Starting phenix.real_space_refine
on Tue Jul 29 08:51:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xso_33429/07_2025/7xso_33429.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xso_33429/07_2025/7xso_33429.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xso_33429/07_2025/7xso_33429.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xso_33429/07_2025/7xso_33429.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xso_33429/07_2025/7xso_33429.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xso_33429/07_2025/7xso_33429.cif"
  }
  resolution = 3.01
  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=   0.004 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P      35      5.49       5
     S      33      5.16       5
     C    6836      2.51       5
     N    1913      2.21       5
     O    2150      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10971
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 10232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1271, 10232
          Classifications: {'peptide': 1271}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 60, 'TRANS': 1210}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 735
          Classifications: {'RNA': 35}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 18, 'rna3p': 16}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    676  SG  CYS A  88      77.755  24.345  20.422  1.00 56.77           S
  ATOM    947  SG  CYS A 121      81.150  23.663  18.457  1.00 61.88           S
  ATOM    993  SG  CYS A 127      80.468  27.509  19.938  1.00 55.76           S
  ATOM   1017  SG  CYS A 130      81.117  24.681  22.142  1.00 54.16           S
  ATOM   3605  SG  CYS A 491      55.617  30.294  46.468  1.00 54.94           S
  ATOM   3673  SG  CYS A 501      56.577  28.803  43.330  1.00 54.99           S
  ATOM   3687  SG  CYS A 503      54.317  32.071  42.736  1.00 54.55           S
  ATOM   3709  SG  CYS A 506      57.891  32.628  43.859  1.00 50.92           S
  ATOM   5680  SG  CYS A 750      41.443  35.171  73.361  1.00 67.60           S
  ATOM   5693  SG  CYS A 752      39.561  38.582  72.519  1.00 60.45           S
  ATOM   5715  SG  CYS A 755      43.237  38.815  71.688  1.00 54.67           S
  ATOM   7689  SG  CYS A1018      41.329  59.400 103.367  1.00 44.86           S
  ATOM   7914  SG  CYS A1406      42.342  55.852 102.186  1.00 50.92           S
  ATOM   7965  SG  CYS A1414      38.269  57.860 101.887  1.00 45.70           S
  ATOM   7982  SG  CYS A1417      41.074  58.599  99.691  1.00 42.97           S

  Time building chain proxies: 8.51, per 1000 atoms: 0.78
  Number of scatterers: 10971
  At special positions: 0
  Unit cell: (111.15, 115.425, 140.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      4     29.99
     S      33     16.00
     P      35     15.00
     O    2150      8.00
     N    1913      7.00
     C    6836      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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.59
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1801 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 127 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A  88 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 130 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 121 "
      pdb="  ZN A1802 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 491 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 506 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 503 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 501 "
      pdb="  ZN A1803 "
        pdb="ZN    ZN A1803 " - pdb=" ND1 HIS A 747 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 752 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 750 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 755 "
      pdb="  ZN A1804 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1406 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1018 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1414 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1417 "
      Number of angles added : 21


  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2324

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 17 sheets defined
      29.0% alpha, 22.5% beta
      0 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 3.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 31
      removed outlier: 3.570A  pdb=" N   LYS A  30 " --> pdb=" O   TRP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 38
    Processing helix  chain 'A' and resid 59 through 78
      removed outlier: 3.605A  pdb=" N   VAL A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 134
    Processing helix  chain 'A' and resid 169 through 172
      No H-bonds generated for 'chain 'A' and resid 169 through 172'
    Processing helix  chain 'A' and resid 214 through 224
      removed outlier: 4.166A  pdb=" N   LEU A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 287
      removed outlier: 3.848A  pdb=" N   ASN A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 303
      removed outlier: 4.226A  pdb=" N   ILE A 295 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 307
      removed outlier: 5.788A  pdb=" N   GLY A 307 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 304 through 307'
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 338 through 348
    Processing helix  chain 'A' and resid 354 through 375
      removed outlier: 3.554A  pdb=" N   PHE A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 488
    Processing helix  chain 'A' and resid 503 through 510
    Processing helix  chain 'A' and resid 569 through 580
      removed outlier: 3.526A  pdb=" N   SER A 573 " --> pdb=" O   PRO A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 598
    Processing helix  chain 'A' and resid 617 through 625
    Processing helix  chain 'A' and resid 626 through 628
      No H-bonds generated for 'chain 'A' and resid 626 through 628'
    Processing helix  chain 'A' and resid 631 through 637
      removed outlier: 3.952A  pdb=" N   LEU A 635 " --> pdb=" O   GLU A 631 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   GLU A 636 " --> pdb=" O   LYS A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 658
      removed outlier: 3.530A  pdb=" N   CYS A 657 " --> pdb=" O   GLU A 654 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 658 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 654 through 658'
    Processing helix  chain 'A' and resid 665 through 667
      No H-bonds generated for 'chain 'A' and resid 665 through 667'
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'A' and resid 723 through 739
      removed outlier: 3.627A  pdb=" N   HIS A 727 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ARG A 738 " --> pdb=" O   ALA A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 758
    Processing helix  chain 'A' and resid 831 through 848
    Processing helix  chain 'A' and resid 855 through 859
    Processing helix  chain 'A' and resid 873 through 881
      removed outlier: 3.523A  pdb=" N   LYS A 877 " --> pdb=" O   PRO A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 914
      removed outlier: 3.813A  pdb=" N   ASP A 914 " --> pdb=" O   SER A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1015
      removed outlier: 3.848A  pdb=" N   LEU A1003 " --> pdb=" O   PRO A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1414 through 1421
    Processing helix  chain 'A' and resid 1486 through 1493
      removed outlier: 3.816A  pdb=" N   ILE A1490 " --> pdb=" O   GLY A1486 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LYS A1493 " --> pdb=" O   ILE A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1493 through 1499
    Processing helix  chain 'A' and resid 1528 through 1540
      removed outlier: 3.540A  pdb=" N   ASP A1540 " --> pdb=" O   LEU A1536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1583 through 1603
    Processing helix  chain 'A' and resid 1615 through 1618
      removed outlier: 3.600A  pdb=" N   VAL A1618 " --> pdb=" O   GLN A1615 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1615 through 1618'
    Processing helix  chain 'A' and resid 1619 through 1629
    Processing helix  chain 'A' and resid 1673 through 1683
    Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153
      removed outlier: 3.699A  pdb=" N   LEU A 158 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   SER A  56 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   ALA A  53 " --> pdb=" O   LYS A  47 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TRP A 195 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      removed outlier: 9.409A  pdb=" N   GLU A  22 " --> pdb=" O   ARG A 193 " (cutoff:3.500A)
      removed outlier: 13.588A  pdb=" N   ARG A 193 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP A 190 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE A 192 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168
      removed outlier: 3.966A  pdb=" N   LEU A 167 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   SER A  56 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 158 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   THR A   9 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82
    Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111
      removed outlier: 6.184A  pdb=" N   THR A 110 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 514
      removed outlier: 6.616A  pdb=" N   GLU A 415 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLU A 611 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE A 417 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ILE A 609 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 419 " --> pdb=" O   ILE A 607 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ILE A 607 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   GLY A 600 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514
      removed outlier: 6.616A  pdb=" N   GLU A 415 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLU A 611 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE A 417 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ILE A 609 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 419 " --> pdb=" O   ILE A 607 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ILE A 607 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432
      removed outlier: 3.788A  pdb=" N   VAL A 432 " --> pdb=" O   ASN A 459 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ASN A 459 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470
    Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 530
    Processing sheet with id=AB1, first strand: chain 'A' and resid 533 through 534
      removed outlier: 3.804A  pdb=" N   THR A 539 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704
      removed outlier: 3.777A  pdb=" N   ARG A 719 " --> pdb=" O   LYS A 704 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   PHE A 720 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704
      removed outlier: 3.777A  pdb=" N   ARG A 719 " --> pdb=" O   LYS A 704 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   PHE A 720 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 789
    Processing sheet with id=AB5, first strand: chain 'A' and resid 924 through 927
    Processing sheet with id=AB6, first strand: chain 'A' and resid 991 through 992
      removed outlier: 6.562A  pdb=" N   LEU A 996 " --> pdb=" O   TYR A1436 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL A1517 " --> pdb=" O   GLU A1437 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992
      removed outlier: 6.562A  pdb=" N   LEU A 996 " --> pdb=" O   TYR A1436 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL A1517 " --> pdb=" O   GLU A1437 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   VAL A1517 " --> pdb=" O   THR A 960 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   THR A 960 " --> pdb=" O   VAL A1517 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   SER A1519 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU A 958 " --> pdb=" O   SER A1519 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   ASP A1521 " --> pdb=" O   CYS A 956 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   CYS A 956 " --> pdb=" O   ASP A1521 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   ARG A1523 " --> pdb=" O   ILE A 954 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ILE A 954 " --> pdb=" O   ARG A1523 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   GLU A1525 " --> pdb=" O   GLY A 952 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   GLY A 952 " --> pdb=" O   GLU A1525 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LYS A 957 " --> pdb=" O   ILE A1564 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   ILE A1564 " --> pdb=" O   LYS A 957 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   GLU A 959 " --> pdb=" O   ILE A1562 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ILE A1562 " --> pdb=" O   GLU A 959 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 985 through 987
      removed outlier: 6.555A  pdb=" N   LYS A 985 " --> pdb=" O   THR A1508 " (cutoff:3.500A)

    358 hydrogen bonds defined for protein.
    987 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 4.59

  Time building geometry restraints manager: 3.15 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1766
        1.28 -     1.41: 2987
        1.41 -     1.54: 6409
        1.54 -     1.68: 85
        1.68 -     1.81: 45
  Bond restraints: 11292
  Sorted by residual:
  bond pdb=" C   PRO A1687 "
       pdb=" O   PRO A1687 "
    ideal  model  delta    sigma   weight residual
    1.233  1.149  0.084 1.16e-02 7.43e+03 5.20e+01
  bond pdb=" O3'   C D  15 "
       pdb=" P     G D  16 "
    ideal  model  delta    sigma   weight residual
    1.607  1.500  0.107 1.50e-02 4.44e+03 5.13e+01
  bond pdb=" C   PRO A1690 "
       pdb=" O   PRO A1690 "
    ideal  model  delta    sigma   weight residual
    1.235  1.183  0.052 7.90e-03 1.60e+04 4.40e+01
  bond pdb=" O3'   U D  -2 "
       pdb=" P     A D  -1 "
    ideal  model  delta    sigma   weight residual
    1.607  1.517  0.090 1.50e-02 4.44e+03 3.63e+01
  bond pdb=" C   PRO A1684 "
       pdb=" O   PRO A1684 "
    ideal  model  delta    sigma   weight residual
    1.234  1.169  0.065 1.14e-02 7.69e+03 3.22e+01
  ... (remaining 11287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.42: 15146
        3.42 -     6.83: 221
        6.83 -    10.25: 23
       10.25 -    13.66: 0
       13.66 -    17.08: 1
  Bond angle restraints: 15391
  Sorted by residual:
  angle pdb=" N   PRO A1690 "
        pdb=" CA  PRO A1690 "
        pdb=" C   PRO A1690 "
      ideal   model   delta    sigma   weight residual
     110.74   93.66   17.08 1.66e+00 3.63e-01 1.06e+02
  angle pdb=" N   LEU A 975 "
        pdb=" CA  LEU A 975 "
        pdb=" C   LEU A 975 "
      ideal   model   delta    sigma   weight residual
     113.30  103.67    9.63 1.34e+00 5.57e-01 5.17e+01
  angle pdb=" O3'   C D  -7 "
        pdb=" C3'   C D  -7 "
        pdb=" C2'   C D  -7 "
      ideal   model   delta    sigma   weight residual
     113.70  104.35    9.35 1.50e+00 4.44e-01 3.89e+01
  angle pdb=" O2'   C D  -7 "
        pdb=" C2'   C D  -7 "
        pdb=" C1'   C D  -7 "
      ideal   model   delta    sigma   weight residual
     108.40   99.06    9.34 1.50e+00 4.44e-01 3.87e+01
  angle pdb=" O4'   A D  -1 "
        pdb=" C1'   A D  -1 "
        pdb=" C2'   A D  -1 "
      ideal   model   delta    sigma   weight residual
     105.80  100.12    5.68 1.00e+00 1.00e+00 3.22e+01
  ... (remaining 15386 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.24: 6534
       35.24 -    70.47: 261
       70.47 -   105.71: 19
      105.71 -   140.95: 0
      140.95 -   176.18: 9
  Dihedral angle restraints: 6823
    sinusoidal: 3192
      harmonic: 3631
  Sorted by residual:
  dihedral pdb=" O4'   U D -13 "
           pdb=" C1'   U D -13 "
           pdb=" N1    U D -13 "
           pdb=" C2    U D -13 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   16.18 -176.18     1      1.50e+01 4.44e-03 8.52e+01
  dihedral pdb=" O4'   U D -10 "
           pdb=" C1'   U D -10 "
           pdb=" N1    U D -10 "
           pdb=" C2    U D -10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   32.16  167.84     1      1.50e+01 4.44e-03 8.44e+01
  dihedral pdb=" O4'   U D   8 "
           pdb=" C1'   U D   8 "
           pdb=" N1    U D   8 "
           pdb=" C2    U D   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   41.91  158.09     1      1.50e+01 4.44e-03 8.23e+01
  ... (remaining 6820 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1441
       0.092 -    0.185: 182
       0.185 -    0.277: 24
       0.277 -    0.369: 5
       0.369 -    0.461: 1
  Chirality restraints: 1653
  Sorted by residual:
  chirality pdb=" CA  ASN A1649 "
            pdb=" N   ASN A1649 "
            pdb=" C   ASN A1649 "
            pdb=" CB  ASN A1649 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.32e+00
  chirality pdb=" C1'   U D -13 "
            pdb=" O4'   U D -13 "
            pdb=" C2'   U D -13 "
            pdb=" N1    U D -13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.10    0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" CA  PRO A1690 "
            pdb=" N   PRO A1690 "
            pdb=" C   PRO A1690 "
            pdb=" CB  PRO A1690 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    3.05   -0.33 2.00e-01 2.50e+01 2.73e+00
  ... (remaining 1650 not shown)

  Planarity restraints: 1868
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 391 "   -0.018 2.00e-02 2.50e+03   3.73e-02 1.39e+01
        pdb=" C   SER A 391 "    0.064 2.00e-02 2.50e+03
        pdb=" O   SER A 391 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LYS A 392 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  -1 "    0.047 2.00e-02 2.50e+03   2.19e-02 1.31e+01
        pdb=" N9    A D  -1 "   -0.050 2.00e-02 2.50e+03
        pdb=" C8    A D  -1 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  -1 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A D  -1 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  -1 "    0.010 2.00e-02 2.50e+03
        pdb=" N6    A D  -1 "    0.003 2.00e-02 2.50e+03
        pdb=" N1    A D  -1 "    0.014 2.00e-02 2.50e+03
        pdb=" C2    A D  -1 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    A D  -1 "   -0.013 2.00e-02 2.50e+03
        pdb=" C4    A D  -1 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 972 "    0.016 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   GLU A 972 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   GLU A 972 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ASN A 973 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1865 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 501
        2.71 -     3.25: 9439
        3.25 -     3.80: 16900
        3.80 -     4.35: 21160
        4.35 -     4.90: 36860
  Nonbonded interactions: 84860
  Sorted by model distance:
  nonbonded pdb=" O   SER A 438 "
            pdb=" OG  SER A 438 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" O   THR A 751 "
            pdb=" OG1 THR A 751 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OH  TYR A1645 "
            pdb=" OP1   C D  14 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OG  SER A 813 "
            pdb=" OE1 GLU A 995 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OD1 ASN A1448 "
            pdb=" NH1 ARG A1498 "
     model   vdw
     2.338 3.120
  ... (remaining 84855 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     37.220
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
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      :  0.010   0.208  11308  Z= 0.495
  Angle     :  1.105  31.570  15412  Z= 0.619
  Chirality :  0.066   0.461   1653
  Planarity :  0.008   0.082   1868
  Dihedral  : 18.965 176.183   4499
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.96 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 14.60 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.34 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.19), residues: 1259
  helix: -2.12 (0.21), residues: 321
  sheet: -0.33 (0.34), residues: 208
  loop : -2.49 (0.18), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A1685 
 HIS   0.009   0.002   HIS A 924 
 PHE   0.023   0.003   PHE A 192 
 TYR   0.019   0.002   TYR A 860 
 ARG   0.008   0.001   ARG A 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17227 (  324)
  hydrogen bonds       : angle       6.10480 (  987)
  metal coordination   : bond        0.12343 (   16)
  metal coordination   : angle      11.56902 (   21)
  covalent geometry    : bond        0.00923 (11292)
  covalent geometry    : angle       1.02007 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 264
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.5940 (m-30)
REVERT: A   51 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8279 (mtp-110)
REVERT: A   73 GLU cc_start: 0.7227 (tt0) cc_final: 0.6854 (mt-10)
REVERT: A  142 VAL cc_start: 0.8871 (t) cc_final: 0.8487 (p)
REVERT: A  287 ASN cc_start: 0.8153 (m110) cc_final: 0.7895 (m110)
REVERT: A  291 GLU cc_start: 0.7169 (tp30) cc_final: 0.6959 (tp30)
REVERT: A  293 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7573 (tp)
REVERT: A  318 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6242 (p0)
REVERT: A  334 VAL cc_start: 0.8029 (t) cc_final: 0.7756 (m)
REVERT: A  401 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8137 (tp)
REVERT: A  509 MET cc_start: 0.8247 (mmm) cc_final: 0.7419 (mmm)
REVERT: A  567 LYS cc_start: 0.8244 (ptmt) cc_final: 0.8023 (ptmm)
REVERT: A  581 GLU cc_start: 0.6926 (pp20) cc_final: 0.6581 (pp20)
REVERT: A  623 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8022 (ttpp)
REVERT: A  646 LEU cc_start: 0.7862 (tp) cc_final: 0.7661 (tp)
REVERT: A  651 PHE cc_start: 0.8274 (m-80) cc_final: 0.7820 (m-80)
REVERT: A  653 GLU cc_start: 0.6614 (mp0) cc_final: 0.6309 (mp0)
REVERT: A  689 SER cc_start: 0.8436 (m) cc_final: 0.8037 (t)
REVERT: A  778 ASN cc_start: 0.8190 (p0) cc_final: 0.7956 (p0)
REVERT: A  847 ASP cc_start: 0.7148 (m-30) cc_final: 0.6917 (m-30)
REVERT: A  944 GLU cc_start: 0.7397 (pm20) cc_final: 0.7042 (pm20)
REVERT: A 1488 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7398 (mtt180)
REVERT: A 1489 ILE cc_start: 0.8124 (pt) cc_final: 0.7875 (mp)
REVERT: A 1493 LYS cc_start: 0.8230 (ptpp) cc_final: 0.7988 (pttp)
REVERT: A 1497 ILE cc_start: 0.8047 (mm) cc_final: 0.7815 (mt)
REVERT: A 1570 PHE cc_start: 0.7920 (p90) cc_final: 0.7340 (p90)
  outliers start: 44
  outliers final: 18
  residues processed: 299
  average time/residue: 0.3038
  time to fit residues: 120.8556
Evaluate side-chains
  238 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  980 ASN
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1637 SER
Chi-restraints excluded: chain A residue 1653 LYS
Chi-restraints excluded: chain A residue 1656 ILE
Chi-restraints excluded: chain A residue 1679 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 118 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 492 ASN
A 708 ASN
A 871 ASN
A 901 ASN
A1449 ASN
A1537 GLN
A1544 ASN
A1604 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.109114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.094219 restraints weight = 15182.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.86
r_work: 0.3022 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11308  Z= 0.139
  Angle     :  0.610   9.314  15412  Z= 0.313
  Chirality :  0.045   0.256   1653
  Planarity :  0.006   0.063   1868
  Dihedral  : 18.316 175.839   1963
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.31 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.21), residues: 1259
  helix: -0.14 (0.28), residues: 328
  sheet: -0.09 (0.35), residues: 196
  loop : -1.95 (0.19), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 612 
 HIS   0.004   0.001   HIS A 789 
 PHE   0.016   0.002   PHE A 824 
 TYR   0.016   0.001   TYR A 808 
 ARG   0.007   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04489 (  324)
  hydrogen bonds       : angle       4.50247 (  987)
  metal coordination   : bond        0.00676 (   16)
  metal coordination   : angle       3.71815 (   21)
  covalent geometry    : bond        0.00320 (11292)
  covalent geometry    : angle       0.59461 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 226
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6251 (m-30)
REVERT: A   52 THR cc_start: 0.8568 (p) cc_final: 0.8355 (t)
REVERT: A  229 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8180 (ttmm)
REVERT: A  287 ASN cc_start: 0.8114 (m110) cc_final: 0.7841 (m110)
REVERT: A  334 VAL cc_start: 0.8152 (t) cc_final: 0.7871 (m)
REVERT: A  509 MET cc_start: 0.8548 (mmm) cc_final: 0.7592 (mmm)
REVERT: A  545 LEU cc_start: 0.8501 (tt) cc_final: 0.8278 (tp)
REVERT: A  567 LYS cc_start: 0.8656 (ptmt) cc_final: 0.8447 (ptmm)
REVERT: A  623 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8154 (ttpp)
REVERT: A  637 MET cc_start: 0.7842 (mtt) cc_final: 0.7596 (ttm)
REVERT: A  651 PHE cc_start: 0.8411 (m-80) cc_final: 0.7863 (m-80)
REVERT: A  653 GLU cc_start: 0.7282 (mp0) cc_final: 0.6855 (mp0)
REVERT: A  689 SER cc_start: 0.8187 (m) cc_final: 0.7828 (p)
REVERT: A  705 ARG cc_start: 0.8508 (mtp85) cc_final: 0.8243 (mtp-110)
REVERT: A  741 ASP cc_start: 0.8128 (m-30) cc_final: 0.7785 (m-30)
REVERT: A  821 LYS cc_start: 0.8398 (tttt) cc_final: 0.8114 (tttp)
REVERT: A  847 ASP cc_start: 0.7699 (m-30) cc_final: 0.7465 (m-30)
REVERT: A  944 GLU cc_start: 0.8085 (pm20) cc_final: 0.7642 (pm20)
REVERT: A  977 LEU cc_start: 0.8160 (mt) cc_final: 0.7919 (mp)
REVERT: A 1401 LYS cc_start: 0.8397 (tttt) cc_final: 0.8040 (tptt)
REVERT: A 1497 ILE cc_start: 0.7960 (mm) cc_final: 0.7700 (mt)
REVERT: A 1570 PHE cc_start: 0.8093 (p90) cc_final: 0.7493 (p90)
REVERT: A 1649 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7690 (p0)
  outliers start: 32
  outliers final: 15
  residues processed: 245
  average time/residue: 0.3230
  time to fit residues: 104.4469
Evaluate side-chains
  236 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 219
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue 1582 VAL
Chi-restraints excluded: chain A residue 1649 ASN
Chi-restraints excluded: chain A residue 1653 LYS
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 126 optimal weight:    0.0040
   chunk 81 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 993 ASN
A1596 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.109967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.095085 restraints weight = 15320.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.87
r_work: 0.3042 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11308  Z= 0.106
  Angle     :  0.541   7.012  15412  Z= 0.277
  Chirality :  0.042   0.223   1653
  Planarity :  0.005   0.060   1868
  Dihedral  : 17.983 179.297   1937
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.67 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.00 (0.22), residues: 1259
  helix:  0.78 (0.29), residues: 327
  sheet:  0.10 (0.35), residues: 203
  loop : -1.65 (0.20), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 612 
 HIS   0.005   0.001   HIS A 727 
 PHE   0.014   0.001   PHE A 824 
 TYR   0.012   0.001   TYR A 808 
 ARG   0.005   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  324)
  hydrogen bonds       : angle       4.07730 (  987)
  metal coordination   : bond        0.00303 (   16)
  metal coordination   : angle       2.82673 (   21)
  covalent geometry    : bond        0.00240 (11292)
  covalent geometry    : angle       0.53111 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 231
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7750 (tp30) cc_final: 0.7318 (tp30)
REVERT: A   51 ARG cc_start: 0.8456 (ptp-170) cc_final: 0.8164 (mtp-110)
REVERT: A  206 THR cc_start: 0.8592 (t) cc_final: 0.8113 (m)
REVERT: A  287 ASN cc_start: 0.8008 (m110) cc_final: 0.7750 (m110)
REVERT: A  509 MET cc_start: 0.8539 (mmm) cc_final: 0.7606 (mmm)
REVERT: A  637 MET cc_start: 0.7845 (mtt) cc_final: 0.7642 (ttm)
REVERT: A  651 PHE cc_start: 0.8409 (m-80) cc_final: 0.8200 (m-80)
REVERT: A  653 GLU cc_start: 0.7328 (mp0) cc_final: 0.6910 (mp0)
REVERT: A  689 SER cc_start: 0.8199 (m) cc_final: 0.7860 (p)
REVERT: A  705 ARG cc_start: 0.8480 (mtp85) cc_final: 0.8235 (mtp-110)
REVERT: A  719 ARG cc_start: 0.8373 (mmt90) cc_final: 0.7925 (mmt90)
REVERT: A  763 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7554 (tt0)
REVERT: A  808 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7449 (m-80)
REVERT: A  847 ASP cc_start: 0.7578 (m-30) cc_final: 0.7361 (m-30)
REVERT: A  944 GLU cc_start: 0.8086 (pm20) cc_final: 0.7632 (pm20)
REVERT: A 1401 LYS cc_start: 0.8450 (tttt) cc_final: 0.8102 (tptt)
REVERT: A 1489 ILE cc_start: 0.8290 (pt) cc_final: 0.8026 (mm)
REVERT: A 1493 LYS cc_start: 0.8336 (ptpt) cc_final: 0.7914 (pttp)
REVERT: A 1497 ILE cc_start: 0.8012 (mm) cc_final: 0.7806 (mt)
REVERT: A 1570 PHE cc_start: 0.8184 (p90) cc_final: 0.7499 (p90)
  outliers start: 27
  outliers final: 18
  residues processed: 246
  average time/residue: 0.2910
  time to fit residues: 96.7605
Evaluate side-chains
  238 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 218
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  656 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain A residue  808 TYR
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1582 VAL
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 95 optimal weight:    0.4980
   chunk 64 optimal weight:    2.9990
   chunk 105 optimal weight:    0.1980
   chunk 123 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 118 optimal weight:    5.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 109 HIS
A 498 GLN
A 502 ASN
A 673 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.109443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.094773 restraints weight = 15245.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.84
r_work: 0.3043 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11308  Z= 0.115
  Angle     :  0.541   7.165  15412  Z= 0.277
  Chirality :  0.043   0.229   1653
  Planarity :  0.005   0.060   1868
  Dihedral  : 17.925 178.792   1931
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.67 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.22), residues: 1259
  helix:  1.11 (0.29), residues: 330
  sheet:  0.30 (0.36), residues: 203
  loop : -1.51 (0.20), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 612 
 HIS   0.005   0.001   HIS A 727 
 PHE   0.014   0.001   PHE A 824 
 TYR   0.011   0.001   TYR A 149 
 ARG   0.007   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  324)
  hydrogen bonds       : angle       4.01921 (  987)
  metal coordination   : bond        0.00423 (   16)
  metal coordination   : angle       2.60255 (   21)
  covalent geometry    : bond        0.00269 (11292)
  covalent geometry    : angle       0.53274 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 228
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6322 (m-30)
REVERT: A   51 ARG cc_start: 0.8464 (ptp-170) cc_final: 0.8184 (mtp-110)
REVERT: A  287 ASN cc_start: 0.8010 (m110) cc_final: 0.7742 (m110)
REVERT: A  499 ILE cc_start: 0.8385 (mm) cc_final: 0.8065 (mm)
REVERT: A  653 GLU cc_start: 0.7326 (mp0) cc_final: 0.6920 (mp0)
REVERT: A  689 SER cc_start: 0.8211 (m) cc_final: 0.7950 (p)
REVERT: A  705 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8212 (mtp-110)
REVERT: A  719 ARG cc_start: 0.8326 (mmt90) cc_final: 0.7891 (mmt90)
REVERT: A  748 GLU cc_start: 0.7856 (pp20) cc_final: 0.7438 (pp20)
REVERT: A  763 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7491 (tt0)
REVERT: A  944 GLU cc_start: 0.8050 (pm20) cc_final: 0.7617 (pm20)
REVERT: A 1401 LYS cc_start: 0.8486 (tttt) cc_final: 0.8160 (tptt)
REVERT: A 1489 ILE cc_start: 0.8307 (pt) cc_final: 0.8094 (mm)
REVERT: A 1493 LYS cc_start: 0.8444 (ptpt) cc_final: 0.8050 (pttp)
REVERT: A 1570 PHE cc_start: 0.8230 (p90) cc_final: 0.7605 (p90)
  outliers start: 33
  outliers final: 20
  residues processed: 245
  average time/residue: 0.3051
  time to fit residues: 99.5650
Evaluate side-chains
  241 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 219
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  656 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain A residue  808 TYR
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 106 optimal weight:    0.1980
   chunk 15 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0870
   chunk 112 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 103 optimal weight:    0.3980
   chunk 101 optimal weight:    0.6980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
A1544 ASN
A1596 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.111911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.096961 restraints weight = 15298.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.91
r_work: 0.3069 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11308  Z= 0.090
  Angle     :  0.507   7.052  15412  Z= 0.260
  Chirality :  0.041   0.220   1653
  Planarity :  0.004   0.058   1868
  Dihedral  : 17.766 177.715   1930
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.13 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.23), residues: 1259
  helix:  1.65 (0.30), residues: 318
  sheet:  0.31 (0.36), residues: 206
  loop : -1.31 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 612 
 HIS   0.006   0.001   HIS A 727 
 PHE   0.013   0.001   PHE A 824 
 TYR   0.010   0.001   TYR A 707 
 ARG   0.006   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02974 (  324)
  hydrogen bonds       : angle       3.80290 (  987)
  metal coordination   : bond        0.00276 (   16)
  metal coordination   : angle       2.33172 (   21)
  covalent geometry    : bond        0.00201 (11292)
  covalent geometry    : angle       0.49955 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 233
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8438 (ptp-170) cc_final: 0.8146 (mtp-110)
REVERT: A   72 GLU cc_start: 0.7885 (tt0) cc_final: 0.7623 (tt0)
REVERT: A  110 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8340 (m)
REVERT: A  206 THR cc_start: 0.8540 (t) cc_final: 0.8146 (m)
REVERT: A  229 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8160 (mtpt)
REVERT: A  287 ASN cc_start: 0.7920 (m110) cc_final: 0.7643 (m110)
REVERT: A  499 ILE cc_start: 0.8369 (mm) cc_final: 0.8010 (mm)
REVERT: A  503 CYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7098 (p)
REVERT: A  509 MET cc_start: 0.8567 (mmm) cc_final: 0.7562 (mmm)
REVERT: A  651 PHE cc_start: 0.8452 (m-10) cc_final: 0.8052 (m-80)
REVERT: A  653 GLU cc_start: 0.7344 (mp0) cc_final: 0.6960 (mp0)
REVERT: A  689 SER cc_start: 0.8177 (m) cc_final: 0.7947 (p)
REVERT: A  705 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8260 (mtp-110)
REVERT: A  719 ARG cc_start: 0.8346 (mmt90) cc_final: 0.7908 (mmt90)
REVERT: A  748 GLU cc_start: 0.7889 (pp20) cc_final: 0.7462 (pp20)
REVERT: A  763 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7595 (tt0)
REVERT: A  944 GLU cc_start: 0.8006 (pm20) cc_final: 0.7614 (pm20)
REVERT: A 1389 LYS cc_start: 0.5404 (mmtm) cc_final: 0.4913 (ttpp)
REVERT: A 1401 LYS cc_start: 0.8521 (tttt) cc_final: 0.8202 (tptt)
REVERT: A 1489 ILE cc_start: 0.8311 (pt) cc_final: 0.8082 (mm)
REVERT: A 1570 PHE cc_start: 0.8126 (p90) cc_final: 0.7583 (p90)
  outliers start: 32
  outliers final: 19
  residues processed: 249
  average time/residue: 0.3208
  time to fit residues: 107.7599
Evaluate side-chains
  245 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 223
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 TRP
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  503 CYS
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  656 GLU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  808 TYR
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1544 ASN
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0050
   chunk 92 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0570
   chunk 122 optimal weight:    3.9990
   overall best weight:    1.6118

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 328 HIS
A 455 HIS
A 986 ASN
A1449 ASN
A1544 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.106994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.092040 restraints weight = 15415.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.89
r_work: 0.2992 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  11308  Z= 0.204
  Angle     :  0.623   9.099  15412  Z= 0.319
  Chirality :  0.047   0.249   1653
  Planarity :  0.005   0.060   1868
  Dihedral  : 17.963 179.912   1930
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 20.67 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.52 (0.22), residues: 1259
  helix:  1.23 (0.29), residues: 331
  sheet:  0.54 (0.37), residues: 195
  loop : -1.42 (0.20), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 612 
 HIS   0.005   0.001   HIS A1621 
 PHE   0.016   0.002   PHE A 192 
 TYR   0.015   0.002   TYR A 149 
 ARG   0.004   0.000   ARG A 935 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05046 (  324)
  hydrogen bonds       : angle       4.20054 (  987)
  metal coordination   : bond        0.00798 (   16)
  metal coordination   : angle       2.90716 (   21)
  covalent geometry    : bond        0.00501 (11292)
  covalent geometry    : angle       0.61389 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 231
  time to evaluate  : 1.475 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6398 (m-30)
REVERT: A   51 ARG cc_start: 0.8470 (ptp-170) cc_final: 0.8129 (mtp-110)
REVERT: A  206 THR cc_start: 0.8733 (t) cc_final: 0.8335 (m)
REVERT: A  287 ASN cc_start: 0.8124 (m110) cc_final: 0.7857 (m110)
REVERT: A  503 CYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7210 (p)
REVERT: A  529 TYR cc_start: 0.8089 (m-80) cc_final: 0.7841 (m-80)
REVERT: A  651 PHE cc_start: 0.8601 (m-10) cc_final: 0.8179 (m-80)
REVERT: A  653 GLU cc_start: 0.7413 (mp0) cc_final: 0.7015 (mp0)
REVERT: A  689 SER cc_start: 0.8218 (m) cc_final: 0.7998 (t)
REVERT: A  705 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8198 (mtp-110)
REVERT: A  714 ILE cc_start: 0.8391 (mt) cc_final: 0.8139 (mt)
REVERT: A  748 GLU cc_start: 0.7847 (pp20) cc_final: 0.7418 (pp20)
REVERT: A  763 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7505 (tt0)
REVERT: A  944 GLU cc_start: 0.8076 (pm20) cc_final: 0.7681 (pm20)
REVERT: A  977 LEU cc_start: 0.8191 (mt) cc_final: 0.7922 (mp)
REVERT: A 1389 LYS cc_start: 0.5577 (mmtm) cc_final: 0.5009 (ttpp)
REVERT: A 1401 LYS cc_start: 0.8552 (tttt) cc_final: 0.8256 (tptt)
REVERT: A 1489 ILE cc_start: 0.8292 (pt) cc_final: 0.8082 (mm)
REVERT: A 1670 ASP cc_start: 0.7811 (m-30) cc_final: 0.7594 (m-30)
  outliers start: 41
  outliers final: 31
  residues processed: 255
  average time/residue: 0.3762
  time to fit residues: 128.3604
Evaluate side-chains
  260 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 226
  time to evaluate  : 2.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  159 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  503 CYS
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  656 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  808 TYR
Chi-restraints excluded: chain A residue  843 SER
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1395 LEU
Chi-restraints excluded: chain A residue 1429 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1527 LEU
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 76 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   chunk 116 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 433 GLN
A 986 ASN
A1576 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.108627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.093762 restraints weight = 15366.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.89
r_work: 0.3016 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11308  Z= 0.125
  Angle     :  0.552   7.685  15412  Z= 0.283
  Chirality :  0.043   0.231   1653
  Planarity :  0.005   0.059   1868
  Dihedral  : 17.800 179.567   1929
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.49 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.23), residues: 1259
  helix:  1.54 (0.30), residues: 325
  sheet:  0.38 (0.36), residues: 205
  loop : -1.35 (0.20), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 612 
 HIS   0.005   0.001   HIS A 727 
 PHE   0.014   0.001   PHE A 824 
 TYR   0.012   0.001   TYR A 987 
 ARG   0.005   0.000   ARG A 738 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03818 (  324)
  hydrogen bonds       : angle       3.99189 (  987)
  metal coordination   : bond        0.00454 (   16)
  metal coordination   : angle       2.56205 (   21)
  covalent geometry    : bond        0.00297 (11292)
  covalent geometry    : angle       0.54454 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 222
  time to evaluate  : 3.123 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.8405 (ptp-170) cc_final: 0.8091 (mtp-110)
REVERT: A  206 THR cc_start: 0.8662 (t) cc_final: 0.8295 (m)
REVERT: A  287 ASN cc_start: 0.8046 (m110) cc_final: 0.7787 (m110)
REVERT: A  322 GLU cc_start: 0.3463 (OUTLIER) cc_final: 0.3165 (mp0)
REVERT: A  503 CYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7202 (p)
REVERT: A  651 PHE cc_start: 0.8515 (m-10) cc_final: 0.8120 (m-80)
REVERT: A  653 GLU cc_start: 0.7406 (mp0) cc_final: 0.7022 (mp0)
REVERT: A  689 SER cc_start: 0.8220 (m) cc_final: 0.7929 (p)
REVERT: A  705 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8221 (mtp-110)
REVERT: A  748 GLU cc_start: 0.7854 (pp20) cc_final: 0.7424 (pp20)
REVERT: A  763 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7509 (tt0)
REVERT: A  944 GLU cc_start: 0.7994 (pm20) cc_final: 0.7635 (pm20)
REVERT: A 1389 LYS cc_start: 0.5508 (mmtm) cc_final: 0.5046 (ttpp)
REVERT: A 1401 LYS cc_start: 0.8563 (tttt) cc_final: 0.8247 (tptt)
REVERT: A 1489 ILE cc_start: 0.8260 (pt) cc_final: 0.8049 (mm)
REVERT: A 1589 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7418 (tm-30)
  outliers start: 37
  outliers final: 25
  residues processed: 245
  average time/residue: 0.4076
  time to fit residues: 134.3250
Evaluate side-chains
  249 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 220
  time to evaluate  : 1.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   55 LYS
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  503 CYS
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  808 TYR
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1429 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1589 GLU
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0970
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 328 HIS
A 986 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.106691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.091901 restraints weight = 15274.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.87
r_work: 0.2985 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  11308  Z= 0.203
  Angle     :  0.617   8.804  15412  Z= 0.317
  Chirality :  0.047   0.247   1653
  Planarity :  0.005   0.061   1868
  Dihedral  : 17.909 179.704   1929
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 21.31 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.50 (0.22), residues: 1259
  helix:  1.27 (0.29), residues: 331
  sheet:  0.55 (0.36), residues: 195
  loop : -1.42 (0.20), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 612 
 HIS   0.006   0.001   HIS A1621 
 PHE   0.016   0.002   PHE A 192 
 TYR   0.017   0.002   TYR A 987 
 ARG   0.003   0.000   ARG A 935 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04938 (  324)
  hydrogen bonds       : angle       4.16182 (  987)
  metal coordination   : bond        0.00810 (   16)
  metal coordination   : angle       2.78575 (   21)
  covalent geometry    : bond        0.00499 (11292)
  covalent geometry    : angle       0.60891 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 228
  time to evaluate  : 1.447 
Fit side-chains
REVERT: A   27 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6372 (m-30)
REVERT: A   51 ARG cc_start: 0.8449 (ptp-170) cc_final: 0.8093 (mtp-110)
REVERT: A  206 THR cc_start: 0.8709 (t) cc_final: 0.8353 (m)
REVERT: A  287 ASN cc_start: 0.8171 (m110) cc_final: 0.7923 (m110)
REVERT: A  322 GLU cc_start: 0.3494 (OUTLIER) cc_final: 0.3241 (pt0)
REVERT: A  503 CYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7281 (p)
REVERT: A  651 PHE cc_start: 0.8604 (m-10) cc_final: 0.8251 (m-80)
REVERT: A  689 SER cc_start: 0.8235 (m) cc_final: 0.7908 (p)
REVERT: A  714 ILE cc_start: 0.8446 (mt) cc_final: 0.8193 (mt)
REVERT: A  748 GLU cc_start: 0.7842 (pp20) cc_final: 0.7424 (pp20)
REVERT: A  763 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7522 (tt0)
REVERT: A  944 GLU cc_start: 0.8041 (pm20) cc_final: 0.7686 (pm20)
REVERT: A 1389 LYS cc_start: 0.5720 (mmtm) cc_final: 0.5170 (ttpt)
REVERT: A 1401 LYS cc_start: 0.8549 (tttt) cc_final: 0.8243 (tptt)
REVERT: A 1589 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7454 (tm-30)
  outliers start: 42
  outliers final: 33
  residues processed: 255
  average time/residue: 0.3483
  time to fit residues: 120.5139
Evaluate side-chains
  263 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 225
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   55 LYS
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  503 CYS
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  782 LYS
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  808 TYR
Chi-restraints excluded: chain A residue  875 ASP
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1429 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1527 LEU
Chi-restraints excluded: chain A residue 1589 GLU
Chi-restraints excluded: chain A residue 1656 ILE
Chi-restraints excluded: chain A residue 1669 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 348 GLN
A 433 GLN
A 986 ASN
A1596 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.108699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.093808 restraints weight = 15337.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.89
r_work: 0.3016 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11308  Z= 0.122
  Angle     :  0.557   7.506  15412  Z= 0.286
  Chirality :  0.043   0.234   1653
  Planarity :  0.005   0.060   1868
  Dihedral  : 17.786 179.834   1929
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.67 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.34 (0.23), residues: 1259
  helix:  1.66 (0.30), residues: 322
  sheet:  0.41 (0.36), residues: 205
  loop : -1.35 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 612 
 HIS   0.005   0.001   HIS A 727 
 PHE   0.014   0.001   PHE A 546 
 TYR   0.011   0.001   TYR A 707 
 ARG   0.004   0.000   ARG A 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03872 (  324)
  hydrogen bonds       : angle       3.99878 (  987)
  metal coordination   : bond        0.00404 (   16)
  metal coordination   : angle       2.55571 (   21)
  covalent geometry    : bond        0.00289 (11292)
  covalent geometry    : angle       0.54961 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 220
  time to evaluate  : 1.257 
Fit side-chains
REVERT: A   27 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6180 (m-30)
REVERT: A   51 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.8043 (mtp-110)
REVERT: A  206 THR cc_start: 0.8651 (t) cc_final: 0.8303 (m)
REVERT: A  287 ASN cc_start: 0.8033 (m110) cc_final: 0.7786 (m110)
REVERT: A  322 GLU cc_start: 0.3339 (OUTLIER) cc_final: 0.3131 (pt0)
REVERT: A  503 CYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7220 (p)
REVERT: A  646 LEU cc_start: 0.7918 (tp) cc_final: 0.7609 (mp)
REVERT: A  651 PHE cc_start: 0.8540 (m-10) cc_final: 0.8213 (m-80)
REVERT: A  689 SER cc_start: 0.8190 (m) cc_final: 0.7899 (p)
REVERT: A  705 ARG cc_start: 0.8473 (mtp85) cc_final: 0.8166 (mtp-110)
REVERT: A  714 ILE cc_start: 0.8451 (mt) cc_final: 0.8194 (mt)
REVERT: A  748 GLU cc_start: 0.7809 (pp20) cc_final: 0.7386 (pp20)
REVERT: A  763 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7549 (tt0)
REVERT: A  800 LEU cc_start: 0.8198 (tp) cc_final: 0.7982 (mp)
REVERT: A  944 GLU cc_start: 0.8015 (pm20) cc_final: 0.7687 (pm20)
REVERT: A 1389 LYS cc_start: 0.5621 (mmtm) cc_final: 0.5132 (ttpp)
REVERT: A 1401 LYS cc_start: 0.8568 (tttt) cc_final: 0.8264 (tptt)
REVERT: A 1589 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7441 (tm-30)
  outliers start: 39
  outliers final: 26
  residues processed: 247
  average time/residue: 0.3032
  time to fit residues: 99.9218
Evaluate side-chains
  251 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 220
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   55 LYS
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  503 CYS
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  581 GLU
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  808 TYR
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1429 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1589 GLU
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 109 optimal weight:    0.3980
   chunk 115 optimal weight:    7.9990
   chunk 60 optimal weight:    0.1980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 119 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 121 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 348 GLN
A 986 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.109616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.094771 restraints weight = 15193.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.88
r_work: 0.3034 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11308  Z= 0.109
  Angle     :  0.541   7.291  15412  Z= 0.277
  Chirality :  0.042   0.228   1653
  Planarity :  0.005   0.060   1868
  Dihedral  : 17.730 179.562   1929
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.03 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.25 (0.23), residues: 1259
  helix:  1.75 (0.29), residues: 324
  sheet:  0.44 (0.36), residues: 205
  loop : -1.31 (0.21), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 612 
 HIS   0.005   0.001   HIS A 727 
 PHE   0.014   0.001   PHE A 546 
 TYR   0.009   0.001   TYR A 149 
 ARG   0.004   0.000   ARG A 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03502 (  324)
  hydrogen bonds       : angle       3.87945 (  987)
  metal coordination   : bond        0.00345 (   16)
  metal coordination   : angle       2.38854 (   21)
  covalent geometry    : bond        0.00252 (11292)
  covalent geometry    : angle       0.53384 (15391)

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

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

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2518 Ramachandran restraints generated.
    1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 228
  time to evaluate  : 1.314 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.8344 (ptp-170) cc_final: 0.8012 (mtp-110)
REVERT: A  206 THR cc_start: 0.8619 (t) cc_final: 0.8275 (m)
REVERT: A  287 ASN cc_start: 0.7994 (m110) cc_final: 0.7727 (m110)
REVERT: A  298 ASP cc_start: 0.7267 (m-30) cc_final: 0.7056 (m-30)
REVERT: A  503 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7123 (p)
REVERT: A  646 LEU cc_start: 0.7907 (tp) cc_final: 0.7592 (mp)
REVERT: A  651 PHE cc_start: 0.8513 (m-10) cc_final: 0.8179 (m-80)
REVERT: A  689 SER cc_start: 0.8168 (m) cc_final: 0.7873 (p)
REVERT: A  705 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8206 (mtp-110)
REVERT: A  748 GLU cc_start: 0.7772 (pp20) cc_final: 0.7371 (pp20)
REVERT: A  763 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7554 (tt0)
REVERT: A  944 GLU cc_start: 0.8003 (pm20) cc_final: 0.7657 (pm20)
REVERT: A  977 LEU cc_start: 0.8122 (mt) cc_final: 0.7828 (mp)
REVERT: A 1389 LYS cc_start: 0.5618 (mmtm) cc_final: 0.5110 (ttpp)
REVERT: A 1401 LYS cc_start: 0.8560 (tttt) cc_final: 0.8250 (tptt)
REVERT: A 1589 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7402 (tm-30)
  outliers start: 34
  outliers final: 25
  residues processed: 250
  average time/residue: 0.3089
  time to fit residues: 103.3225
Evaluate side-chains
  254 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 226
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LYS
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  503 CYS
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  636 GLU
Chi-restraints excluded: chain A residue  656 GLU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  711 ASN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  763 GLU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  808 TYR
Chi-restraints excluded: chain A residue  875 ASP
Chi-restraints excluded: chain A residue  948 GLU
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1589 GLU
Chi-restraints excluded: chain A residue 1656 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 102 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 119 optimal weight:    0.0970
   chunk 128 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   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  79 ASN
A  89 ASN
A 348 GLN
A 433 GLN
A 986 ASN
A1449 ASN
A1596 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.109790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.094988 restraints weight = 15215.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.88
r_work: 0.3038 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11308  Z= 0.109
  Angle     :  0.540   7.197  15412  Z= 0.276
  Chirality :  0.043   0.227   1653
  Planarity :  0.005   0.061   1868
  Dihedral  : 17.714 179.168   1929
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.30 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.23 (0.23), residues: 1259
  helix:  1.81 (0.29), residues: 324
  sheet:  0.43 (0.36), residues: 198
  loop : -1.30 (0.20), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 612 
 HIS   0.005   0.001   HIS A 727 
 PHE   0.014   0.001   PHE A 546 
 TYR   0.011   0.001   TYR A 707 
 ARG   0.004   0.000   ARG A 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  324)
  hydrogen bonds       : angle       3.85126 (  987)
  metal coordination   : bond        0.00369 (   16)
  metal coordination   : angle       2.38333 (   21)
  covalent geometry    : bond        0.00255 (11292)
  covalent geometry    : angle       0.53323 (15391)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6998.01 seconds
wall clock time: 124 minutes 53.25 seconds (7493.25 seconds total)