  Chirality :  0.040   0.138   1335
  Planarity :  0.004   0.037   1373
  Dihedral  :  5.979  92.801   1262
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.94 %
    Favored  : 86.49 %
  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:  2.25 (0.27), residues: 1024
  helix:  2.48 (0.23), residues: 507
  sheet:  0.48 (0.43), residues: 144
  loop :  0.63 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A 817 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 681 

*********************** 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
  55 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8547 (mp)
REVERT: A  415 LYS cc_start: 0.7739 (tttt) cc_final: 0.7278 (tttt)
REVERT: A 1144 LEU cc_start: 0.8807 (tp) cc_final: 0.8349 (tt)
REVERT: A 1151 LYS cc_start: 0.8213 (ptpp) cc_final: 0.7884 (ptpp)
  outliers start: 13
  outliers final: 6
  residues processed: 51
  average time/residue: 1.0694
  time to fit residues: 59.4372
Evaluate side-chains
  49 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0870
   chunk 28 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 98 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.5558

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8036  Z= 0.162
  Angle     :  0.830  29.737  10991  Z= 0.323
  Chirality :  0.040   0.137   1335
  Planarity :  0.004   0.038   1373
  Dihedral  :  5.876  91.843   1262
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.67 %
    Favored  : 86.25 %
  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:  2.31 (0.27), residues: 1024
  helix:  2.53 (0.23), residues: 507
  sheet:  0.52 (0.43), residues: 144
  loop :  0.64 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A 817 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.009   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 740 

*********************** 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
  51 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   90 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8520 (mp)
REVERT: A  415 LYS cc_start: 0.7731 (tttt) cc_final: 0.7264 (tttt)
REVERT: A 1144 LEU cc_start: 0.8750 (tp) cc_final: 0.8296 (tt)
REVERT: A 1151 LYS cc_start: 0.8162 (ptpp) cc_final: 0.7846 (ptpp)
  outliers start: 9
  outliers final: 5
  residues processed: 49
  average time/residue: 1.0264
  time to fit residues: 54.9222
Evaluate side-chains
  48 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 103 optimal weight:    0.4980
   chunk 95 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS
A 377 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8036  Z= 0.179
  Angle     :  0.842  29.712  10991  Z= 0.329
  Chirality :  0.040   0.136   1335
  Planarity :  0.004   0.038   1373
  Dihedral  :  5.847  92.467   1262
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.30 %
    Favored  : 86.25 %
  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:  2.27 (0.27), residues: 1024
  helix:  2.52 (0.23), residues: 507
  sheet:  0.29 (0.42), residues: 154
  loop :  0.71 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 170 
 HIS   0.003   0.001   HIS A 817 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.010   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 281 

********************** 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
  54 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8255 (pp)
REVERT: A   90 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8492 (mp)
REVERT: A  415 LYS cc_start: 0.7733 (tttt) cc_final: 0.7306 (tttm)
REVERT: A 1144 LEU cc_start: 0.8730 (tp) cc_final: 0.8277 (tt)
REVERT: A 1151 LYS cc_start: 0.8180 (ptpp) cc_final: 0.7861 (ptpp)
  outliers start: 12
  outliers final: 5
  residues processed: 52
  average time/residue: 1.0838
  time to fit residues: 61.2001
Evaluate side-chains
  49 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  787 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0770
   chunk 84 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS
A 377 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.092318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.070533 restraints weight = 17190.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.70
r_work: 0.3016 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8036  Z= 0.153
  Angle     :  0.828  29.799  10991  Z= 0.323
  Chirality :  0.039   0.136   1335
  Planarity :  0.004   0.037   1373
  Dihedral  :  5.738  90.375   1262
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.55 %
    Favored  : 86.25 %
  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:  2.29 (0.27), residues: 1024
  helix:  2.54 (0.23), residues: 508
  sheet:  0.56 (0.43), residues: 144
  loop :  0.56 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 817 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.009   0.001   TYR A 161 
 ARG   0.001   0.000   ARG A 740 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2249.57 seconds
wall clock time: 41 minutes 18.03 seconds (2478.03 seconds total)