Starting phenix.real_space_refine (version: dev)
on Mon Apr  4 19:34:48 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2022/7rph_24614_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2022/7rph_24614.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2022/7rph_24614.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2022/7rph_24614.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2022/7rph_24614_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2022/7rph_24614_updated.pdb"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.006 sd=   0.579
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  258": "OE1" <-> "OE2"
    Residue "A PHE  304": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  310": "OE1" <-> "OE2"
    Residue "A GLU  371": "OE1" <-> "OE2"
    Residue "A ARG  372": "NH1" <-> "NH2"
    Residue "A ARG  382": "NH1" <-> "NH2"
    Residue "A GLU  472": "OE1" <-> "OE2"
    Residue "A TYR  545": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  552": "OE1" <-> "OE2"
    Residue "A GLU  591": "OE1" <-> "OE2"
    Residue "A GLU  698": "OE1" <-> "OE2"
    Residue "A GLU  746": "OE1" <-> "OE2"
    Residue "A GLU  807": "OE1" <-> "OE2"
    Residue "A GLU  842": "OE1" <-> "OE2"
    Residue "A GLU  852": "OE1" <-> "OE2"
    Residue "A GLU  859": "OE1" <-> "OE2"
    Residue "A GLU  882": "OE1" <-> "OE2"
    Residue "A GLU  894": "OE1" <-> "OE2"
    Residue "A ARG  897": "NH1" <-> "NH2"
    Residue "A PHE  929": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  944": "OE1" <-> "OE2"
    Residue "A GLU  958": "OE1" <-> "OE2"
    Residue "A GLU  970": "OE1" <-> "OE2"
    Residue "A ARG 1059": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 8573
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8573
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1048, 8565
          Unusual residues: {' NA': 3, 'Y01': 26, 'AV0': 2, 'NAG': 5}
          Classifications: {'undetermined': 36, 'water': 86, 'peptide': 926}
          Link IDs: {'PTRANS': 39, 'TRANS': 885, None: 122, 'PCIS': 1}
            Not linked:
              pdbres="PHE A1143 "
              pdbres=" NA A1601 "
            Not linked:
              pdbres=" NA A1601 "
              pdbres=" NA A1602 "
            Not linked:
              pdbres=" NA A1602 "
              pdbres=" NA A1603 "
            Not linked:
              pdbres=" NA A1603 "
              pdbres="Y01 A1604 "
            Not linked:
              pdbres="Y01 A1604 "
              pdbres="Y01 A1605 "
            ... (remaining 117 not shown)
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
      Conformer: "B"
        Number of residues, atoms: 1048, 8565
          Unusual residues: {' NA': 3, 'Y01': 26, 'AV0': 2, 'NAG': 5}
          Classifications: {'undetermined': 36, 'water': 86, 'peptide': 926}
          Link IDs: {'PTRANS': 39, 'TRANS': 885, None: 122, 'PCIS': 1}
            Not linked:
              pdbres="PHE A1143 "
              pdbres=" NA A1601 "
            Not linked:
              pdbres=" NA A1601 "
              pdbres=" NA A1602 "
            Not linked:
              pdbres=" NA A1602 "
              pdbres=" NA A1603 "
            Not linked:
              pdbres=" NA A1603 "
              pdbres="Y01 A1604 "
            Not linked:
              pdbres="Y01 A1604 "
              pdbres="Y01 A1605 "
            ... (remaining 117 not shown)
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
          bond proxies already assigned to first conformer: 8749
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AMET A 557 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A 557 " occ=0.50
  Time building chain proxies: 9.64, per 1000 atoms: 1.12
  Number of scatterers: 8573
  At special positions: 0
  Unit cell: (88.51, 88.51, 127.755, 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      65     16.00
     Na      3     11.00
     O    1578      8.00
     N    1185      7.00
     C    5742      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 292 " - pdb=" SG  CYS A 348 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 366 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 347 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS A 417 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 397 " - pdb=" SG  CYS A 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 829 " - pdb=" SG  CYS A 849 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 863 " - pdb=" SG  CYS A 872 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 871 " - pdb=" SG  CYS A 887 " distance=2.05

  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
  Links applied
    NAG-ASN
      " NAG A1632 " - " ASN A 915 "
      " NAG A1633 " - " ASN A 475 "
      " NAG A1634 " - " ASN A 834 "
      " NAG A1635 " - " ASN A 362 "
      " NAG A1636 " - " ASN A 390 "
  Time building additional restraints: 3.43
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1766

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      37 helices and 2 sheets defined
      60.8% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 180 through 186
    Processing helix  chain 'A' and resid 188 through 208
    Processing helix  chain 'A' and resid 228 through 241
    Processing helix  chain 'A' and resid 254 through 261
    Processing helix  chain 'A' and resid 315 through 328
      removed outlier: 3.547A  pdb=" N   CYS A 322 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 338
      No H-bonds generated for 'chain 'A' and resid 335 through 338'
    Processing helix  chain 'A' and resid 353 through 360
    Processing helix  chain 'A' and resid 366 through 368
      No H-bonds generated for 'chain 'A' and resid 366 through 368'
    Processing helix  chain 'A' and resid 371 through 389
      removed outlier: 5.423A  pdb=" N   LYS A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   HIS A 387 " --> pdb=" O   THR A 383 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TYR A 388 " --> pdb=" O   CYS A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 429
      removed outlier: 3.625A  pdb=" N   LYS A 419 " --> pdb=" O   ARG A 415 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   TYR A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   ASN A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ALA A 422 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   VAL A 423 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   TYR A 424 " --> pdb=" O   TYR A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 441
      No H-bonds generated for 'chain 'A' and resid 438 through 441'
    Processing helix  chain 'A' and resid 461 through 470
      removed outlier: 3.546A  pdb=" N   MET A 464 " --> pdb=" O   GLU A 461 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ASN A 465 " --> pdb=" O   SER A 462 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A 467 " --> pdb=" O   MET A 464 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ASP A 469 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN A 470 " --> pdb=" O   TYR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 521
      removed outlier: 3.795A  pdb=" N   THR A 503 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   VAL A 504 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   TYR A 505 " --> pdb=" O   MET A 501 " (cutoff:3.500A)
      Proline residue:  A 506  - end of helix
    Processing helix  chain 'A' and resid 524 through 547
      removed outlier: 3.813A  pdb=" N   LEU A 538 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 568
      removed outlier: 3.523A  pdb=" N   ILE A 564 " --> pdb=" O   ALA A 561 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 566 " --> pdb=" O   ILE A 563 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 568 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 586
      removed outlier: 3.619A  pdb=" N   PHE A 574 " --> pdb=" O   ASP A 571 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 576 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   CYS A 577 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASP A 586 " --> pdb=" O   THR A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 623
      removed outlier: 5.641A  pdb=" N   LEU A 605 " --> pdb=" O   GLN A 601 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   SER A 606 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   THR A 614 " --> pdb=" O   THR A 610 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASN A 621 " --> pdb=" O   ALA A 617 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   TYR A 622 " --> pdb=" O   PHE A 618 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   VAL A 623 " --> pdb=" O   TYR A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 648
    Processing helix  chain 'A' and resid 650 through 661
    Processing helix  chain 'A' and resid 682 through 705
    Processing helix  chain 'A' and resid 707 through 714
    Processing helix  chain 'A' and resid 716 through 735
      removed outlier: 3.527A  pdb=" N   ILE A 721 " --> pdb=" O   TYR A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 749
      No H-bonds generated for 'chain 'A' and resid 747 through 749'
    Processing helix  chain 'A' and resid 758 through 764
      removed outlier: 3.646A  pdb=" N   ASP A 763 " --> pdb=" O   PHE A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 768
      No H-bonds generated for 'chain 'A' and resid 766 through 768'
    Processing helix  chain 'A' and resid 771 through 778
      removed outlier: 4.013A  pdb=" N   HIS A 776 " --> pdb=" O   PHE A 772 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   HIS A 777 " --> pdb=" O   GLU A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 834
      removed outlier: 3.547A  pdb=" N   ASN A 834 " --> pdb=" O   GLN A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 860
      removed outlier: 3.572A  pdb=" N   ASN A 860 " --> pdb=" O   GLN A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 871
      Proline residue:  A 870  - end of helix
    Processing helix  chain 'A' and resid 881 through 898
      removed outlier: 4.099A  pdb=" N   LYS A 889 " --> pdb=" O   GLU A 885 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A 897 " --> pdb=" O   MET A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 935 through 955
      removed outlier: 3.514A  pdb=" N   GLN A 940 " --> pdb=" O   GLU A 936 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   SER A 955 " --> pdb=" O   HIS A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 1001
    Processing helix  chain 'A' and resid 1004 through 1027
    Processing helix  chain 'A' and resid 1034 through 1060
      removed outlier: 3.719A  pdb=" N   VAL A1038 " --> pdb=" O   VAL A1034 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A1040 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER A1041 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   VAL A1044 " --> pdb=" O   ILE A1040 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   ASP A1049 " --> pdb=" O   GLY A1045 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   PHE A1050 " --> pdb=" O   LEU A1046 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ALA A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1095
      removed outlier: 5.233A  pdb=" N   SER A1079 " --> pdb=" O   SER A1075 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   ALA A1080 " --> pdb=" O   ARG A1076 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   MET A1095 " --> pdb=" O   ALA A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1122
    Processing helix  chain 'A' and resid 1124 through 1132
    Processing sheet with id=  A, first strand: chain 'A' and resid 964 through 966
      removed outlier: 6.637A  pdb=" N   ARG A 911 " --> pdb=" O   ARG A 919 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 450 through 458
      removed outlier: 3.952A  pdb=" N   SER A 300 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ALA A 305 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   VAL A 483 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1089 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 3.70 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1239
        1.29 -     1.42: 2196
        1.42 -     1.56: 4867
        1.56 -     1.69: 367
        1.69 -     1.83: 98
  Bond restraints: 8767
  Sorted by residual:
  bond pdb=" C   LEU A1086 "
       pdb=" O   LEU A1086 "
    ideal  model  delta    sigma   weight residual
    1.237  1.156  0.081 1.17e-02 7.31e+03 4.75e+01
  bond pdb=" C   THR A 613 "
       pdb=" O   THR A 613 "
    ideal  model  delta    sigma   weight residual
    1.236  1.150  0.086 1.26e-02 6.30e+03 4.71e+01
  bond pdb=" C   ALA A 615 "
       pdb=" O   ALA A 615 "
    ideal  model  delta    sigma   weight residual
    1.237  1.159  0.078 1.16e-02 7.43e+03 4.53e+01
  bond pdb=" C   PHE A 608 "
       pdb=" O   PHE A 608 "
    ideal  model  delta    sigma   weight residual
    1.237  1.162  0.075 1.16e-02 7.43e+03 4.18e+01
  bond pdb=" C   ALA A 573 "
       pdb=" O   ALA A 573 "
    ideal  model  delta    sigma   weight residual
    1.237  1.161  0.076 1.19e-02 7.06e+03 4.08e+01
  ... (remaining 8762 not shown)

  Histogram of bond angle deviations from ideal:
       98.94 -   106.29: 421
      106.29 -   113.65: 4784
      113.65 -   121.00: 4592
      121.00 -   128.35: 2212
      128.35 -   135.70: 57
  Bond angle restraints: 12066
  Sorted by residual:
  angle pdb=" N   PHE A 612 "
        pdb=" CA  PHE A 612 "
        pdb=" C   PHE A 612 "
      ideal   model   delta    sigma   weight residual
     111.71  121.40   -9.69 1.15e+00 7.56e-01 7.10e+01
  angle pdb=" N   LEU A1086 "
        pdb=" CA  LEU A1086 "
        pdb=" C   LEU A1086 "
      ideal   model   delta    sigma   weight residual
     111.28  119.12   -7.84 1.09e+00 8.42e-01 5.17e+01
  angle pdb=" CA  PHE A 759 "
        pdb=" CB  PHE A 759 "
        pdb=" CG  PHE A 759 "
      ideal   model   delta    sigma   weight residual
     113.80  120.09   -6.29 1.00e+00 1.00e+00 3.96e+01
  angle pdb=" N   ASP A1049 "
        pdb=" CA  ASP A1049 "
        pdb=" C   ASP A1049 "
      ideal   model   delta    sigma   weight residual
     111.07  117.58   -6.51 1.07e+00 8.73e-01 3.70e+01
  angle pdb=" N   ASP A 571 "
        pdb=" CA  ASP A 571 "
        pdb=" C   ASP A 571 "
      ideal   model   delta    sigma   weight residual
     111.33  118.66   -7.33 1.21e+00 6.83e-01 3.67e+01
  ... (remaining 12061 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.95: 4668
       27.95 -    55.91: 171
       55.91 -    83.86: 20
       83.86 -   111.82: 2
      111.82 -   139.77: 3
  Dihedral angle restraints: 4864
    sinusoidal: 2136
      harmonic: 2728
  Sorted by residual:
  dihedral pdb=" CB  CYS A 863 "
           pdb=" SG  CYS A 863 "
           pdb=" SG  CYS A 872 "
           pdb=" CB  CYS A 872 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.15   77.15     1      1.00e+01 1.00e-02 7.46e+01
  dihedral pdb=" CA  VAL A1048 "
           pdb=" C   VAL A1048 "
           pdb=" N   ASP A1049 "
           pdb=" CA  ASP A1049 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.08  -27.92     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CB  CYS A 384 "
           pdb=" SG  CYS A 384 "
           pdb=" SG  CYS A 417 "
           pdb=" CB  CYS A 417 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.34  -41.34     1      1.00e+01 1.00e-02 2.39e+01
  ... (remaining 4861 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 975
       0.109 -    0.219: 384
       0.219 -    0.328: 66
       0.328 -    0.437: 14
       0.437 -    0.546: 2
  Chirality restraints: 1441
  Sorted by residual:
  chirality pdb=" CA  LEU A1086 "
            pdb=" N   LEU A1086 "
            pdb=" C   LEU A1086 "
            pdb=" CB  LEU A1086 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.46e+00
  chirality pdb=" CA  PHE A 612 "
            pdb=" N   PHE A 612 "
            pdb=" C   PHE A 612 "
            pdb=" CB  PHE A 612 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.45 2.00e-01 2.50e+01 4.95e+00
  chirality pdb=" CA  GLN A 334 "
            pdb=" N   GLN A 334 "
            pdb=" C   GLN A 334 "
            pdb=" CB  GLN A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.71e+00
  ... (remaining 1438 not shown)

  Planarity restraints: 1345
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 475 "    0.125 2.00e-02 2.50e+03   1.32e-01 2.17e+02
        pdb=" CG  ASN A 475 "   -0.073 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 475 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 475 "   -0.202 2.00e-02 2.50e+03
        pdb=" C1  NAG A1633 "    0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 313 "    0.134 2.00e-02 2.50e+03   6.63e-02 1.10e+02
        pdb=" CG  TRP A 313 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 313 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 313 "   -0.037 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 313 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 313 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 313 "   -0.079 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 313 "    0.078 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 313 "   -0.045 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 313 "    0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 351 "   -0.106 2.00e-02 2.50e+03   5.66e-02 8.00e+01
        pdb=" CG  TRP A 351 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 351 "    0.084 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 351 "    0.026 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 351 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 351 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 351 "    0.082 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 351 "   -0.050 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 351 "    0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 351 "   -0.052 2.00e-02 2.50e+03
  ... (remaining 1342 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 19
        2.54 -     3.13: 6303
        3.13 -     3.72: 12603
        3.72 -     4.31: 19818
        4.31 -     4.90: 31325
  Nonbonded interactions: 70068
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 571 "
            pdb="NA    NA A1602 "
     model   vdw
     1.952 2.470
  nonbonded pdb=" OD1 ASP A1049 "
            pdb="NA    NA A1601 "
     model   vdw
     2.174 2.470
  nonbonded pdb=" O   GLY A 567 "
            pdb="NA    NA A1602 "
     model   vdw
     2.186 2.470
  nonbonded pdb=" OG1 THR A 613 "
            pdb="NA    NA A1601 "
     model   vdw
     2.201 2.470
  nonbonded pdb=" OD2 ASP A 572 "
            pdb="NA    NA A1603 "
     model   vdw
     2.251 2.470
  ... (remaining 70063 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
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     Na      3      4.78       5
     C    5742      2.51       5
     N    1185      2.21       5
     O    1578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          7.420
  Check model and map are aligned:         0.140
  Convert atoms to be neutral:             0.070
  Process input model:                     31.920
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Set scattering table:                    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:13.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
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      :  0.017   0.128   8767  Z= 1.015
  Angle     :  1.887   9.687  12066  Z= 1.232
  Chirality :  0.115   0.546   1441
  Planarity :  0.014   0.105   1340
  Dihedral  : 14.660 139.770   3074
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer Outliers :  0.61 %
  Cbeta Deviations :  0.45 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.70 (0.25), residues: 921
  helix: -0.48 (0.19), residues: 563
  sheet: -0.16 (0.97), residues: 29
  loop : -0.11 (0.34), residues: 329

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 146
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 0
  residues processed: 148
  average time/residue: 1.1123
  time to fit residues: 176.4700
Evaluate side-chains
  100 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.936 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2355
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN
A 367 GLN
A 376 HIS
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 389 GLN
A 856 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8767  Z= 0.171
  Angle     :  0.650   8.655  12066  Z= 0.310
  Chirality :  0.043   0.282   1441
  Planarity :  0.004   0.041   1340
  Dihedral  : 12.366 148.694   1403
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer Outliers :  1.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.46 (0.28), residues: 921
  helix:  1.29 (0.21), residues: 571
  sheet:  0.22 (0.88), residues: 31
  loop :  0.68 (0.38), residues: 319

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 5
  residues processed: 132
  average time/residue: 1.0437
  time to fit residues: 148.5187
Evaluate side-chains
  97 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.954 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 2.3067
  time to fit residues: 3.6062
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   chunk 102 optimal weight:   50.0000
   chunk 84 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 32 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8767  Z= 0.320
  Angle     :  0.739   7.962  12066  Z= 0.350
  Chirality :  0.047   0.252   1441
  Planarity :  0.004   0.037   1340
  Dihedral  : 12.655 146.686   1403
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer Outliers :  3.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.25 (0.28), residues: 921
  helix:  1.23 (0.21), residues: 568
  sheet:  0.50 (0.91), residues: 29
  loop :  0.33 (0.37), residues: 324

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 93
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 30
  outliers final: 13
  residues processed: 113
  average time/residue: 1.0226
  time to fit residues: 125.1670
Evaluate side-chains
  101 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.991 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 3
  average time/residue: 1.5271
  time to fit residues: 6.0521
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 94 optimal weight:    9.9990
   chunk 100 optimal weight:   50.0000
   chunk 89 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   overall best weight:    2.3188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8767  Z= 0.341
  Angle     :  0.742   7.587  12066  Z= 0.349
  Chirality :  0.047   0.242   1441
  Planarity :  0.005   0.039   1340
  Dihedral  : 12.550 144.530   1403
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer Outliers :  3.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.01 (0.27), residues: 921
  helix:  1.08 (0.21), residues: 569
  sheet:  0.29 (0.91), residues: 29
  loop :  0.14 (0.36), residues: 323

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 27
  outliers final: 17
  residues processed: 111
  average time/residue: 1.0095
  time to fit residues: 121.4532
Evaluate side-chains
  105 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.960 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 12
  residues processed: 5
  average time/residue: 0.9593
  time to fit residues: 6.4230
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 856 GLN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8767  Z= 0.188
  Angle     :  0.617   6.878  12066  Z= 0.287
  Chirality :  0.041   0.214   1441
  Planarity :  0.004   0.034   1340
  Dihedral  : 11.932 145.439   1403
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer Outliers :  3.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.28), residues: 921
  helix:  1.45 (0.22), residues: 564
  sheet:  0.13 (0.87), residues: 31
  loop :  0.23 (0.36), residues: 326

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
  outliers start: 26
  outliers final: 12
  residues processed: 112
  average time/residue: 1.0215
  time to fit residues: 123.7752
Evaluate side-chains
  100 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.732 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 11
  residues processed: 1
  average time/residue: 0.1098
  time to fit residues: 1.1295
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 100 optimal weight:   50.0000
   chunk 83 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 97 optimal weight:   50.0000
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 856 GLN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8767  Z= 0.216
  Angle     :  0.639  10.530  12066  Z= 0.297
  Chirality :  0.042   0.208   1441
  Planarity :  0.004   0.035   1340
  Dihedral  : 11.853 145.130   1403
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer Outliers :  3.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.42 (0.28), residues: 921
  helix:  1.51 (0.22), residues: 565
  sheet:  0.24 (0.88), residues: 31
  loop :  0.14 (0.36), residues: 325

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 29
  outliers final: 15
  residues processed: 111
  average time/residue: 1.0513
  time to fit residues: 126.3211
Evaluate side-chains
  104 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.846 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 13
  residues processed: 2
  average time/residue: 0.6186
  time to fit residues: 2.5297
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0970
   chunk 100 optimal weight:   50.0000
   chunk 62 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 856 GLN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8767  Z= 0.149
  Angle     :  0.569   8.551  12066  Z= 0.266
  Chirality :  0.040   0.205   1441
  Planarity :  0.004   0.035   1340
  Dihedral  : 11.432 145.511   1403
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer Outliers :  3.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.68 (0.28), residues: 921
  helix:  1.68 (0.22), residues: 567
  sheet:  0.50 (0.87), residues: 31
  loop :  0.29 (0.37), residues: 323

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 16
  residues processed: 111
  average time/residue: 1.0318
  time to fit residues: 123.9069
Evaluate side-chains
  102 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.860 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 14
  residues processed: 2
  average time/residue: 0.6092
  time to fit residues: 2.5192
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    0.0970
   chunk 19 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0010
   chunk 78 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 96 optimal weight:   40.0000
   chunk 87 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 856 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8767  Z= 0.188
  Angle     :  0.607  10.621  12066  Z= 0.282
  Chirality :  0.041   0.204   1441
  Planarity :  0.004   0.034   1340
  Dihedral  : 11.482 145.231   1403
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer Outliers :  2.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.59 (0.28), residues: 921
  helix:  1.64 (0.22), residues: 568
  sheet:  0.44 (0.86), residues: 31
  loop :  0.18 (0.37), residues: 322

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 20
  outliers final: 17
  residues processed: 100
  average time/residue: 1.1465
  time to fit residues: 124.2877
Evaluate side-chains
  99 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.969 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 14
  residues processed: 3
  average time/residue: 0.4441
  time to fit residues: 2.7585
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:   30.0000
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 93 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 98 optimal weight:   50.0000
   chunk 60 optimal weight:    0.7980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 856 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8767  Z= 0.196
  Angle     :  0.608  11.559  12066  Z= 0.284
  Chirality :  0.042   0.310   1441
  Planarity :  0.004   0.035   1340
  Dihedral  : 11.480 144.580   1403
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer Outliers :  2.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.28), residues: 921
  helix:  1.59 (0.22), residues: 568
  sheet:  0.44 (0.85), residues: 31
  loop :  0.18 (0.37), residues: 322

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 16
  residues processed: 103
  average time/residue: 1.1179
  time to fit residues: 124.1040
Evaluate side-chains
  103 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.907 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 14
  residues processed: 2
  average time/residue: 0.6067
  time to fit residues: 2.6480
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 103 optimal weight:   50.0000
   chunk 95 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0770
   overall best weight:    1.2942

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

Flipped N/Q/H residues before XYZ refinement:
A 856 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8767  Z= 0.221
  Angle     :  0.654  12.753  12066  Z= 0.308
  Chirality :  0.049   0.942   1441
  Planarity :  0.004   0.035   1340
  Dihedral  : 11.607 144.194   1403
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer Outliers :  2.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  1.46 (0.28), residues: 921
  helix:  1.54 (0.22), residues: 565
  sheet:  0.39 (0.85), residues: 31
  loop :  0.15 (0.36), residues: 325

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 20
  outliers final: 16
  residues processed: 103
  average time/residue: 1.1635
  time to fit residues: 128.8948
Evaluate side-chains
  102 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.952 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 14
  residues processed: 2
  average time/residue: 0.6200
  time to fit residues: 2.6301
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0470
   chunk 59 optimal weight:    0.0970
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A 856 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.182797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.137298 restraints weight = 18212.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.10
r_work: 0.3531 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 1.99 restraints_weight: 0.2500
r_work: 0.3479 rms_B_bonded: 2.28 restraints_weight: 0.1250
r_work: 0.3447 rms_B_bonded: 2.74 restraints_weight: 0.0625
r_work: 0.3409 rms_B_bonded: 3.40 restraints_weight: 0.0312
r_work: 0.3362 rms_B_bonded: 4.34 restraints_weight: 0.0156
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4101 r_free = 0.4101    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4101 r_free = 0.4101    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8767  Z= 0.133
  Angle     :  0.562  12.320  12066  Z= 0.261
  Chirality :  0.042   0.638   1441
  Planarity :  0.004   0.035   1340
  Dihedral  : 11.244 144.507   1403
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer Outliers :  2.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  1.75 (0.28), residues: 921
  helix:  1.74 (0.22), residues: 567
  sheet:  0.64 (0.84), residues: 31
  loop :  0.30 (0.37), residues: 323

===============================================================================
Job complete
usr+sys time: 2792.94 seconds
wall clock time: 50 minutes 40.50 seconds (3040.50 seconds total)