Starting phenix.real_space_refine
on Tue Nov 14 06:22:25 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/11_2023/7e7s_31003.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/11_2023/7e7s_31003.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/11_2023/7e7s_31003.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/11_2023/7e7s_31003.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/11_2023/7e7s_31003.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/11_2023/7e7s_31003.pdb"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      58      5.16       5
     C    5027      2.51       5
     N    1314      2.21       5
     O    1483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   59": "OD1" <-> "OD2"
    Residue "A GLU  121": "OE1" <-> "OE2"
    Residue "A GLU  125": "OE1" <-> "OE2"
    Residue "A TYR  295": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  394": "OE1" <-> "OE2"
    Residue "A GLU  439": "OE1" <-> "OE2"
    Residue "A PHE  483": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  518": "OE1" <-> "OE2"
    Residue "A ASP  694": "OD1" <-> "OD2"
    Residue "A TYR  867": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  882": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1040": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 7884
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1022, 7884
          Unusual residues: {' CA': 2}
          Classifications: {'peptide': 1020, 'undetermined': 2}
          Link IDs: {'PTRANS': 46, 'TRANS': 973, None: 2}
            Not linked:
              pdbres="SER A1042 "
              pdbres=" CA A4001 "
            Not linked:
              pdbres=" CA A4001 "
              pdbres=" CA A4002 "
          Chain breaks: 2
  Time building chain proxies: 4.32, per 1000 atoms: 0.55
  Number of scatterers: 7884
  At special positions: 0
  Unit cell: (78.435, 84.66, 150.645, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      58     16.00
     O    1483      8.00
     N    1314      7.00
     C    5027      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 875 " - pdb=" SG  CYS A 887 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.27
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1910

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      55.0% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
      removed outlier: 3.599A  pdb=" N   THR A   6 " --> pdb=" O   ASN A   3 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS A   7 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3 through 7'
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 25 through 36
      removed outlier: 3.588A  pdb=" N   GLU A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 59 through 76
    Processing helix  chain 'A' and resid 88 through 123
      removed outlier: 3.509A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.976A  pdb=" N   ASN A 229 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 274
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.748A  pdb=" N   HIS A 278 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ASN A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 287 through 307
      removed outlier: 3.631A  pdb=" N   PHE A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 329
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.690A  pdb=" N   THR A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 407 through 420
      removed outlier: 3.745A  pdb=" N   VAL A 411 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 453
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 4.106A  pdb=" N   ALA A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 478
    Processing helix  chain 'A' and resid 516 through 523
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.622A  pdb=" N   GLN A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 586
      removed outlier: 3.859A  pdb=" N   PHE A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.502A  pdb=" N   ASN A 671 " --> pdb=" O   ASP A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.868A  pdb=" N   LYS A 683 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER A 684 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 723 through 729
      removed outlier: 3.639A  pdb=" N   LYS A 727 " --> pdb=" O   THR A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 781
      removed outlier: 3.705A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 800
      removed outlier: 3.676A  pdb=" N   GLY A 800 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 806 through 809
    Processing helix  chain 'A' and resid 829 through 858
      removed outlier: 3.557A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE A 855 " --> pdb=" O   ALA A 851 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A 858 " --> pdb=" O   TRP A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 871
    Processing helix  chain 'A' and resid 872 through 875
    Processing helix  chain 'A' and resid 886 through 891
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.425A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 916
      No H-bonds generated for 'chain 'A' and resid 914 through 916'
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 946
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 962 through 974
      removed outlier: 3.621A  pdb=" N   MET A 968 " --> pdb=" O   THR A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.632A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1030
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129
    Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153
      removed outlier: 6.861A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE A 163 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 208 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176
      removed outlier: 6.552A  pdb=" N   ARG A 174 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASN A 213 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 651 through 653
      removed outlier: 8.069A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A 734 " --> pdb=" O   ALA A 718 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.446A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 368 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 365 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.034A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.946A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 515 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA A 564 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.446A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 368 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 365 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.034A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.946A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   CYS A 524 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE A 592 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   GLY A 594 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 9.299A  pdb=" N   ARG A 528 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
      removed outlier: 13.026A  pdb=" N   VAL A 596 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428

    413 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.91

  Time building geometry restraints manager: 3.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2577
        1.34 -     1.46: 1658
        1.46 -     1.58: 3706
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 8031
  Sorted by residual:
  bond pdb=" CA  VAL A 529 "
       pdb=" CB  VAL A 529 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.72e-01
  bond pdb=" CG  LEU A 806 "
       pdb=" CD1 LEU A 806 "
    ideal  model  delta    sigma   weight residual
    1.521  1.498  0.023 3.30e-02 9.18e+02 4.87e-01
  bond pdb=" N   PRO A 819 "
       pdb=" CA  PRO A 819 "
    ideal  model  delta    sigma   weight residual
    1.457  1.466 -0.009 1.31e-02 5.83e+03 4.68e-01
  bond pdb=" C   PRO A 819 "
       pdb=" O   PRO A 819 "
    ideal  model  delta    sigma   weight residual
    1.246  1.240  0.005 8.50e-03 1.38e+04 4.18e-01
  bond pdb=" CG  PRO A 312 "
       pdb=" CD  PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.503  1.481  0.022 3.40e-02 8.65e+02 4.14e-01
  ... (remaining 8026 not shown)

  Histogram of bond angle deviations from ideal:
       99.97 -   106.79: 239
      106.79 -   113.60: 4553
      113.60 -   120.41: 2910
      120.41 -   127.22: 3113
      127.22 -   134.03: 84
  Bond angle restraints: 10899
  Sorted by residual:
  angle pdb=" CB  MET A 908 "
        pdb=" CG  MET A 908 "
        pdb=" SD  MET A 908 "
      ideal   model   delta    sigma   weight residual
     112.70  121.00   -8.30 3.00e+00 1.11e-01 7.65e+00
  angle pdb=" N   ILE A 232 "
        pdb=" CA  ILE A 232 "
        pdb=" C   ILE A 232 "
      ideal   model   delta    sigma   weight residual
     113.07  109.43    3.64 1.36e+00 5.41e-01 7.18e+00
  angle pdb=" C   VAL A 223 "
        pdb=" N   VAL A 224 "
        pdb=" CA  VAL A 224 "
      ideal   model   delta    sigma   weight residual
     122.66  120.19    2.47 9.70e-01 1.06e+00 6.46e+00
  angle pdb=" CB  LYS A 541 "
        pdb=" CG  LYS A 541 "
        pdb=" CD  LYS A 541 "
      ideal   model   delta    sigma   weight residual
     111.30  116.95   -5.65 2.30e+00 1.89e-01 6.04e+00
  angle pdb=" N   LEU A 952 "
        pdb=" CA  LEU A 952 "
        pdb=" C   LEU A 952 "
      ideal   model   delta    sigma   weight residual
     109.81  115.21   -5.40 2.21e+00 2.05e-01 5.98e+00
  ... (remaining 10894 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4353
       17.73 -    35.45: 426
       35.45 -    53.18: 64
       53.18 -    70.91: 17
       70.91 -    88.63: 8
  Dihedral angle restraints: 4868
    sinusoidal: 1922
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CA  VAL A 949 "
           pdb=" C   VAL A 949 "
           pdb=" N   GLU A 950 "
           pdb=" CA  GLU A 950 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.07  -22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  ASP A1038 "
           pdb=" CB  ASP A1038 "
           pdb=" CG  ASP A1038 "
           pdb=" OD1 ASP A1038 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.97   58.97     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CB  GLU A  79 "
           pdb=" CG  GLU A  79 "
           pdb=" CD  GLU A  79 "
           pdb=" OE1 GLU A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.63  -88.63     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 4865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 919
       0.036 -    0.072: 256
       0.072 -    0.108: 85
       0.108 -    0.144: 18
       0.144 -    0.180: 1
  Chirality restraints: 1279
  Sorted by residual:
  chirality pdb=" CB  ILE A 150 "
            pdb=" CA  ILE A 150 "
            pdb=" CG1 ILE A 150 "
            pdb=" CG2 ILE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  ILE A 527 "
            pdb=" N   ILE A 527 "
            pdb=" C   ILE A 527 "
            pdb=" CB  ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  PRO A 788 "
            pdb=" N   PRO A 788 "
            pdb=" C   PRO A 788 "
            pdb=" CB  PRO A 788 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.96e-01
  ... (remaining 1276 not shown)

  Planarity restraints: 1389
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 400 "    0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO A 401 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 401 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 401 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 247 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO A 248 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 892 "   -0.025 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO A 893 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 893 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 893 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1386 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 222
        2.71 -     3.26: 8253
        3.26 -     3.81: 12642
        3.81 -     4.35: 15906
        4.35 -     4.90: 26753
  Nonbonded interactions: 63776
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 879 "
            pdb=" OD1 ASP A 881 "
     model   vdw
     2.166 2.520
  nonbonded pdb=" O   ILE A 307 "
            pdb=" OE1 GLU A 309 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NH2 ARG A 619 "
            pdb=" O   CYS A 669 "
     model   vdw
     2.264 2.520
  nonbonded pdb=" O   PHE A 209 "
            pdb=" OG1 THR A 212 "
     model   vdw
     2.284 2.440
  nonbonded pdb=" OG  SER A  38 "
            pdb=" O   LYS A 143 "
     model   vdw
     2.296 2.440
  ... (remaining 63771 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          1.410
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     25.470
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8031  Z= 0.171
  Angle     :  0.496   8.299  10899  Z= 0.261
  Chirality :  0.040   0.180   1279
  Planarity :  0.004   0.054   1389
  Dihedral  : 14.410  88.632   2955
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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: -0.13 (0.26), residues: 1014
  helix:  0.30 (0.23), residues: 482
  sheet: -1.14 (0.48), residues: 109
  loop : -0.03 (0.32), residues: 423

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.935 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2051
  time to fit residues: 29.9215
Evaluate side-chains
  80 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.809 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2441
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0570
   chunk 48 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0770
   overall best weight:    0.7860

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 403 ASN
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 913 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8031  Z= 0.187
  Angle     :  0.524   6.976  10899  Z= 0.273
  Chirality :  0.042   0.171   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.865  22.467   1078
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  7.10 %
    Favored  : 92.67 %
  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:  0.66 (0.27), residues: 1014
  helix:  1.29 (0.23), residues: 501
  sheet: -1.17 (0.48), residues: 102
  loop : -0.05 (0.32), residues: 411

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.829 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 97
  average time/residue: 0.1942
  time to fit residues: 26.6421
Evaluate side-chains
  82 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.809 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0708
  time to fit residues: 1.3060
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8031  Z= 0.239
  Angle     :  0.531   6.853  10899  Z= 0.273
  Chirality :  0.042   0.146   1279
  Planarity :  0.004   0.045   1389
  Dihedral  :  3.941  24.598   1078
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 10.54 %
    Favored  : 88.66 %
  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:  0.84 (0.27), residues: 1014
  helix:  1.49 (0.24), residues: 501
  sheet: -1.01 (0.48), residues: 102
  loop : -0.07 (0.32), residues: 411

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.863 
Fit side-chains
  outliers start: 7
  outliers final: 2
  residues processed: 95
  average time/residue: 0.2038
  time to fit residues: 27.5223
Evaluate side-chains
  88 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.866 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0744
  time to fit residues: 1.5189
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 48 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8031  Z= 0.175
  Angle     :  0.495   5.866  10899  Z= 0.254
  Chirality :  0.042   0.199   1279
  Planarity :  0.004   0.046   1389
  Dihedral  :  3.840  23.774   1078
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.60 %
    Favored  : 86.25 %
  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:  1.05 (0.27), residues: 1014
  helix:  1.68 (0.24), residues: 500
  sheet: -0.85 (0.53), residues: 84
  loop : -0.07 (0.31), residues: 430

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.909 
Fit side-chains
  outliers start: 10
  outliers final: 5
  residues processed: 98
  average time/residue: 0.2060
  time to fit residues: 28.1238
Evaluate side-chains
  95 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.776 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0741
  time to fit residues: 1.8463
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.0270
   chunk 73 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    1.3442

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8031  Z= 0.231
  Angle     :  0.512   6.780  10899  Z= 0.262
  Chirality :  0.042   0.208   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.888  24.434   1078
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 13.97 %
    Favored  : 84.99 %
  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:  1.03 (0.27), residues: 1014
  helix:  1.68 (0.24), residues: 501
  sheet: -0.80 (0.52), residues: 87
  loop : -0.10 (0.31), residues: 426

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.924 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 99
  average time/residue: 0.2064
  time to fit residues: 28.3444
Evaluate side-chains
  97 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.870 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0760
  time to fit residues: 1.9162
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 8 optimal weight:    0.2980
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8031  Z= 0.219
  Angle     :  0.511   7.206  10899  Z= 0.261
  Chirality :  0.043   0.279   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.888  24.480   1078
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 15.01 %
    Favored  : 84.31 %
  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:  1.04 (0.27), residues: 1014
  helix:  1.72 (0.24), residues: 501
  sheet: -0.80 (0.58), residues: 77
  loop : -0.17 (0.31), residues: 436

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.819 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1989
  time to fit residues: 25.8909
Evaluate side-chains
  92 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.826 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0716
  time to fit residues: 1.6649
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8031  Z= 0.210
  Angle     :  0.506   7.666  10899  Z= 0.259
  Chirality :  0.042   0.246   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.879  24.275   1078
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 16.15 %
    Favored  : 83.39 %
  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:  1.06 (0.27), residues: 1014
  helix:  1.75 (0.24), residues: 501
  sheet: -0.76 (0.57), residues: 77
  loop : -0.19 (0.31), residues: 436

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.803 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 92
  average time/residue: 0.1977
  time to fit residues: 25.6224
Evaluate side-chains
  91 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.794 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0722
  time to fit residues: 1.2654
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.0570
   chunk 62 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0980
   chunk 9 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8031  Z= 0.145
  Angle     :  0.499   7.935  10899  Z= 0.251
  Chirality :  0.041   0.221   1279
  Planarity :  0.004   0.046   1389
  Dihedral  :  3.783  22.858   1078
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 16.15 %
    Favored  : 83.51 %
  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:  1.28 (0.27), residues: 1014
  helix:  1.97 (0.24), residues: 500
  sheet: -0.65 (0.57), residues: 77
  loop : -0.12 (0.31), residues: 437

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.909 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2033
  time to fit residues: 27.3215
Evaluate side-chains
  92 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.892 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2744
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.0570
   chunk 71 optimal weight:    0.0060
   chunk 28 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 86 optimal weight:    0.4980
   chunk 91 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.4314

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8031  Z= 0.141
  Angle     :  0.500   8.862  10899  Z= 0.248
  Chirality :  0.041   0.212   1279
  Planarity :  0.003   0.046   1389
  Dihedral  :  3.684  22.644   1078
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 16.61 %
    Favored  : 82.93 %
  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:  1.35 (0.27), residues: 1014
  helix:  2.05 (0.24), residues: 499
  sheet: -0.50 (0.59), residues: 77
  loop : -0.13 (0.31), residues: 438

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.849 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 92
  average time/residue: 0.2069
  time to fit residues: 26.6447
Evaluate side-chains
  92 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.856 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0778
  time to fit residues: 1.5022
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0020
   chunk 8 optimal weight:    0.0020
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8031  Z= 0.145
  Angle     :  0.491   8.609  10899  Z= 0.247
  Chirality :  0.041   0.204   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.666  22.698   1078
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 16.49 %
    Favored  : 83.28 %
  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:  1.39 (0.27), residues: 1014
  helix:  2.08 (0.24), residues: 499
  sheet: -0.46 (0.58), residues: 79
  loop : -0.12 (0.31), residues: 436

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.927 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 92
  average time/residue: 0.1960
  time to fit residues: 25.9259
Evaluate side-chains
  91 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.869 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0987
  time to fit residues: 2.1546
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0370
   chunk 33 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 71 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0870
   chunk 58 optimal weight:    7.9990
   chunk 92 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.187579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.116044 restraints weight = 8301.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.87
r_work: 0.3054 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8031  Z= 0.137
  Angle     :  0.485   8.732  10899  Z= 0.243
  Chirality :  0.041   0.194   1279
  Planarity :  0.003   0.047   1389
  Dihedral  :  3.616  22.444   1078
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.07 %
    Favored  : 82.93 %
  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:  1.42 (0.27), residues: 1014
  helix:  2.12 (0.24), residues: 499
  sheet: -0.46 (0.58), residues: 77
  loop : -0.12 (0.31), residues: 438
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1833.54 seconds
wall clock time: 33 minutes 58.22 seconds (2038.22 seconds total)