Starting phenix.real_space_refine
on Tue Feb 13 12:32:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ygn_33817/02_2024/7ygn_33817_updated.pdb"
  }
  resolution = 3.0
  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=  -0.001 sd=   0.200
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: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      2      5.21       5
     S      43      5.16       5
     C    3896      2.51       5
     N    1057      2.21       5
     O    1126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  236": "OE1" <-> "OE2"
    Residue "A GLU  311": "OE1" <-> "OE2"
    Residue "A PHE  320": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  494": "OE1" <-> "OE2"
    Residue "A GLU  546": "OE1" <-> "OE2"
    Residue "A GLU  569": "OE1" <-> "OE2"
    Residue "A TYR  608": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  848": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 6133
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 739, 5945
          Classifications: {'peptide': 739}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 701}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 186
          Classifications: {'RNA': 9}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 3, 'rna3p': 5}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.07, per 1000 atoms: 0.66
  Number of scatterers: 6133
  At special positions: 0
  Unit cell: (76.09, 84.786, 113.048, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      43     16.00
     P       9     15.00
     Mg      2     11.99
     O    1126      8.00
     N    1057      7.00
     C    3896      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.64
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1402

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      23 helices and 10 sheets defined
      34.2% alpha, 22.5% beta
      0 base pairs and 3 stacking pairs defined.
    Time for finding SS restraints: 2.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 252 through 261
    Processing helix  chain 'A' and resid 263 through 266
      No H-bonds generated for 'chain 'A' and resid 263 through 266'
    Processing helix  chain 'A' and resid 315 through 332
      removed outlier: 4.010A  pdb=" N   ILE A 318 " --> pdb=" O   ASP A 315 " (cutoff:3.500A)
      Proline residue:  A 319  - end of helix
    Processing helix  chain 'A' and resid 344 through 346
      No H-bonds generated for 'chain 'A' and resid 344 through 346'
    Processing helix  chain 'A' and resid 388 through 398
    Processing helix  chain 'A' and resid 403 through 413
      removed outlier: 4.603A  pdb=" N   GLY A 413 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 457
    Processing helix  chain 'A' and resid 503 through 507
      removed outlier: 4.251A  pdb=" N   LYS A 507 " --> pdb=" O   GLU A 503 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 503 through 507'
    Processing helix  chain 'A' and resid 510 through 519
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 541 through 550
      removed outlier: 4.798A  pdb=" N   TRP A 550 " --> pdb=" O   GLU A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 592
      removed outlier: 3.646A  pdb=" N   THR A 591 " --> pdb=" O   VAL A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 630
      removed outlier: 4.008A  pdb=" N   MET A 613 " --> pdb=" O   LYS A 610 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   ASP A 614 " --> pdb=" O   ARG A 611 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   GLN A 615 " --> pdb=" O   ALA A 612 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A 616 " --> pdb=" O   MET A 613 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ILE A 626 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA A 627 " --> pdb=" O   GLU A 624 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLY A 628 " --> pdb=" O   LYS A 625 " (cutoff:3.500A)
      Proline residue:  A 629  - end of helix
    Processing helix  chain 'A' and resid 647 through 660
    Processing helix  chain 'A' and resid 676 through 687
    Processing helix  chain 'A' and resid 699 through 703
    Processing helix  chain 'A' and resid 709 through 723
    Processing helix  chain 'A' and resid 782 through 801
      removed outlier: 3.535A  pdb=" N   LEU A 788 " --> pdb=" O   ASP A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 825
      removed outlier: 4.022A  pdb=" N   LEU A 820 " --> pdb=" O   ASP A 817 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   LYS A 821 " --> pdb=" O   GLY A 818 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASN A 825 " --> pdb=" O   THR A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 837
      removed outlier: 3.512A  pdb=" N   LYS A 833 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   CYS A 834 " --> pdb=" O   GLN A 830 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   PHE A 835 " --> pdb=" O   LEU A 831 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   GLU A 836 " --> pdb=" O   GLN A 832 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ALA A 837 " --> pdb=" O   LYS A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 927
      removed outlier: 3.896A  pdb=" N   HIS A 927 " --> pdb=" O   PHE A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 940 through 954
    Processing helix  chain 'A' and resid 962 through 966
      removed outlier: 4.081A  pdb=" N   GLY A 966 " --> pdb=" O   GLN A 963 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 560 through 565
    Processing sheet with id=  B, first strand: chain 'A' and resid 228 through 230
      removed outlier: 3.614A  pdb=" N   ASN A 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 231 through 233
    Processing sheet with id=  D, first strand: chain 'A' and resid 270 through 272
      removed outlier: 5.825A  pdb=" N   HIS A 242 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   LEU A 306 " --> pdb=" O   HIS A 242 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   THR A 244 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE A 304 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   SER A 246 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   ILE A 302 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 348 through 350
    Processing sheet with id=  F, first strand: chain 'A' and resid 423 through 425
      removed outlier: 3.514A  pdb=" N   ARG A 423 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'A' and resid 429 through 431
    Processing sheet with id=  H, first strand: chain 'A' and resid 570 through 572
    Processing sheet with id=  I, first strand: chain 'A' and resid 638 through 641
      removed outlier: 6.430A  pdb=" N   MET A 666 " --> pdb=" O   ALA A 605 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   PHE A 607 " --> pdb=" O   MET A 666 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL A 668 " --> pdb=" O   PHE A 607 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   CYS A 669 " --> pdb=" O   PRO A 693 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   GLN A 695 " --> pdb=" O   CYS A 669 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   ILE A 671 " --> pdb=" O   GLN A 695 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ILE A 697 " --> pdb=" O   ILE A 671 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'A' and resid 769 through 775
      removed outlier: 3.908A  pdb=" N   ASP A 743 " --> pdb=" O   GLY A 757 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   VAL A 739 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   LYS A 807 " --> pdb=" O   MET A 738 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   ILE A 740 " --> pdb=" O   LYS A 807 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   VAL A 809 " --> pdb=" O   ILE A 740 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   MET A 742 " --> pdb=" O   VAL A 809 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TYR A 811 " --> pdb=" O   MET A 742 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   VAL A 744 " --> pdb=" O   TYR A 811 " (cutoff:3.500A)
      removed outlier: 8.426A  pdb=" N   ASP A 813 " --> pdb=" O   VAL A 744 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LYS A 844 " --> pdb=" O   ILE A 808 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   VAL A 810 " --> pdb=" O   LYS A 844 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL A 846 " --> pdb=" O   VAL A 810 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ARG A 812 " --> pdb=" O   VAL A 846 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   PHE A 848 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 908 " --> pdb=" O   VAL A 847 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   VAL A 849 " --> pdb=" O   CYS A 906 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   CYS A 906 " --> pdb=" O   VAL A 849 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 851 " --> pdb=" O   TYR A 904 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   TYR A 904 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL A 885 " --> pdb=" O   CYS A 906 " (cutoff:3.500A)

    231 hydrogen bonds defined for protein.
    579 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      3 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 963
        1.30 -     1.43: 1632
        1.43 -     1.56: 3607
        1.56 -     1.69: 16
        1.69 -     1.82: 67
  Bond restraints: 6285
  Sorted by residual:
  bond pdb=" O3'   U B   2 "
       pdb=" P     A B   3 "
    ideal  model  delta    sigma   weight residual
    1.607  1.528  0.079 1.50e-02 4.44e+03 2.78e+01
  bond pdb=" P     U B   2 "
       pdb=" OP1   U B   2 "
    ideal  model  delta    sigma   weight residual
    1.485  1.434  0.051 2.00e-02 2.50e+03 6.59e+00
  bond pdb=" N   GLN A 263 "
       pdb=" CA  GLN A 263 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 5.13e+00
  bond pdb=" N   SER A 264 "
       pdb=" CA  SER A 264 "
    ideal  model  delta    sigma   weight residual
    1.453  1.484 -0.031 1.41e-02 5.03e+03 4.92e+00
  bond pdb=" N   HIS A 262 "
       pdb=" CA  HIS A 262 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.32e-02 5.74e+03 4.48e+00
  ... (remaining 6280 not shown)

  Histogram of bond angle deviations from ideal:
       86.40 -    95.92: 2
       95.92 -   105.44: 161
      105.44 -   114.97: 3906
      114.97 -   124.49: 4319
      124.49 -   134.01: 165
  Bond angle restraints: 8553
  Sorted by residual:
  angle pdb=" O3'   U B  25 "
        pdb=" P   OMC B  26 "
        pdb=" OP1 OMC B  26 "
      ideal   model   delta    sigma   weight residual
     108.00   86.40   21.60 3.00e+00 1.11e-01 5.18e+01
  angle pdb=" O3'   U B  25 "
        pdb=" P   OMC B  26 "
        pdb=" OP2 OMC B  26 "
      ideal   model   delta    sigma   weight residual
     108.00   90.04   17.96 3.00e+00 1.11e-01 3.58e+01
  angle pdb=" N   GLN A 263 "
        pdb=" CA  GLN A 263 "
        pdb=" C   GLN A 263 "
      ideal   model   delta    sigma   weight residual
     111.28  105.23    6.05 1.09e+00 8.42e-01 3.09e+01
  angle pdb=" C4'   U B   2 "
        pdb=" C3'   U B   2 "
        pdb=" O3'   U B   2 "
      ideal   model   delta    sigma   weight residual
     113.00  119.62   -6.62 1.50e+00 4.44e-01 1.95e+01
  angle pdb=" N   HIS A 262 "
        pdb=" CA  HIS A 262 "
        pdb=" C   HIS A 262 "
      ideal   model   delta    sigma   weight residual
     113.02  108.23    4.79 1.20e+00 6.94e-01 1.59e+01
  ... (remaining 8548 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3360
       17.79 -    35.59: 355
       35.59 -    53.38: 68
       53.38 -    71.17: 21
       71.17 -    88.97: 8
  Dihedral angle restraints: 3812
    sinusoidal: 1647
      harmonic: 2165
  Sorted by residual:
  dihedral pdb=" C4'   U B   2 "
           pdb=" C3'   U B   2 "
           pdb=" C2'   U B   2 "
           pdb=" C1'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.00    5.39   30.61     1      8.00e+00 1.56e-02 2.09e+01
  dihedral pdb=" O4'   U B   2 "
           pdb=" C2'   U B   2 "
           pdb=" C1'   U B   2 "
           pdb=" C3'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -2.36   27.36     1      8.00e+00 1.56e-02 1.68e+01
  dihedral pdb=" C5'   U B   2 "
           pdb=" C4'   U B   2 "
           pdb=" C3'   U B   2 "
           pdb=" O3'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  109.29  -27.29     1      8.00e+00 1.56e-02 1.67e+01
  ... (remaining 3809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 833
       0.068 -    0.135: 125
       0.135 -    0.203: 13
       0.203 -    0.271: 1
       0.271 -    0.339: 1
  Chirality restraints: 973
  Sorted by residual:
  chirality pdb=" P     U B   2 "
            pdb=" OP1   U B   2 "
            pdb=" OP2   U B   2 "
            pdb=" O5'   U B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.07    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" C3'   U B   2 "
            pdb=" C4'   U B   2 "
            pdb=" O3'   U B   2 "
            pdb=" C2'   U B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.22   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  ILE A 905 "
            pdb=" N   ILE A 905 "
            pdb=" C   ILE A 905 "
            pdb=" CB  ILE A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.73e-01
  ... (remaining 970 not shown)

  Planarity restraints: 1052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' OMC B  26 "    0.029 2.00e-02 2.50e+03   5.58e-01 6.99e+03
        pdb=" C4' OMC B  26 "    0.427 2.00e-02 2.50e+03
        pdb=" O4' OMC B  26 "    0.599 2.00e-02 2.50e+03
        pdb=" C3' OMC B  26 "   -0.592 2.00e-02 2.50e+03
        pdb=" O3' OMC B  26 "   -0.549 2.00e-02 2.50e+03
        pdb=" C2' OMC B  26 "   -0.213 2.00e-02 2.50e+03
        pdb=" O2' OMC B  26 "    0.897 2.00e-02 2.50e+03
        pdb=" C1' OMC B  26 "    0.238 2.00e-02 2.50e+03
        pdb=" N1  OMC B  26 "   -0.836 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   2 "   -0.044 2.00e-02 2.50e+03   2.47e-02 1.38e+01
        pdb=" N1    U B   2 "    0.056 2.00e-02 2.50e+03
        pdb=" C2    U B   2 "    0.014 2.00e-02 2.50e+03
        pdb=" O2    U B   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    U B   2 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4    U B   2 "   -0.013 2.00e-02 2.50e+03
        pdb=" O4    U B   2 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    U B   2 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U B   2 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 220 "   -0.038 5.00e-02 4.00e+02   5.66e-02 5.12e+00
        pdb=" N   PRO A 221 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 221 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 221 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1049 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 29
        2.49 -     3.10: 4066
        3.10 -     3.70: 8669
        3.70 -     4.30: 12877
        4.30 -     4.90: 21966
  Nonbonded interactions: 47607
  Sorted by model distance:
  nonbonded pdb=" OP1   U B   1 "
            pdb="MG    MG A1001 "
     model   vdw
     1.892 2.170
  nonbonded pdb=" O   LEU A 971 "
            pdb="MG    MG A1001 "
     model   vdw
     1.900 2.170
  nonbonded pdb=" OD2 ASP A 743 "
            pdb="MG    MG A1002 "
     model   vdw
     2.039 2.170
  nonbonded pdb=" OP1   A B   3 "
            pdb="MG    MG A1001 "
     model   vdw
     2.114 2.170
  nonbonded pdb=" OG  SER A 439 "
            pdb=" OE2 GLU A 447 "
     model   vdw
     2.209 2.440
  ... (remaining 47602 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:             0.530
  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:          1.970
  Check model and map are aligned:         0.080
  Set scattering table:                    0.060
  Process input model:                     22.980
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
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      :  0.004   0.079   6285  Z= 0.294
  Angle     :  0.827  21.598   8553  Z= 0.436
  Chirality :  0.049   0.339    973
  Planarity :  0.018   0.558   1052
  Dihedral  : 15.541  88.968   2410
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.31), residues: 733
  helix:  1.28 (0.36), residues: 234
  sheet:  0.54 (0.36), residues: 198
  loop : -1.22 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 728 
 HIS   0.010   0.001   HIS A 353 
 PHE   0.017   0.002   PHE A 578 
 TYR   0.013   0.002   TYR A 239 
 ARG   0.008   0.001   ARG A 570 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.711 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 1.1501
  time to fit residues: 93.4204
Evaluate side-chains
  63 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.3980
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 18 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0980
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 GLN
A 746 HIS
** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6285  Z= 0.181
  Angle     :  0.624  13.460   8553  Z= 0.356
  Chirality :  0.044   0.180    973
  Planarity :  0.006   0.118   1052
  Dihedral  : 10.172  81.645    928
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.77 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.31), residues: 733
  helix:  1.13 (0.36), residues: 234
  sheet:  0.78 (0.37), residues: 194
  loop : -1.07 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 884 
 HIS   0.004   0.001   HIS A 927 
 PHE   0.013   0.001   PHE A 320 
 TYR   0.015   0.001   TYR A 239 
 ARG   0.004   0.000   ARG A 570 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A  505 MET cc_start: 0.6649 (mmt) cc_final: 0.6248 (mmt)
REVERT: A  886 ASP cc_start: 0.8169 (p0) cc_final: 0.7917 (p0)
REVERT: A  895 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.5716 (ptp90)
  outliers start: 13
  outliers final: 4
  residues processed: 81
  average time/residue: 1.2984
  time to fit residues: 110.1793
Evaluate side-chains
  70 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 240 GLN
A 263 GLN
** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 ASN
A 539 GLN
A 763 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   6285  Z= 0.357
  Angle     :  0.692  12.724   8553  Z= 0.386
  Chirality :  0.048   0.175    973
  Planarity :  0.006   0.117   1052
  Dihedral  : 10.195  80.965    928
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 14.46 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.31), residues: 733
  helix:  0.81 (0.35), residues: 238
  sheet:  0.41 (0.36), residues: 197
  loop : -1.22 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 604 
 HIS   0.008   0.001   HIS A 927 
 PHE   0.024   0.002   PHE A 320 
 TYR   0.016   0.002   TYR A 239 
 ARG   0.004   0.000   ARG A 327 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6729 (mmp) cc_final: 0.6350 (mmp)
REVERT: A  309 ILE cc_start: 0.7501 (mt) cc_final: 0.7256 (mt)
REVERT: A  505 MET cc_start: 0.6497 (mmt) cc_final: 0.5805 (mmt)
REVERT: A  535 GLN cc_start: 0.7557 (tp40) cc_final: 0.7317 (mm110)
REVERT: A  845 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7446 (ttt)
REVERT: A  895 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.5734 (ptp90)
  outliers start: 22
  outliers final: 7
  residues processed: 86
  average time/residue: 1.2396
  time to fit residues: 112.0703
Evaluate side-chains
  64 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  845 MET
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6285  Z= 0.180
  Angle     :  0.598  12.821   8553  Z= 0.342
  Chirality :  0.043   0.159    973
  Planarity :  0.006   0.114   1052
  Dihedral  :  9.949  79.062    928
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.44 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.31), residues: 733
  helix:  1.18 (0.36), residues: 237
  sheet:  0.51 (0.36), residues: 196
  loop : -1.14 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 604 
 HIS   0.004   0.001   HIS A 927 
 PHE   0.016   0.001   PHE A 320 
 TYR   0.012   0.001   TYR A 239 
 ARG   0.005   0.000   ARG A 423 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6927 (mmp) cc_final: 0.6623 (mmp)
REVERT: A  309 ILE cc_start: 0.7388 (mt) cc_final: 0.7097 (mt)
REVERT: A  663 LYS cc_start: 0.7464 (mtmm) cc_final: 0.7188 (mmmt)
REVERT: A  845 MET cc_start: 0.7670 (ttm) cc_final: 0.7418 (ttt)
REVERT: A  895 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.5847 (ptp90)
  outliers start: 19
  outliers final: 6
  residues processed: 77
  average time/residue: 1.3722
  time to fit residues: 110.6639
Evaluate side-chains
  62 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 40 optimal weight:    0.1980
   chunk 1 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0070
   overall best weight:    0.6002

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN
A 535 GLN
A 539 GLN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6285  Z= 0.157
  Angle     :  0.584  12.687   8553  Z= 0.335
  Chirality :  0.043   0.154    973
  Planarity :  0.006   0.114   1052
  Dihedral  :  9.842  78.230    928
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.78 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.31), residues: 733
  helix:  1.35 (0.36), residues: 237
  sheet:  0.60 (0.36), residues: 196
  loop : -1.02 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 604 
 HIS   0.003   0.000   HIS A 927 
 PHE   0.013   0.001   PHE A 320 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.004   0.000   ARG A 611 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6893 (mmp) cc_final: 0.6656 (mmp)
REVERT: A  309 ILE cc_start: 0.7486 (mt) cc_final: 0.7191 (mt)
REVERT: A  663 LYS cc_start: 0.7373 (mtmm) cc_final: 0.7142 (mmmt)
  outliers start: 17
  outliers final: 7
  residues processed: 78
  average time/residue: 1.4160
  time to fit residues: 115.5907
Evaluate side-chains
  64 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  868 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0670
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8922

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6285  Z= 0.188
  Angle     :  0.607  12.681   8553  Z= 0.342
  Chirality :  0.043   0.175    973
  Planarity :  0.006   0.114   1052
  Dihedral  :  9.781  77.566    928
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.57 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.31), residues: 733
  helix:  1.40 (0.36), residues: 237
  sheet:  0.61 (0.36), residues: 196
  loop : -1.00 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 604 
 HIS   0.003   0.001   HIS A 927 
 PHE   0.021   0.001   PHE A 272 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.007   0.000   ARG A 423 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6910 (mmp) cc_final: 0.6682 (mmp)
REVERT: A  309 ILE cc_start: 0.7479 (mt) cc_final: 0.7170 (mt)
REVERT: A  423 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.7143 (ttm110)
REVERT: A  505 MET cc_start: 0.6495 (mmt) cc_final: 0.5686 (mmt)
REVERT: A  895 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5637 (ptp90)
  outliers start: 15
  outliers final: 9
  residues processed: 68
  average time/residue: 1.3534
  time to fit residues: 96.5260
Evaluate side-chains
  66 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 40 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0970
   chunk 70 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 262 HIS
A 285 GLN
** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6285  Z= 0.167
  Angle     :  0.590  12.592   8553  Z= 0.335
  Chirality :  0.043   0.170    973
  Planarity :  0.005   0.114   1052
  Dihedral  :  9.739  76.104    928
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.27 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.31), residues: 733
  helix:  1.49 (0.36), residues: 237
  sheet:  0.65 (0.36), residues: 194
  loop : -1.02 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 604 
 HIS   0.003   0.001   HIS A 927 
 PHE   0.013   0.001   PHE A 320 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.007   0.000   ARG A 611 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6941 (mmp) cc_final: 0.6693 (mmp)
REVERT: A  309 ILE cc_start: 0.7416 (mt) cc_final: 0.7132 (mt)
REVERT: A  423 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.6886 (ttm110)
REVERT: A  505 MET cc_start: 0.6561 (mmt) cc_final: 0.5720 (mmt)
REVERT: A  610 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7646 (mptt)
REVERT: A  666 MET cc_start: 0.8775 (tpp) cc_final: 0.8575 (ttm)
REVERT: A  895 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5680 (ptp90)
  outliers start: 16
  outliers final: 9
  residues processed: 74
  average time/residue: 1.3929
  time to fit residues: 107.8750
Evaluate side-chains
  67 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
A 520 ASN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6285  Z= 0.174
  Angle     :  0.590  12.517   8553  Z= 0.335
  Chirality :  0.043   0.151    973
  Planarity :  0.005   0.113   1052
  Dihedral  :  9.643  75.037    928
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.97 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.31), residues: 733
  helix:  1.51 (0.36), residues: 238
  sheet:  0.63 (0.36), residues: 196
  loop : -1.02 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 604 
 HIS   0.003   0.001   HIS A 927 
 PHE   0.016   0.001   PHE A 950 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.005   0.000   ARG A 423 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6950 (mmp) cc_final: 0.6694 (mmp)
REVERT: A  309 ILE cc_start: 0.7399 (mt) cc_final: 0.7086 (mt)
REVERT: A  423 ARG cc_start: 0.7399 (mtp-110) cc_final: 0.7082 (ttm110)
REVERT: A  505 MET cc_start: 0.6531 (mmt) cc_final: 0.5752 (mmt)
REVERT: A  666 MET cc_start: 0.8951 (tpp) cc_final: 0.8643 (ttm)
REVERT: A  895 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.5622 (ptp90)
  outliers start: 14
  outliers final: 9
  residues processed: 67
  average time/residue: 1.3846
  time to fit residues: 97.2277
Evaluate side-chains
  66 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6285  Z= 0.239
  Angle     :  0.619  12.509   8553  Z= 0.350
  Chirality :  0.044   0.159    973
  Planarity :  0.005   0.113   1052
  Dihedral  :  9.613  74.456    928
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.97 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.31), residues: 733
  helix:  1.43 (0.36), residues: 238
  sheet:  0.56 (0.36), residues: 194
  loop : -1.16 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 927 
 PHE   0.018   0.001   PHE A 320 
 TYR   0.012   0.001   TYR A 239 
 ARG   0.005   0.000   ARG A 611 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.612 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6981 (mmp) cc_final: 0.6747 (mmp)
REVERT: A  309 ILE cc_start: 0.7458 (mt) cc_final: 0.7141 (mt)
REVERT: A  334 MET cc_start: 0.8269 (mtp) cc_final: 0.8027 (mtp)
REVERT: A  348 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6415 (ptt)
REVERT: A  666 MET cc_start: 0.8955 (tpp) cc_final: 0.8279 (ttt)
REVERT: A  895 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5619 (ptp90)
  outliers start: 15
  outliers final: 10
  residues processed: 71
  average time/residue: 1.3379
  time to fit residues: 99.5921
Evaluate side-chains
  69 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 44 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
A 520 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6285  Z= 0.165
  Angle     :  0.598  12.370   8553  Z= 0.341
  Chirality :  0.043   0.144    973
  Planarity :  0.005   0.113   1052
  Dihedral  :  9.597  73.627    928
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.01 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.31), residues: 733
  helix:  1.51 (0.36), residues: 238
  sheet:  0.64 (0.36), residues: 194
  loop : -1.09 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 884 
 HIS   0.003   0.001   HIS A 927 
 PHE   0.019   0.001   PHE A 272 
 TYR   0.010   0.001   TYR A 239 
 ARG   0.006   0.000   ARG A 423 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6951 (mmp) cc_final: 0.6706 (mmp)
REVERT: A  309 ILE cc_start: 0.7360 (mt) cc_final: 0.7043 (mt)
REVERT: A  334 MET cc_start: 0.8254 (mtp) cc_final: 0.7941 (mtp)
REVERT: A  755 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7837 (t)
REVERT: A  895 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.5624 (ptp90)
  outliers start: 13
  outliers final: 9
  residues processed: 67
  average time/residue: 1.3201
  time to fit residues: 92.7993
Evaluate side-chains
  67 residues out of total 671 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  677 ASP
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.170285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123905 restraints weight = 6741.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.69
r_work: 0.3069 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   6285  Z= 0.377
  Angle     :  0.685  12.489   8553  Z= 0.381
  Chirality :  0.047   0.174    973
  Planarity :  0.006   0.113   1052
  Dihedral  :  9.693  73.976    928
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 21.61 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.30), residues: 733
  helix:  1.25 (0.35), residues: 237
  sheet:  0.31 (0.36), residues: 197
  loop : -1.26 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 604 
 HIS   0.007   0.001   HIS A 927 
 PHE   0.023   0.002   PHE A 320 
 TYR   0.015   0.002   TYR A 239 
 ARG   0.007   0.001   ARG A 423 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2453.27 seconds
wall clock time: 44 minutes 25.83 seconds (2665.83 seconds total)