Starting phenix.real_space_refine
on Sun Jul 21 15:36:40 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/07_2024/8pjj_17711.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/07_2024/8pjj_17711.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/07_2024/8pjj_17711.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/07_2024/8pjj_17711.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/07_2024/8pjj_17711.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjj_17711/07_2024/8pjj_17711.cif"
  }
  resolution = 4.24
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7392 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P      42      5.49       5
     S      47      5.16       5
     C    5137      2.51       5
     N    1438      2.21       5
     O    1684      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  551": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  603": "OD1" <-> "OD2"
    Residue "A ASP  605": "OD1" <-> "OD2"
    Residue "A ASP  882": "OD1" <-> "OD2"
    Residue "A GLU  896": "OE1" <-> "OE2"
    Residue "A GLU 1025": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 8348
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7474
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 946, 7463
          Classifications: {'peptide': 946}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 898}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
      Conformer: "B"
        Number of residues, atoms: 946, 7463
          Classifications: {'peptide': 946}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 898}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
          bond proxies already assigned to first conformer: 7593
    Chain: "B"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 847
          Classifications: {'RNA': 40}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 2, 'rna3p': 37}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.55, per 1000 atoms: 1.02
  Number of scatterers: 8348
  At special positions: 0
  Unit cell: (74.56, 102.52, 137.004, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P      42     15.00
     O    1684      8.00
     N    1438      7.00
     C    5137      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: 3.74
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 7 sheets defined
      47.1% alpha, 10.8% beta
      10 base pairs and 15 stacking pairs defined.
    Time for finding SS restraints: 2.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 171 through 181
    Processing helix  chain 'A' and resid 223 through 242
    Processing helix  chain 'A' and resid 268 through 283
    Processing helix  chain 'A' and resid 347 through 351
    Processing helix  chain 'A' and resid 352 through 371
    Processing helix  chain 'A' and resid 371 through 384
    Processing helix  chain 'A' and resid 385 through 388
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.741A  pdb=" N   ASN A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 415
      removed outlier: 3.601A  pdb=" N   THR A 415 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 412 through 415'
    Processing helix  chain 'A' and resid 416 through 428
      removed outlier: 3.564A  pdb=" N   SER A 428 " --> pdb=" O   ASP A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 458
    Processing helix  chain 'A' and resid 486 through 494
    Processing helix  chain 'A' and resid 513 through 530
      removed outlier: 3.585A  pdb=" N   ASP A 525 " --> pdb=" O   VAL A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 551
    Processing helix  chain 'A' and resid 570 through 578
    Processing helix  chain 'A' and resid 621 through 629
    Processing helix  chain 'A' and resid 636 through 651
      removed outlier: 3.737A  pdb=" N   LEU A 640 " --> pdb=" O   SER A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 676
    Processing helix  chain 'A' and resid 695 through 703
      removed outlier: 3.785A  pdb=" N   GLN A 699 " --> pdb=" O   PRO A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 722
      removed outlier: 3.554A  pdb=" N   GLU A 721 " --> pdb=" O   THR A 717 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR A 722 " --> pdb=" O   ASN A 718 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 717 through 722'
    Processing helix  chain 'A' and resid 758 through 767
    Processing helix  chain 'A' and resid 782 through 789
      removed outlier: 3.584A  pdb=" N   LEU A 789 " --> pdb=" O   ARG A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 812
    Processing helix  chain 'A' and resid 816 through 823
    Processing helix  chain 'A' and resid 829 through 842
      removed outlier: 3.620A  pdb=" N   VAL A 833 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 862
      removed outlier: 3.739A  pdb=" N   ARG A 861 " --> pdb=" O   ARG A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 878
      removed outlier: 5.040A  pdb=" N   MET A 871 " --> pdb=" O   ARG A 867 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU A 874 " --> pdb=" O   LYS A 870 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA A 876 " --> pdb=" O   MET A 872 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A 877 " --> pdb=" O   VAL A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 893
    Processing helix  chain 'A' and resid 908 through 914
    Processing helix  chain 'A' and resid 920 through 937
    Processing helix  chain 'A' and resid 940 through 950
      removed outlier: 3.923A  pdb=" N   ARG A 945 " --> pdb=" O   HIS A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 975
    Processing helix  chain 'A' and resid 977 through 981
      removed outlier: 3.821A  pdb=" N   CYS A 980 " --> pdb=" O   PRO A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1008
    Processing helix  chain 'A' and resid 1101 through 1110
      removed outlier: 3.573A  pdb=" N   ALA A1105 " --> pdb=" O   GLU A1101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1111 through 1125
    Processing helix  chain 'A' and resid 1126 through 1129
      removed outlier: 3.678A  pdb=" N   ILE A1129 " --> pdb=" O   PRO A1126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1126 through 1129'
    Processing helix  chain 'A' and resid 1133 through 1147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192
      removed outlier: 3.689A  pdb=" N   LEU A 204 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192
    Processing sheet with id=AA3, first strand: chain 'A' and resid 465 through 468
      removed outlier: 7.478A  pdb=" N   ILE A 436 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
      removed outlier: 9.157A  pdb=" N   CYS A 485 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ILE A 504 " --> pdb=" O   ILE A 536 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   MET A 538 " --> pdb=" O   ILE A 504 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL A 403 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   SER A 539 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ILE A 405 " --> pdb=" O   SER A 539 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   LEU A 557 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   ILE A 404 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   VAL A 559 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ARG A 406 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 569
      removed outlier: 5.252A  pdb=" N   PHE A 569 " --> pdb=" O   THR A 779 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL A 730 " --> pdb=" O   PHE A 776 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   PHE A 778 " --> pdb=" O   VAL A 730 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   VAL A 732 " --> pdb=" O   PHE A 778 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   ALA A 655 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   ILE A 656 " --> pdb=" O   ILE A 714 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   SER A 716 " --> pdb=" O   ILE A 656 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   VAL A 658 " --> pdb=" O   SER A 716 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   GLN A 686 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   LEU A 715 " --> pdb=" O   GLN A 686 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   LEU A 688 " --> pdb=" O   LEU A 715 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 744
      removed outlier: 3.861A  pdb=" N   ALA A 738 " --> pdb=" O   VAL A 755 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   VAL A 755 " --> pdb=" O   ALA A 738 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA A 753 " --> pdb=" O   MET A 740 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1055 through 1056
      removed outlier: 3.880A  pdb=" N   SER A1062 " --> pdb=" O   ILE A1056 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   CYS A1063 " --> pdb=" O   ALA A1028 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   LEU A1030 " --> pdb=" O   CYS A1063 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS A1027 " --> pdb=" O   THR A1023 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   LYS A1020 " --> pdb=" O   LYS A1016 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1090 through 1092

    325 hydrogen bonds defined for protein.
    933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      15 stacking parallelities
  Total time for adding SS restraints: 3.33

  Time building geometry restraints manager: 3.98 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: 2475
        1.34 -     1.46: 1525
        1.46 -     1.58: 4440
        1.58 -     1.70: 81
        1.70 -     1.82: 71
  Bond restraints: 8592
  Sorted by residual:
  bond pdb=" N   ASP A 605 "
       pdb=" CA  ASP A 605 "
    ideal  model  delta    sigma   weight residual
    1.460  1.489 -0.029 1.02e-02 9.61e+03 8.03e+00
  bond pdb=" N   ASP A 603 "
       pdb=" CA  ASP A 603 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.23e-02 6.61e+03 6.80e+00
  bond pdb=" N   LYS A 604 "
       pdb=" CA  LYS A 604 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.27e+00
  bond pdb=" N   GLU A 608 "
       pdb=" CA  GLU A 608 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.23e-02 6.61e+03 5.46e+00
  bond pdb=" N   GLU A 602 "
       pdb=" CA  GLU A 602 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 5.17e+00
  ... (remaining 8587 not shown)

  Histogram of bond angle deviations from ideal:
       98.58 -   106.11: 425
      106.11 -   113.63: 4874
      113.63 -   121.15: 4228
      121.15 -   128.67: 2227
      128.67 -   136.20: 81
  Bond angle restraints: 11835
  Sorted by residual:
  angle pdb=" N   GLU A 379 "
        pdb=" CA  GLU A 379 "
        pdb=" CB  GLU A 379 "
      ideal   model   delta    sigma   weight residual
     110.39  117.65   -7.26 1.66e+00 3.63e-01 1.91e+01
  angle pdb=" N   LEU A 630 "
        pdb=" CA  LEU A 630 "
        pdb=" CB  LEU A 630 "
      ideal   model   delta    sigma   weight residual
     110.49  116.86   -6.37 1.69e+00 3.50e-01 1.42e+01
  angle pdb=" C   MET A 629 "
        pdb=" N   LEU A 630 "
        pdb=" CA  LEU A 630 "
      ideal   model   delta    sigma   weight residual
     121.54  128.60   -7.06 1.91e+00 2.74e-01 1.37e+01
  angle pdb=" C   GLU A 608 "
        pdb=" N   ILE A 609 "
        pdb=" CA  ILE A 609 "
      ideal   model   delta    sigma   weight residual
     123.14  118.37    4.77 1.31e+00 5.83e-01 1.33e+01
  angle pdb=" C   LEU A 378 "
        pdb=" N   GLU A 379 "
        pdb=" CA  GLU A 379 "
      ideal   model   delta    sigma   weight residual
     120.72  114.76    5.96 1.67e+00 3.59e-01 1.27e+01
  ... (remaining 11830 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 5117
       35.95 -    71.89: 165
       71.89 -   107.84: 21
      107.84 -   143.79: 3
      143.79 -   179.73: 2
  Dihedral angle restraints: 5308
    sinusoidal: 2528
      harmonic: 2780
  Sorted by residual:
  dihedral pdb=" O4'   C B  45 "
           pdb=" C1'   C B  45 "
           pdb=" N1    C B  45 "
           pdb=" C2    C B  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   51.73 -179.73     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O1B ADP A1201 "
           pdb=" O3A ADP A1201 "
           pdb=" PB  ADP A1201 "
           pdb=" PA  ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  170.25  129.75     1      2.00e+01 2.50e-03 3.93e+01
  dihedral pdb=" O4'   U B   4 "
           pdb=" C1'   U B   4 "
           pdb=" N1    U B   4 "
           pdb=" C2    U B   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -77.44  -82.56     1      1.50e+01 4.44e-03 3.71e+01
  ... (remaining 5305 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 950
       0.035 -    0.071: 289
       0.071 -    0.106: 113
       0.106 -    0.142: 35
       0.142 -    0.177: 4
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" C1'   U B   9 "
            pdb=" O4'   U B   9 "
            pdb=" C2'   U B   9 "
            pdb=" N1    U B   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.29    0.18 2.00e-01 2.50e+01 7.86e-01
  chirality pdb=" CA  GLU A 608 "
            pdb=" N   GLU A 608 "
            pdb=" C   GLU A 608 "
            pdb=" CB  GLU A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.54e-01
  chirality pdb=" CB  ILE A 735 "
            pdb=" CA  ILE A 735 "
            pdb=" CG1 ILE A 735 "
            pdb=" CG2 ILE A 735 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.85e-01
  ... (remaining 1388 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1134 "   -0.030 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO A1135 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A1135 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1135 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   9 "   -0.024 2.00e-02 2.50e+03   1.20e-02 3.22e+00
        pdb=" N1    U B   9 "    0.025 2.00e-02 2.50e+03
        pdb=" C2    U B   9 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U B   9 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    U B   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U B   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" O4    U B   9 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5    U B   9 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    U B   9 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   8 "   -0.018 2.00e-02 2.50e+03   8.11e-03 1.81e+00
        pdb=" N9    A B   8 "    0.017 2.00e-02 2.50e+03
        pdb=" C8    A B   8 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A B   8 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A B   8 "    0.000 2.00e-02 2.50e+03
        pdb=" N6    A B   8 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A B   8 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A B   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A B   8 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A B   8 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 289
        2.68 -     3.23: 8761
        3.23 -     3.79: 14214
        3.79 -     4.34: 18337
        4.34 -     4.90: 27342
  Nonbonded interactions: 68943
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 332 "
            pdb=" OH  TYR A 479 "
     model   vdw
     2.120 2.440
  nonbonded pdb=" NH1 ARG A 198 "
            pdb=" O2    U B  29 "
     model   vdw
     2.171 2.520
  nonbonded pdb=" OG BSER A1070 "
            pdb=" OE1 GLN A1073 "
     model   vdw
     2.189 2.440
  nonbonded pdb=" OG1 THR A 744 "
            pdb=" OD1 ASN A 747 "
     model   vdw
     2.212 2.440
  nonbonded pdb=" OG  SER A 548 "
            pdb=" O   CYS A 554 "
     model   vdw
     2.226 2.440
  ... (remaining 68938 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=0.00 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:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     33.660
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
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      :  0.003   0.032   8592  Z= 0.181
  Angle     :  0.755  10.234  11835  Z= 0.384
  Chirality :  0.042   0.177   1391
  Planarity :  0.004   0.046   1374
  Dihedral  : 17.529 179.735   3498
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 19.23
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.57 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  0.24 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.28), residues: 942
  helix: -0.09 (0.26), residues: 415
  sheet: -1.24 (0.51), residues: 113
  loop : -1.20 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 328 
 HIS   0.003   0.001   HIS A1032 
 PHE   0.009   0.001   PHE A 518 
 TYR   0.009   0.001   TYR A 530 
 ARG   0.008   0.000   ARG A 375 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9628 (mmp) cc_final: 0.9366 (mmm)
REVERT: A  389 MET cc_start: 0.8688 (pmm) cc_final: 0.8301 (pmm)
REVERT: A  483 LEU cc_start: 0.9233 (tp) cc_final: 0.9002 (tp)
REVERT: A  538 MET cc_start: 0.4037 (ttt) cc_final: 0.3358 (ttt)
REVERT: A  670 MET cc_start: 0.9229 (mmp) cc_final: 0.8980 (mmm)
REVERT: A  797 MET cc_start: 0.8448 (ppp) cc_final: 0.7691 (ppp)
REVERT: A  872 MET cc_start: 0.9050 (mmp) cc_final: 0.8831 (mmm)
REVERT: A  966 GLN cc_start: 0.9527 (tt0) cc_final: 0.9254 (mp10)
  outliers start: 4
  outliers final: 1
  residues processed: 67
  average time/residue: 0.1661
  time to fit residues: 16.9072
Evaluate side-chains
  53 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 41 optimal weight:    9.9990
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   8592  Z= 0.193
  Angle     :  0.693   8.155  11835  Z= 0.340
  Chirality :  0.042   0.191   1391
  Planarity :  0.004   0.044   1374
  Dihedral  : 18.642 178.227   1649
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 23.15
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.47 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  3.25 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.28), residues: 942
  helix: -0.08 (0.25), residues: 424
  sheet: -1.05 (0.50), residues: 112
  loop : -1.39 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 328 
 HIS   0.002   0.001   HIS A 339 
 PHE   0.021   0.001   PHE A 200 
 TYR   0.016   0.001   TYR A 550 
 ARG   0.007   0.000   ARG A 198 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 ASN cc_start: 0.8729 (p0) cc_final: 0.8518 (t0)
REVERT: A  358 MET cc_start: 0.9637 (mmp) cc_final: 0.9363 (mmm)
REVERT: A  389 MET cc_start: 0.8748 (pmm) cc_final: 0.8379 (pmm)
REVERT: A  440 GLN cc_start: 0.8835 (tt0) cc_final: 0.8506 (tt0)
REVERT: A  483 LEU cc_start: 0.9293 (tp) cc_final: 0.9040 (tp)
REVERT: A  538 MET cc_start: 0.4211 (ttt) cc_final: 0.3733 (ttt)
REVERT: A  629 MET cc_start: 0.6994 (tmm) cc_final: 0.6642 (tpp)
REVERT: A  797 MET cc_start: 0.8658 (ppp) cc_final: 0.8021 (ppp)
REVERT: A  807 LEU cc_start: 0.9553 (mt) cc_final: 0.9123 (tt)
REVERT: A 1004 LEU cc_start: 0.8916 (mm) cc_final: 0.8701 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1575
  time to fit residues: 15.7477
Evaluate side-chains
  49 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 96 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   8592  Z= 0.177
  Angle     :  0.668   7.721  11835  Z= 0.326
  Chirality :  0.041   0.195   1391
  Planarity :  0.004   0.045   1374
  Dihedral  : 18.487 178.322   1649
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 22.53
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.83 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  1.68 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.28), residues: 942
  helix:  0.05 (0.25), residues: 426
  sheet: -1.06 (0.49), residues: 112
  loop : -1.48 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 328 
 HIS   0.002   0.001   HIS A 503 
 PHE   0.017   0.001   PHE A 200 
 TYR   0.012   0.001   TYR A 550 
 ARG   0.007   0.000   ARG A 198 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 ASN cc_start: 0.8742 (p0) cc_final: 0.8529 (t0)
REVERT: A  358 MET cc_start: 0.9640 (mmp) cc_final: 0.9370 (mmm)
REVERT: A  389 MET cc_start: 0.8799 (pmm) cc_final: 0.8451 (pmm)
REVERT: A  483 LEU cc_start: 0.9306 (tp) cc_final: 0.9058 (tp)
REVERT: A  484 PHE cc_start: 0.9605 (m-10) cc_final: 0.9359 (m-10)
REVERT: A  538 MET cc_start: 0.3932 (ttt) cc_final: 0.3499 (ttt)
REVERT: A  670 MET cc_start: 0.9207 (mmp) cc_final: 0.8993 (mmm)
REVERT: A  807 LEU cc_start: 0.9562 (mt) cc_final: 0.9160 (tt)
REVERT: A  872 MET cc_start: 0.8979 (mmp) cc_final: 0.8711 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1611
  time to fit residues: 16.3365
Evaluate side-chains
  49 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 9 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 94 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
A 179 GLN
A 238 GLN
A 419 GLN
A 684 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   8592  Z= 0.166
  Angle     :  0.676   8.749  11835  Z= 0.328
  Chirality :  0.041   0.198   1391
  Planarity :  0.004   0.053   1374
  Dihedral  : 18.355 178.271   1649
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.51 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  2.88 %
    Favored  : 96.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.28), residues: 942
  helix:  0.02 (0.25), residues: 429
  sheet: -1.53 (0.50), residues: 103
  loop : -1.31 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 328 
 HIS   0.002   0.001   HIS A 503 
 PHE   0.016   0.001   PHE A 200 
 TYR   0.007   0.001   TYR A 550 
 ARG   0.004   0.000   ARG A 198 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9634 (mmp) cc_final: 0.9359 (mmm)
REVERT: A  389 MET cc_start: 0.8818 (pmm) cc_final: 0.8489 (pmm)
REVERT: A  440 GLN cc_start: 0.8892 (tt0) cc_final: 0.8457 (tt0)
REVERT: A  483 LEU cc_start: 0.9312 (tp) cc_final: 0.9043 (tp)
REVERT: A  538 MET cc_start: 0.3758 (ttt) cc_final: 0.3296 (ttt)
REVERT: A  629 MET cc_start: 0.6783 (tmm) cc_final: 0.6413 (tpp)
REVERT: A  670 MET cc_start: 0.9198 (mmp) cc_final: 0.8979 (mmm)
REVERT: A  807 LEU cc_start: 0.9570 (mt) cc_final: 0.9173 (tt)
REVERT: A  872 MET cc_start: 0.9005 (mmp) cc_final: 0.8705 (mmp)
REVERT: A 1004 LEU cc_start: 0.8908 (mm) cc_final: 0.8690 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1897
  time to fit residues: 18.5002
Evaluate side-chains
  51 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:   40.0000
   chunk 48 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 GLN
A 958 ASN
** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   8592  Z= 0.404
  Angle     :  0.879   9.134  11835  Z= 0.440
  Chirality :  0.047   0.247   1391
  Planarity :  0.006   0.060   1374
  Dihedral  : 18.886 177.566   1649
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 41.88
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 10.53 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.16 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.27), residues: 942
  helix: -0.34 (0.24), residues: 416
  sheet: -1.54 (0.47), residues: 109
  loop : -1.54 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A 328 
 HIS   0.011   0.002   HIS A1015 
 PHE   0.034   0.003   PHE A 200 
 TYR   0.018   0.003   TYR A 420 
 ARG   0.010   0.001   ARG A1091 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9559 (mmp) cc_final: 0.9291 (mmm)
REVERT: A  440 GLN cc_start: 0.8991 (tt0) cc_final: 0.8515 (tt0)
REVERT: A  577 MET cc_start: 0.8187 (pmm) cc_final: 0.7592 (pmm)
REVERT: A  670 MET cc_start: 0.9263 (mmp) cc_final: 0.9015 (mmm)
REVERT: A  797 MET cc_start: 0.8785 (ppp) cc_final: 0.8117 (ppp)
REVERT: A  871 MET cc_start: 0.8737 (ptp) cc_final: 0.8136 (pmm)
REVERT: A  872 MET cc_start: 0.8903 (mmp) cc_final: 0.8663 (mmp)
REVERT: A 1004 LEU cc_start: 0.9111 (mm) cc_final: 0.8839 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1771
  time to fit residues: 14.0617
Evaluate side-chains
  43 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 94 optimal weight:   10.0000
   chunk 78 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 430 GLN
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   8592  Z= 0.194
  Angle     :  0.738   8.861  11835  Z= 0.357
  Chirality :  0.044   0.293   1391
  Planarity :  0.004   0.065   1374
  Dihedral  : 18.596 177.309   1649
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 25.41
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  9.36 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  1.08 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.27), residues: 942
  helix: -0.13 (0.25), residues: 426
  sheet: -1.50 (0.50), residues: 96
  loop : -1.55 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 328 
 HIS   0.003   0.001   HIS A 510 
 PHE   0.020   0.002   PHE A 200 
 TYR   0.018   0.002   TYR A 685 
 ARG   0.005   0.000   ARG A 375 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9567 (mmp) cc_final: 0.9308 (mmm)
REVERT: A  389 MET cc_start: 0.8852 (pmm) cc_final: 0.8547 (pmm)
REVERT: A  440 GLN cc_start: 0.9084 (tt0) cc_final: 0.8587 (tt0)
REVERT: A  483 LEU cc_start: 0.9383 (tp) cc_final: 0.9164 (tp)
REVERT: A  538 MET cc_start: 0.3399 (ttt) cc_final: 0.2882 (ttt)
REVERT: A  577 MET cc_start: 0.8113 (pmm) cc_final: 0.7507 (pmm)
REVERT: A  629 MET cc_start: 0.7187 (tmm) cc_final: 0.6882 (tpp)
REVERT: A  670 MET cc_start: 0.9213 (mmp) cc_final: 0.8929 (mmm)
REVERT: A  797 MET cc_start: 0.8689 (ppp) cc_final: 0.7964 (ppp)
REVERT: A  807 LEU cc_start: 0.9652 (mt) cc_final: 0.9298 (tt)
REVERT: A  872 MET cc_start: 0.9128 (mmp) cc_final: 0.8769 (mmp)
REVERT: A 1004 LEU cc_start: 0.9061 (mm) cc_final: 0.8854 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1649
  time to fit residues: 14.8734
Evaluate side-chains
  43 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 79 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 958 ASN
** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   8592  Z= 0.241
  Angle     :  0.737   8.959  11835  Z= 0.360
  Chirality :  0.044   0.256   1391
  Planarity :  0.005   0.066   1374
  Dihedral  : 18.655 178.432   1649
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 28.84
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 10.00 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.96 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.27), residues: 942
  helix: -0.15 (0.24), residues: 426
  sheet: -1.68 (0.49), residues: 103
  loop : -1.53 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 328 
 HIS   0.006   0.001   HIS A 510 
 PHE   0.023   0.002   PHE A 200 
 TYR   0.023   0.002   TYR A 685 
 ARG   0.004   0.001   ARG A 524 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9552 (mmp) cc_final: 0.9296 (mmm)
REVERT: A  389 MET cc_start: 0.8872 (pmm) cc_final: 0.8598 (pmm)
REVERT: A  440 GLN cc_start: 0.9052 (tt0) cc_final: 0.8608 (tt0)
REVERT: A  538 MET cc_start: 0.3432 (ttt) cc_final: 0.3138 (ttt)
REVERT: A  577 MET cc_start: 0.8153 (pmm) cc_final: 0.7817 (pmm)
REVERT: A  797 MET cc_start: 0.8726 (ppp) cc_final: 0.8050 (ppp)
REVERT: A  872 MET cc_start: 0.9243 (mmp) cc_final: 0.8909 (mmp)
REVERT: A 1004 LEU cc_start: 0.9047 (mm) cc_final: 0.8757 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1734
  time to fit residues: 14.5875
Evaluate side-chains
  44 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 74 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   8592  Z= 0.216
  Angle     :  0.727   9.596  11835  Z= 0.353
  Chirality :  0.043   0.233   1391
  Planarity :  0.005   0.073   1374
  Dihedral  : 18.616 178.575   1649
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 26.51
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.89 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.60 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.27), residues: 942
  helix: -0.05 (0.24), residues: 426
  sheet: -1.22 (0.55), residues: 84
  loop : -1.61 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 328 
 HIS   0.004   0.001   HIS A 510 
 PHE   0.020   0.002   PHE A 200 
 TYR   0.021   0.002   TYR A 685 
 ARG   0.003   0.000   ARG A 524 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9537 (mmp) cc_final: 0.9281 (mmm)
REVERT: A  389 MET cc_start: 0.8898 (pmm) cc_final: 0.8599 (pmm)
REVERT: A  440 GLN cc_start: 0.9151 (tt0) cc_final: 0.8672 (tt0)
REVERT: A  483 LEU cc_start: 0.9397 (tp) cc_final: 0.9188 (tp)
REVERT: A  577 MET cc_start: 0.8287 (pmm) cc_final: 0.7918 (pmm)
REVERT: A  637 PHE cc_start: 0.8651 (m-10) cc_final: 0.8406 (m-80)
REVERT: A  670 MET cc_start: 0.9118 (mmm) cc_final: 0.8801 (mmm)
REVERT: A  797 MET cc_start: 0.8757 (ppp) cc_final: 0.8134 (ppp)
REVERT: A  807 LEU cc_start: 0.9680 (mt) cc_final: 0.9329 (tt)
REVERT: A  872 MET cc_start: 0.9192 (mmp) cc_final: 0.8907 (mmp)
REVERT: A 1004 LEU cc_start: 0.9035 (mm) cc_final: 0.8821 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1787
  time to fit residues: 15.1667
Evaluate side-chains
  44 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   8592  Z= 0.168
  Angle     :  0.715   8.460  11835  Z= 0.345
  Chirality :  0.043   0.220   1391
  Planarity :  0.004   0.068   1374
  Dihedral  : 18.412 179.714   1649
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.47 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.24 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.28), residues: 942
  helix:  0.02 (0.25), residues: 420
  sheet: -1.27 (0.49), residues: 109
  loop : -1.51 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 328 
 HIS   0.002   0.001   HIS A 503 
 PHE   0.015   0.001   PHE A1052 
 TYR   0.019   0.001   TYR A 685 
 ARG   0.003   0.000   ARG A1158 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9535 (mmp) cc_final: 0.9276 (mmm)
REVERT: A  389 MET cc_start: 0.8907 (pmm) cc_final: 0.8594 (pmm)
REVERT: A  440 GLN cc_start: 0.9131 (tt0) cc_final: 0.8724 (tt0)
REVERT: A  483 LEU cc_start: 0.9351 (tp) cc_final: 0.9066 (tp)
REVERT: A  577 MET cc_start: 0.8322 (pmm) cc_final: 0.7969 (pmm)
REVERT: A  629 MET cc_start: 0.6812 (tmm) cc_final: 0.6125 (tpp)
REVERT: A  637 PHE cc_start: 0.8639 (m-10) cc_final: 0.8392 (m-80)
REVERT: A  670 MET cc_start: 0.9066 (mmm) cc_final: 0.8861 (mmm)
REVERT: A  797 MET cc_start: 0.8698 (ppp) cc_final: 0.8089 (ppp)
REVERT: A  807 LEU cc_start: 0.9668 (mt) cc_final: 0.9292 (tt)
REVERT: A  872 MET cc_start: 0.9077 (mmp) cc_final: 0.8648 (mmp)
REVERT: A  957 MET cc_start: 0.9312 (ppp) cc_final: 0.9103 (ppp)
REVERT: A  966 GLN cc_start: 0.9579 (tt0) cc_final: 0.9251 (mt0)
REVERT: A 1004 LEU cc_start: 0.8960 (mm) cc_final: 0.8674 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1686
  time to fit residues: 15.7890
Evaluate side-chains
  50 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 56 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 64 optimal weight:    8.9990
   chunk 97 optimal weight:    9.9990
   chunk 89 optimal weight:    0.5980
   chunk 77 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0270
   chunk 47 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0020
   overall best weight:    3.3250

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   8592  Z= 0.249
  Angle     :  0.744  10.110  11835  Z= 0.366
  Chirality :  0.044   0.232   1391
  Planarity :  0.005   0.069   1374
  Dihedral  : 18.571 179.891   1649
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 28.53
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.21 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.00 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.27), residues: 942
  helix:  0.02 (0.25), residues: 418
  sheet: -1.39 (0.51), residues: 96
  loop : -1.60 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 328 
 HIS   0.006   0.002   HIS A1015 
 PHE   0.023   0.002   PHE A 200 
 TYR   0.022   0.002   TYR A 685 
 ARG   0.006   0.001   ARG A1091 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9532 (mmp) cc_final: 0.9264 (mmm)
REVERT: A  389 MET cc_start: 0.8910 (pmm) cc_final: 0.8636 (pmm)
REVERT: A  440 GLN cc_start: 0.9165 (tt0) cc_final: 0.8705 (tt0)
REVERT: A  577 MET cc_start: 0.8452 (pmm) cc_final: 0.8108 (pmm)
REVERT: A  629 MET cc_start: 0.6993 (tmm) cc_final: 0.6315 (tpp)
REVERT: A  637 PHE cc_start: 0.8641 (m-10) cc_final: 0.8401 (m-80)
REVERT: A  670 MET cc_start: 0.9090 (mmm) cc_final: 0.8859 (mmm)
REVERT: A  797 MET cc_start: 0.8778 (ppp) cc_final: 0.8182 (ppp)
REVERT: A  807 LEU cc_start: 0.9684 (mt) cc_final: 0.9329 (tt)
REVERT: A 1004 LEU cc_start: 0.8980 (mm) cc_final: 0.8766 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1777
  time to fit residues: 15.8989
Evaluate side-chains
  45 residues out of total 833 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 23 optimal weight:   20.0000
   chunk 71 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 79 optimal weight:    0.4980
   chunk 9 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0060
   overall best weight:    1.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.061808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.043947 restraints weight = 248030.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.046537 restraints weight = 116604.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.047066 restraints weight = 70281.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   8592  Z= 0.188
  Angle     :  0.730   9.307  11835  Z= 0.354
  Chirality :  0.044   0.222   1391
  Planarity :  0.004   0.069   1374
  Dihedral  : 18.464 179.949   1649
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 23.57
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.89 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.12 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.27), residues: 942
  helix: -0.01 (0.25), residues: 419
  sheet: -1.05 (0.55), residues: 84
  loop : -1.54 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 328 
 HIS   0.002   0.001   HIS A 510 
 PHE   0.017   0.001   PHE A 200 
 TYR   0.020   0.001   TYR A 685 
 ARG   0.009   0.000   ARG A 173 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1599.61 seconds
wall clock time: 29 minutes 48.58 seconds (1788.58 seconds total)