Starting phenix.real_space_refine
on Mon Mar 11 08:15:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/03_2024/6xou_22280.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/03_2024/6xou_22280.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/03_2024/6xou_22280.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/03_2024/6xou_22280.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/03_2024/6xou_22280.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/03_2024/6xou_22280.pdb"
  }
  resolution = 4.0
  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=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4897      2.51       5
     N    1304      2.21       5
     O    1457      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   59": "OE1" <-> "OE2"
    Residue "A GLU  185": "OE1" <-> "OE2"
    Residue "A GLU  244": "OE1" <-> "OE2"
    Residue "A ARG  264": "NH1" <-> "NH2"
    Residue "A PHE  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  388": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  417": "OE1" <-> "OE2"
    Residue "A GLU  480": "OE1" <-> "OE2"
    Residue "A GLU  518": "OE1" <-> "OE2"
    Residue "A GLU  527": "OE1" <-> "OE2"
    Residue "A GLU  539": "OE1" <-> "OE2"
    Residue "A GLU  543": "OE1" <-> "OE2"
    Residue "A GLU  640": "OE1" <-> "OE2"
    Residue "A GLU  686": "OE1" <-> "OE2"
    Residue "A GLU  695": "OE1" <-> "OE2"
    Residue "A GLU  696": "OE1" <-> "OE2"
    Residue "A GLU  709": "OE1" <-> "OE2"
    Residue "A GLU  754": "OE1" <-> "OE2"
    Residue "A GLU  793": "OE1" <-> "OE2"
    Residue "A PHE  848": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  901": "OE1" <-> "OE2"
    Residue "A GLU 1024": "OE1" <-> "OE2"
  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: 7697
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7697
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 965, 7691
          Classifications: {'peptide': 965}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 902}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 965, 7691
          Classifications: {'peptide': 965}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 902}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7875
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER A 723 " occ=0.42
      ... (10 atoms not shown)
      pdb=" OG BSER A 723 " occ=0.58
  Time building chain proxies: 8.08, per 1000 atoms: 1.05
  Number of scatterers: 7697
  At special positions: 0
  Unit cell: (84.744, 98.44, 103.576, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1457      8.00
     N    1304      7.00
     C    4897      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: 3.19
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1824

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      53.6% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 4.096A  pdb=" N   ARG A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 61
    Processing helix  chain 'A' and resid 101 through 111
      removed outlier: 3.927A  pdb=" N   LEU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 3.532A  pdb=" N   MET A 126 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LEU A 127 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 123 through 127'
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 200 through 210
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.725A  pdb=" N   VAL A 233 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 245
      removed outlier: 3.866A  pdb=" N   GLU A 244 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 272 through 284
      removed outlier: 3.916A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 288
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.566A  pdb=" N   ILE A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 457
      removed outlier: 4.750A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 5.254A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   HIS A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 481
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 509 through 527
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 608 through 613
      removed outlier: 3.639A  pdb=" N   ARG A 612 " --> pdb=" O   GLU A 609 " (cutoff:3.500A)
      Proline residue:  A 613  - end of helix
    Processing helix  chain 'A' and resid 614 through 622
    Processing helix  chain 'A' and resid 631 through 642
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 695 through 713
      removed outlier: 3.703A  pdb=" N   PHE A 699 " --> pdb=" O   GLU A 695 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 701 " --> pdb=" O   GLU A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 716
      No H-bonds generated for 'chain 'A' and resid 714 through 716'
    Processing helix  chain 'A' and resid 717 through 727
    Processing helix  chain 'A' and resid 728 through 730
      No H-bonds generated for 'chain 'A' and resid 728 through 730'
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
      removed outlier: 3.550A  pdb=" N   VAL A 746 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 763 through 773
      removed outlier: 4.294A  pdb=" N   ARG A 767 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 878 through 894
      removed outlier: 4.323A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 901
    Processing helix  chain 'A' and resid 928 through 945
      removed outlier: 3.505A  pdb=" N   LEU A 932 " --> pdb=" O   THR A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 964
    Processing helix  chain 'A' and resid 968 through 972
      removed outlier: 3.566A  pdb=" N   LYS A 972 " --> pdb=" O   PRO A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 979
      removed outlier: 3.947A  pdb=" N   PHE A 977 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 996
    Processing helix  chain 'A' and resid 997 through 1008
    Processing helix  chain 'A' and resid 1025 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.798A  pdb=" N   LYS A  66 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   SER A  56 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   LEU A  62 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   MET A 135 " --> pdb=" O   PRO A 147 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   SER A 149 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.798A  pdb=" N   LYS A  66 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   SER A  56 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   LEU A  62 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186
    Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313
      removed outlier: 5.721A  pdb=" N   THR A 326 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ALA A 387 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ASP A 373 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313
      removed outlier: 5.721A  pdb=" N   THR A 326 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ALA A 387 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579
      removed outlier: 3.554A  pdb=" N   ASP A 575 " --> pdb=" O   TYR A 587 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE A 598 " --> pdb=" O   SER A 670 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLY A 645 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LEU A 673 " --> pdb=" O   THR A 643 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   THR A 643 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912
      removed outlier: 6.325A  pdb=" N   THR A 855 " --> pdb=" O   ILE A1020 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   GLY A1022 " --> pdb=" O   THR A 855 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   PHE A 857 " --> pdb=" O   GLY A1022 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   LYS A 854 " --> pdb=" O   ILE A1035 " (cutoff:3.500A)

    471 hydrogen bonds defined for protein.
    1360 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: 2.92

  Time building geometry restraints manager: 3.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2447
        1.34 -     1.46: 1495
        1.46 -     1.58: 3885
        1.58 -     1.70: 0
        1.70 -     1.81: 62
  Bond restraints: 7889
  Sorted by residual:
  bond pdb=" C   ILE A 242 "
       pdb=" N   PRO A 243 "
    ideal  model  delta    sigma   weight residual
    1.334  1.406 -0.072 2.34e-02 1.83e+03 9.46e+00
  bond pdb=" C   ILE A 714 "
       pdb=" N   PRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.026 1.36e-02 5.41e+03 3.76e+00
  bond pdb=" C   VAL A 615 "
       pdb=" N   PRO A 616 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.026 1.36e-02 5.41e+03 3.71e+00
  bond pdb=" CB  ASN A 712 "
       pdb=" CG  ASN A 712 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.40e+00
  bond pdb=" CG1 ILE A 885 "
       pdb=" CD1 ILE A 885 "
    ideal  model  delta    sigma   weight residual
    1.513  1.444  0.069 3.90e-02 6.57e+02 3.10e+00
  ... (remaining 7884 not shown)

  Histogram of bond angle deviations from ideal:
       99.37 -   106.60: 315
      106.60 -   113.82: 4252
      113.82 -   121.05: 3915
      121.05 -   128.27: 2152
      128.27 -   135.50: 64
  Bond angle restraints: 10698
  Sorted by residual:
  angle pdb=" N   ASP A 458 "
        pdb=" CA  ASP A 458 "
        pdb=" C   ASP A 458 "
      ideal   model   delta    sigma   weight residual
     111.54  117.53   -5.99 1.36e+00 5.41e-01 1.94e+01
  angle pdb=" N   LEU A 131 "
        pdb=" CA  LEU A 131 "
        pdb=" C   LEU A 131 "
      ideal   model   delta    sigma   weight residual
     111.30  106.10    5.20 1.43e+00 4.89e-01 1.32e+01
  angle pdb=" C   ALA A 580 "
        pdb=" N   GLY A 581 "
        pdb=" CA  GLY A 581 "
      ideal   model   delta    sigma   weight residual
     121.70  128.18   -6.48 1.80e+00 3.09e-01 1.30e+01
  angle pdb=" C   LYS A 893 "
        pdb=" N   PHE A 894 "
        pdb=" CA  PHE A 894 "
      ideal   model   delta    sigma   weight residual
     121.54  114.71    6.83 1.91e+00 2.74e-01 1.28e+01
  angle pdb=" CA  VAL A 615 "
        pdb=" C   VAL A 615 "
        pdb=" N   PRO A 616 "
      ideal   model   delta    sigma   weight residual
     118.88  124.27   -5.39 1.54e+00 4.22e-01 1.23e+01
  ... (remaining 10693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 4386
       17.76 -    35.52: 295
       35.52 -    53.27: 65
       53.27 -    71.03: 15
       71.03 -    88.79: 10
  Dihedral angle restraints: 4771
    sinusoidal: 1952
      harmonic: 2819
  Sorted by residual:
  dihedral pdb=" CA  PHE A 210 "
           pdb=" C   PHE A 210 "
           pdb=" N   THR A 211 "
           pdb=" CA  THR A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.00   24.00     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  PRO A 170 "
           pdb=" C   PRO A 170 "
           pdb=" N   CYS A 171 "
           pdb=" CA  CYS A 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.64   21.36     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" C   VAL A 102 "
           pdb=" N   VAL A 102 "
           pdb=" CA  VAL A 102 "
           pdb=" CB  VAL A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.21    9.21     0      2.50e+00 1.60e-01 1.36e+01
  ... (remaining 4768 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 921
       0.070 -    0.140: 213
       0.140 -    0.209: 32
       0.209 -    0.279: 5
       0.279 -    0.349: 1
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" CG  LEU A 467 "
            pdb=" CB  LEU A 467 "
            pdb=" CD1 LEU A 467 "
            pdb=" CD2 LEU A 467 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" CA  VAL A 102 "
            pdb=" N   VAL A 102 "
            pdb=" C   VAL A 102 "
            pdb=" CB  VAL A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.18    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CB  THR A  94 "
            pdb=" CA  THR A  94 "
            pdb=" OG1 THR A  94 "
            pdb=" CG2 THR A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 1169 not shown)

  Planarity restraints: 1397
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 301 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.29e+00
        pdb=" C   THR A 301 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   THR A 301 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PRO A 302 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 334 "   -0.036 5.00e-02 4.00e+02   5.56e-02 4.94e+00
        pdb=" N   PRO A 335 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 335 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 335 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 793 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.61e+00
        pdb=" C   GLU A 793 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU A 793 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LYS A 794 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1394 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1748
        2.79 -     3.32: 6901
        3.32 -     3.84: 12652
        3.84 -     4.37: 14147
        4.37 -     4.90: 24954
  Nonbonded interactions: 60402
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 783 "
            pdb=" O   PRO A 969 "
     model   vdw
     2.261 2.520
  nonbonded pdb=" OH  TYR A 146 "
            pdb=" OH  TYR A 258 "
     model   vdw
     2.270 2.440
  nonbonded pdb=" O   SER A 351 "
            pdb=" OG  SER A 355 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" OD1 ASP A  98 "
            pdb=" OG1 THR A 100 "
     model   vdw
     2.302 2.440
  nonbonded pdb=" O   HIS A 457 "
            pdb=" OD1 ASP A 458 "
     model   vdw
     2.310 3.040
  ... (remaining 60397 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=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          3.970
  Check model and map are aligned:         0.110
  Set scattering table:                    0.090
  Process input model:                     31.360
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.050
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
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   0.075   7889  Z= 0.332
  Angle     :  1.064  10.498  10698  Z= 0.563
  Chirality :  0.061   0.349   1172
  Planarity :  0.007   0.056   1397
  Dihedral  : 13.628  88.791   2947
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.10 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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: -1.51 (0.24), residues: 964
  helix: -1.05 (0.21), residues: 447
  sheet:  0.29 (0.36), residues: 178
  loop : -1.42 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 684 
 HIS   0.008   0.001   HIS A 430 
 PHE   0.021   0.002   PHE A 848 
 TYR   0.016   0.002   TYR A 662 
 ARG   0.006   0.001   ARG A  81 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 THR cc_start: 0.8860 (m) cc_final: 0.8624 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2109
  time to fit residues: 43.2915
Evaluate side-chains
  94 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 29 optimal weight:   20.0000
   chunk 45 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
A 151 GLN
A 204 ASN
** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 430 HIS
A 637 GLN
A 638 GLN
A 690 ASN
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 787 GLN
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7889  Z= 0.317
  Angle     :  0.788  10.856  10698  Z= 0.397
  Chirality :  0.045   0.208   1172
  Planarity :  0.005   0.045   1397
  Dihedral  :  4.517  23.076   1036
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.79 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.43 (0.26), residues: 964
  helix:  0.86 (0.24), residues: 453
  sheet:  1.04 (0.38), residues: 176
  loop : -0.85 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 455 
 HIS   0.008   0.001   HIS A 108 
 PHE   0.023   0.002   PHE A 918 
 TYR   0.015   0.002   TYR A 587 
 ARG   0.006   0.001   ARG A 751 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 LEU cc_start: 0.8416 (pp) cc_final: 0.8208 (pt)
  outliers start: 14
  outliers final: 9
  residues processed: 99
  average time/residue: 0.2199
  time to fit residues: 30.8130
Evaluate side-chains
  89 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  851 TRP
Chi-restraints excluded: chain A residue  866 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 59 optimal weight:    0.2980
   chunk 24 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   chunk 77 optimal weight:    0.4980
   chunk 86 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7889  Z= 0.190
  Angle     :  0.724  12.572  10698  Z= 0.353
  Chirality :  0.044   0.202   1172
  Planarity :  0.005   0.045   1397
  Dihedral  :  4.212  20.424   1036
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 13.30 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.85 (0.27), residues: 964
  helix:  1.24 (0.25), residues: 454
  sheet:  1.24 (0.38), residues: 170
  loop : -0.67 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 455 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.014   0.001   PHE A 474 
 TYR   0.022   0.001   TYR A 388 
 ARG   0.003   0.000   ARG A 779 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  911 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8181 (ptpp)
  outliers start: 6
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1705
  time to fit residues: 23.2397
Evaluate side-chains
  81 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  851 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 83 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7889  Z= 0.252
  Angle     :  0.720  10.019  10698  Z= 0.354
  Chirality :  0.043   0.151   1172
  Planarity :  0.004   0.041   1397
  Dihedral  :  4.300  20.719   1036
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.54 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.03 (0.27), residues: 964
  helix:  1.37 (0.25), residues: 455
  sheet:  1.21 (0.37), residues: 169
  loop : -0.46 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 455 
 HIS   0.005   0.001   HIS A 108 
 PHE   0.011   0.001   PHE A 474 
 TYR   0.019   0.001   TYR A 388 
 ARG   0.002   0.000   ARG A 779 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1818
  time to fit residues: 20.0345
Evaluate side-chains
  78 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  851 TRP
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  872 THR
Chi-restraints excluded: chain A residue  895 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 83 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 856 HIS
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7889  Z= 0.322
  Angle     :  0.762  11.680  10698  Z= 0.376
  Chirality :  0.044   0.157   1172
  Planarity :  0.005   0.039   1397
  Dihedral  :  4.522  23.604   1036
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 14.12 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.91 (0.27), residues: 964
  helix:  1.22 (0.25), residues: 449
  sheet:  1.07 (0.37), residues: 168
  loop : -0.36 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 455 
 HIS   0.007   0.001   HIS A 108 
 PHE   0.013   0.002   PHE A 177 
 TYR   0.017   0.002   TYR A 388 
 ARG   0.003   0.000   ARG A 534 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 PHE cc_start: 0.7223 (t80) cc_final: 0.6630 (t80)
REVERT: A  431 LYS cc_start: 0.9295 (tppt) cc_final: 0.8987 (tppt)
  outliers start: 13
  outliers final: 13
  residues processed: 75
  average time/residue: 0.1847
  time to fit residues: 20.2062
Evaluate side-chains
  80 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  851 TRP
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  872 THR
Chi-restraints excluded: chain A residue  895 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 89 optimal weight:    0.5980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7889  Z= 0.215
  Angle     :  0.724  11.709  10698  Z= 0.349
  Chirality :  0.043   0.189   1172
  Planarity :  0.004   0.042   1397
  Dihedral  :  4.314  17.724   1036
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.94 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.10 (0.27), residues: 964
  helix:  1.46 (0.25), residues: 447
  sheet:  1.12 (0.37), residues: 166
  loop : -0.36 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 941 
 HIS   0.004   0.001   HIS A 108 
 PHE   0.015   0.001   PHE A 935 
 TYR   0.017   0.001   TYR A 388 
 ARG   0.003   0.000   ARG A 924 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 MET cc_start: 0.7852 (tpt) cc_final: 0.7485 (tpt)
REVERT: A  431 LYS cc_start: 0.9271 (tppt) cc_final: 0.8959 (tppt)
REVERT: A  659 MET cc_start: 0.6523 (mmt) cc_final: 0.6233 (mmt)
  outliers start: 10
  outliers final: 9
  residues processed: 78
  average time/residue: 0.1806
  time to fit residues: 20.5536
Evaluate side-chains
  77 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  872 THR
Chi-restraints excluded: chain A residue  895 LEU
Chi-restraints excluded: chain A residue  918 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 42 optimal weight:    0.3980
   chunk 36 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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: 0.8018
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7889  Z= 0.199
  Angle     :  0.726  11.295  10698  Z= 0.347
  Chirality :  0.043   0.178   1172
  Planarity :  0.004   0.041   1397
  Dihedral  :  4.256  16.914   1036
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.17 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.14 (0.27), residues: 964
  helix:  1.44 (0.25), residues: 455
  sheet:  0.92 (0.37), residues: 169
  loop : -0.17 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 851 
 HIS   0.004   0.001   HIS A 108 
 PHE   0.012   0.001   PHE A 935 
 TYR   0.016   0.001   TYR A 388 
 ARG   0.002   0.000   ARG A 924 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7399 (t80)
REVERT: A  431 LYS cc_start: 0.9268 (tppt) cc_final: 0.8974 (tppt)
REVERT: A  659 MET cc_start: 0.6559 (mmt) cc_final: 0.6328 (mmt)
REVERT: A  964 ASP cc_start: 0.8698 (p0) cc_final: 0.8401 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1639
  time to fit residues: 19.2885
Evaluate side-chains
  80 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  268 TYR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  872 THR
Chi-restraints excluded: chain A residue  918 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   chunk 84 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7889  Z= 0.181
  Angle     :  0.745  11.303  10698  Z= 0.350
  Chirality :  0.042   0.187   1172
  Planarity :  0.004   0.041   1397
  Dihedral  :  4.134  18.852   1036
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 16.34 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.23 (0.27), residues: 964
  helix:  1.44 (0.25), residues: 463
  sheet:  0.96 (0.38), residues: 169
  loop : -0.02 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 851 
 HIS   0.003   0.001   HIS A 457 
 PHE   0.012   0.001   PHE A 935 
 TYR   0.016   0.001   TYR A 388 
 ARG   0.002   0.000   ARG A 675 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 LYS cc_start: 0.9271 (tppt) cc_final: 0.8965 (tppt)
  outliers start: 6
  outliers final: 5
  residues processed: 79
  average time/residue: 0.1667
  time to fit residues: 19.3830
Evaluate side-chains
  76 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  918 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0570
   chunk 77 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 56 optimal weight:    0.3980
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.8904

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.4638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7889  Z= 0.207
  Angle     :  0.773  18.447  10698  Z= 0.358
  Chirality :  0.043   0.211   1172
  Planarity :  0.004   0.040   1397
  Dihedral  :  4.159  18.662   1036
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 16.34 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.22 (0.27), residues: 964
  helix:  1.42 (0.25), residues: 459
  sheet:  0.96 (0.38), residues: 169
  loop : -0.00 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 851 
 HIS   0.004   0.001   HIS A 108 
 PHE   0.011   0.001   PHE A 474 
 TYR   0.026   0.001   TYR A 510 
 ARG   0.002   0.000   ARG A 924 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
REVERT: A  268 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7537 (t80)
REVERT: A  431 LYS cc_start: 0.9293 (tppt) cc_final: 0.8991 (tppt)
  outliers start: 8
  outliers final: 7
  residues processed: 77
  average time/residue: 0.1551
  time to fit residues: 18.1306
Evaluate side-chains
  78 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  268 TYR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  453 SER
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  855 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 88 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 514 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.4720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7889  Z= 0.184
  Angle     :  0.771  15.743  10698  Z= 0.357
  Chirality :  0.043   0.195   1172
  Planarity :  0.004   0.041   1397
  Dihedral  :  4.130  18.825   1036
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 16.80 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.18 (0.27), residues: 964
  helix:  1.31 (0.25), residues: 465
  sheet:  0.92 (0.37), residues: 169
  loop :  0.09 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 851 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.026   0.001   PHE A 318 
 TYR   0.021   0.001   TYR A 510 
 ARG   0.003   0.000   ARG A 725 

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7528 (t80)
REVERT: A  431 LYS cc_start: 0.9279 (tppt) cc_final: 0.8971 (tppt)
REVERT: A  743 MET cc_start: 0.8008 (mmm) cc_final: 0.7787 (mmp)
  outliers start: 6
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1571
  time to fit residues: 17.7469
Evaluate side-chains
  74 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  268 TYR
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  617 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0980
   chunk 66 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.044152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.035046 restraints weight = 48481.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.036511 restraints weight = 27354.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.037554 restraints weight = 18138.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.4793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7889  Z= 0.178
  Angle     :  0.778  17.191  10698  Z= 0.356
  Chirality :  0.043   0.189   1172
  Planarity :  0.004   0.041   1397
  Dihedral  :  4.057  19.130   1036
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 16.80 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  1.24 (0.27), residues: 964
  helix:  1.33 (0.25), residues: 464
  sheet:  0.95 (0.38), residues: 168
  loop :  0.19 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 182 
 HIS   0.002   0.001   HIS A 229 
 PHE   0.016   0.001   PHE A 318 
 TYR   0.023   0.001   TYR A 510 
 ARG   0.002   0.000   ARG A 725 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1659.55 seconds
wall clock time: 31 minutes 24.64 seconds (1884.64 seconds total)