Starting phenix.real_space_refine
on Mon Mar 11 15:22:26 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h5b_34490/03_2024/8h5b_34490.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h5b_34490/03_2024/8h5b_34490.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h5b_34490/03_2024/8h5b_34490.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h5b_34490/03_2024/8h5b_34490.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h5b_34490/03_2024/8h5b_34490.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h5b_34490/03_2024/8h5b_34490.pdb"
  }
  resolution = 4.03
  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=   0.002 sd=   0.040
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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    5514      2.51       5
     N    1389      2.21       5
     O    1630      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   73": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  113": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  264": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  266": "NH1" <-> "NH2"
    Residue "A PHE  277": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  356": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  379": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  400": "OE1" <-> "OE2"
    Residue "A TYR  414": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  450": "OE1" <-> "OE2"
    Residue "A TYR  511": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  513": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  543": "OD1" <-> "OD2"
    Residue "A PHE  578": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  582": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  587": "OE1" <-> "OE2"
    Residue "A ASP  607": "OD1" <-> "OD2"
    Residue "A GLU  693": "OE1" <-> "OE2"
    Residue "A GLU  719": "OE1" <-> "OE2"
    Residue "A PHE  782": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  798": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  933": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  993": "OD1" <-> "OD2"
    Residue "B GLU   93": "OE1" <-> "OE2"
    Residue "B GLU  108": "OE1" <-> "OE2"
    Residue "B PHE  155": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  196": "NH1" <-> "NH2"
    Residue "B TYR  231": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 8570
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 902, 7213
          Classifications: {'peptide': 902}
          Link IDs: {'PTRANS': 25, 'TRANS': 876}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 1357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 173, 1357
          Classifications: {'peptide': 173}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 164}
  Time building chain proxies: 4.87, per 1000 atoms: 0.57
  Number of scatterers: 8570
  At special positions: 0
  Unit cell: (108.73, 113.71, 101.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1630      8.00
     N    1389      7.00
     C    5514      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.61
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2094

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 1 sheets defined
      76.9% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 11
    Processing helix  chain 'A' and resid 17 through 31
      removed outlier: 3.861A  pdb=" N   GLN A  24 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER A  31 " --> pdb=" O   GLN A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 46
      removed outlier: 3.832A  pdb=" N   LYS A  38 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 69
      removed outlier: 4.168A  pdb=" N   LYS A  63 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   MET A  67 " --> pdb=" O   LYS A  63 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   TYR A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 100
      removed outlier: 3.791A  pdb=" N   LYS A  96 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 127
      removed outlier: 3.559A  pdb=" N   CYS A 114 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 121 " --> pdb=" O   GLN A 117 " (cutoff:3.500A)
      Proline residue:  A 124  - end of helix
    Processing helix  chain 'A' and resid 129 through 141
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.137A  pdb=" N   ASP A 155 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ASP A 156 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 165
    Processing helix  chain 'A' and resid 167 through 182
      removed outlier: 3.512A  pdb=" N   ALA A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 207
      removed outlier: 3.630A  pdb=" N   ALA A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLN A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 204 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   HIS A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 236
      removed outlier: 3.698A  pdb=" N   GLN A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 264
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 270 through 291
    Processing helix  chain 'A' and resid 303 through 321
      removed outlier: 3.552A  pdb=" N   ILE A 312 " --> pdb=" O   HIS A 308 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TYR A 313 " --> pdb=" O   ASP A 309 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 314 " --> pdb=" O   CYS A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 342
      removed outlier: 4.153A  pdb=" N   ILE A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 355
    Processing helix  chain 'A' and resid 355 through 364
      removed outlier: 4.326A  pdb=" N   PHE A 359 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER A 361 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 382
      removed outlier: 3.977A  pdb=" N   ASN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLU A 378 " --> pdb=" O   ASP A 374 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   SER A 382 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 403
      removed outlier: 3.665A  pdb=" N   GLU A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 422
      removed outlier: 3.758A  pdb=" N   LEU A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASN A 422 " --> pdb=" O   CYS A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 448
      removed outlier: 4.318A  pdb=" N   GLN A 433 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 470
      Proline residue:  A 464  - end of helix
    Processing helix  chain 'A' and resid 476 through 494
      removed outlier: 3.617A  pdb=" N   SER A 482 " --> pdb=" O   LYS A 478 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS A 494 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 515
      removed outlier: 4.620A  pdb=" N   ILE A 506 " --> pdb=" O   SER A 502 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TYR A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   PHE A 514 " --> pdb=" O   TYR A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 521
    Processing helix  chain 'A' and resid 522 through 542
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'A' and resid 570 through 588
      removed outlier: 3.766A  pdb=" N   GLU A 587 " --> pdb=" O   THR A 583 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASP A 588 " --> pdb=" O   ILE A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 606
      removed outlier: 3.713A  pdb=" N   VAL A 595 " --> pdb=" O   ASN A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 634
      removed outlier: 4.753A  pdb=" N   ASN A 616 " --> pdb=" O   ASP A 612 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR A 617 " --> pdb=" O   ASN A 613 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
      removed outlier: 3.875A  pdb=" N   ALA A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 656
    Processing helix  chain 'A' and resid 664 through 682
      removed outlier: 3.780A  pdb=" N   ASN A 668 " --> pdb=" O   PRO A 664 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   GLU A 673 " --> pdb=" O   GLN A 669 " (cutoff:3.500A)
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 684 through 702
      removed outlier: 3.988A  pdb=" N   ALA A 694 " --> pdb=" O   LEU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 706
      removed outlier: 3.555A  pdb=" N   ALA A 706 " --> pdb=" O   ASP A 703 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 703 through 706'
    Processing helix  chain 'A' and resid 707 through 722
      removed outlier: 4.483A  pdb=" N   MET A 712 " --> pdb=" O   GLU A 708 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   ASP A 713 " --> pdb=" O   PRO A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 732
    Processing helix  chain 'A' and resid 733 through 745
      removed outlier: 4.749A  pdb=" N   LEU A 737 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A 745 " --> pdb=" O   ILE A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 767
      removed outlier: 4.192A  pdb=" N   LEU A 752 " --> pdb=" O   GLU A 748 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY A 754 " --> pdb=" O   GLN A 750 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   ARG A 755 " --> pdb=" O   PRO A 751 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS A 766 " --> pdb=" O   VAL A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 787
      removed outlier: 4.080A  pdb=" N   LEU A 780 " --> pdb=" O   LEU A 776 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   CYS A 781 " --> pdb=" O   LEU A 777 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   PHE A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU A 783 " --> pdb=" O   VAL A 779 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP A 787 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 798
      removed outlier: 4.234A  pdb=" N   THR A 791 " --> pdb=" O   ASP A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 820
      removed outlier: 4.467A  pdb=" N   LEU A 808 " --> pdb=" O   ASP A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 838
      removed outlier: 3.577A  pdb=" N   ILE A 826 " --> pdb=" O   GLY A 822 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU A 828 " --> pdb=" O   LYS A 824 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   PHE A 838 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 846
    Processing helix  chain 'A' and resid 878 through 896
      removed outlier: 4.002A  pdb=" N   ILE A 884 " --> pdb=" O   TYR A 880 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LYS A 885 " --> pdb=" O   THR A 881 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 941
      removed outlier: 4.124A  pdb=" N   GLU A 938 " --> pdb=" O   ASP A 934 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP A 941 " --> pdb=" O   LYS A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 978
      removed outlier: 3.554A  pdb=" N   LEU A 968 " --> pdb=" O   SER A 964 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER A 978 " --> pdb=" O   LYS A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 990
      removed outlier: 3.846A  pdb=" N   ILE A 987 " --> pdb=" O   GLY A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1000
      removed outlier: 3.946A  pdb=" N   SER A1000 " --> pdb=" O   ARG A 996 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 128 through 146
    Processing helix  chain 'B' and resid 171 through 180
      removed outlier: 3.940A  pdb=" N   LEU B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   HIS B 179 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 235
      removed outlier: 3.588A  pdb=" N   ILE B 223 " --> pdb=" O   GLN B 219 " (cutoff:3.500A)
      Proline residue:  B 232  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.563A  pdb=" N   VAL B 122 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   VAL B 161 " --> pdb=" O   GLN B  68 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   ILE B  70 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ASN B 159 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA B  72 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ILE B 157 " --> pdb=" O   ALA B  72 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE B 202 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   MET B 197 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)

    542 hydrogen bonds defined for protein.
    1611 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: 2.77

  Time building geometry restraints manager: 3.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2754
        1.34 -     1.46: 1393
        1.46 -     1.58: 4505
        1.58 -     1.69: 2
        1.69 -     1.81: 55
  Bond restraints: 8709
  Sorted by residual:
  bond pdb=" CG  PRO A 567 "
       pdb=" CD  PRO A 567 "
    ideal  model  delta    sigma   weight residual
    1.503  1.318  0.185 3.40e-02 8.65e+02 2.97e+01
  bond pdb=" CB  PRO A 567 "
       pdb=" CG  PRO A 567 "
    ideal  model  delta    sigma   weight residual
    1.492  1.644 -0.152 5.00e-02 4.00e+02 9.30e+00
  bond pdb=" CB  PRO B 169 "
       pdb=" CG  PRO B 169 "
    ideal  model  delta    sigma   weight residual
    1.492  1.602 -0.110 5.00e-02 4.00e+02 4.86e+00
  bond pdb=" N   PRO A 567 "
       pdb=" CA  PRO A 567 "
    ideal  model  delta    sigma   weight residual
    1.466  1.439  0.027 1.50e-02 4.44e+03 3.30e+00
  bond pdb=" C   VAL A 734 "
       pdb=" N   GLY A 735 "
    ideal  model  delta    sigma   weight residual
    1.330  1.356 -0.026 1.49e-02 4.50e+03 2.98e+00
  ... (remaining 8704 not shown)

  Histogram of bond angle deviations from ideal:
       90.01 -    98.80: 4
       98.80 -   107.59: 214
      107.59 -   116.38: 5624
      116.38 -   125.17: 5872
      125.17 -   133.96: 72
  Bond angle restraints: 11786
  Sorted by residual:
  angle pdb=" N   PRO A 567 "
        pdb=" CD  PRO A 567 "
        pdb=" CG  PRO A 567 "
      ideal   model   delta    sigma   weight residual
     103.20   90.01   13.19 1.50e+00 4.44e-01 7.73e+01
  angle pdb=" CA  PRO A 567 "
        pdb=" N   PRO A 567 "
        pdb=" CD  PRO A 567 "
      ideal   model   delta    sigma   weight residual
     112.00  100.64   11.36 1.40e+00 5.10e-01 6.59e+01
  angle pdb=" CA  PRO B 169 "
        pdb=" N   PRO B 169 "
        pdb=" CD  PRO B 169 "
      ideal   model   delta    sigma   weight residual
     112.00  105.15    6.85 1.40e+00 5.10e-01 2.39e+01
  angle pdb=" CA  PRO A 567 "
        pdb=" CB  PRO A 567 "
        pdb=" CG  PRO A 567 "
      ideal   model   delta    sigma   weight residual
     104.50   96.36    8.14 1.90e+00 2.77e-01 1.84e+01
  angle pdb=" C   ALA B  89 "
        pdb=" N   ARG B  90 "
        pdb=" CA  ARG B  90 "
      ideal   model   delta    sigma   weight residual
     121.54  128.43   -6.89 1.91e+00 2.74e-01 1.30e+01
  ... (remaining 11781 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 4855
       17.60 -    35.19: 423
       35.19 -    52.79: 37
       52.79 -    70.38: 13
       70.38 -    87.98: 4
  Dihedral angle restraints: 5332
    sinusoidal: 2141
      harmonic: 3191
  Sorted by residual:
  dihedral pdb=" CA  TYR A 670 "
           pdb=" C   TYR A 670 "
           pdb=" N   LEU A 671 "
           pdb=" CA  LEU A 671 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.95  -19.05     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  PHE A 379 "
           pdb=" C   PHE A 379 "
           pdb=" N   PHE A 380 "
           pdb=" CA  PHE A 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.03  -18.97     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  THR B 111 "
           pdb=" C   THR B 111 "
           pdb=" N   THR B 112 "
           pdb=" CA  THR B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 5329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1199
       0.058 -    0.116: 188
       0.116 -    0.173: 25
       0.173 -    0.231: 0
       0.231 -    0.289: 1
  Chirality restraints: 1413
  Sorted by residual:
  chirality pdb=" CA  PRO A 567 "
            pdb=" N   PRO A 567 "
            pdb=" C   PRO A 567 "
            pdb=" CB  PRO A 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CA  ILE B 202 "
            pdb=" N   ILE B 202 "
            pdb=" C   ILE B 202 "
            pdb=" CB  ILE B 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" CA  ILE B 160 "
            pdb=" N   ILE B 160 "
            pdb=" C   ILE B 160 "
            pdb=" CB  ILE B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.57e-01
  ... (remaining 1410 not shown)

  Planarity restraints: 1484
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 168 "    0.069 5.00e-02 4.00e+02   1.01e-01 1.64e+01
        pdb=" N   PRO B 169 "   -0.175 5.00e-02 4.00e+02
        pdb=" CA  PRO B 169 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B 169 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 255 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   GLU A 255 "    0.034 2.00e-02 2.50e+03
        pdb=" O   GLU A 255 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A 256 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 199 "   -0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO B 200 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 200 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 200 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1481 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.49: 117
        2.49 -     3.09: 7677
        3.09 -     3.69: 13951
        3.69 -     4.30: 20377
        4.30 -     4.90: 31324
  Nonbonded interactions: 73446
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 198 "
            pdb=" OE1 GLU A 255 "
     model   vdw
     1.882 2.520
  nonbonded pdb=" OG  SER A 495 "
            pdb=" O   LYS A 497 "
     model   vdw
     1.909 2.440
  nonbonded pdb=" O   THR A 583 "
            pdb=" OG  SER A 586 "
     model   vdw
     1.945 2.440
  nonbonded pdb=" O   ARG A 720 "
            pdb=" OG  SER A 723 "
     model   vdw
     2.012 2.440
  nonbonded pdb=" O   VAL A  20 "
            pdb=" OG1 THR A  23 "
     model   vdw
     2.067 2.440
  ... (remaining 73441 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:          4.020
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     26.890
  Find NCS groups from input model:        0.240
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
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      :  0.005   0.185   8709  Z= 0.273
  Angle     :  0.736  13.190  11786  Z= 0.433
  Chirality :  0.041   0.289   1413
  Planarity :  0.005   0.101   1484
  Dihedral  : 12.981  87.977   3238
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 23.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -1.67 (0.24), residues: 1057
  helix: -0.81 (0.18), residues: 702
  sheet: -1.38 (0.73), residues: 49
  loop : -1.36 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 813 
 HIS   0.005   0.001   HIS A 579 
 PHE   0.028   0.002   PHE A 177 
 TYR   0.020   0.002   TYR A 614 
 ARG   0.019   0.002   ARG B 107 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8496 (m-80) cc_final: 0.8224 (m-80)
REVERT: A  163 PHE cc_start: 0.7841 (t80) cc_final: 0.7580 (t80)
REVERT: A  190 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8568 (mtmm)
REVERT: A  283 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8396 (tp40)
REVERT: A  410 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6331 (mt-10)
REVERT: A  813 TRP cc_start: 0.7155 (t60) cc_final: 0.6646 (t60)
REVERT: B  153 THR cc_start: 0.9377 (p) cc_final: 0.9168 (p)
REVERT: B  219 GLN cc_start: 0.8100 (mp10) cc_final: 0.7898 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2042
  time to fit residues: 54.7638
Evaluate side-chains
  140 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 43 optimal weight:    0.3980
   chunk 83 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8709  Z= 0.234
  Angle     :  0.682   9.796  11786  Z= 0.357
  Chirality :  0.045   0.188   1413
  Planarity :  0.005   0.065   1484
  Dihedral  :  4.919  17.593   1133
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.98 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.05 (0.25), residues: 1057
  helix:  0.45 (0.18), residues: 732
  sheet: -1.12 (0.69), residues: 47
  loop : -0.57 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 813 
 HIS   0.003   0.001   HIS B 179 
 PHE   0.029   0.002   PHE A 249 
 TYR   0.021   0.001   TYR A 135 
 ARG   0.004   0.001   ARG B 220 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.9603 (tt) cc_final: 0.9316 (tt)
REVERT: A  131 LEU cc_start: 0.8918 (mt) cc_final: 0.8691 (mt)
REVERT: A  135 TYR cc_start: 0.8554 (m-80) cc_final: 0.8263 (m-80)
REVERT: A  200 CYS cc_start: 0.8335 (t) cc_final: 0.7985 (t)
REVERT: A  255 GLU cc_start: 0.8112 (pp20) cc_final: 0.7829 (pp20)
REVERT: A  283 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8427 (tp40)
REVERT: A  588 ASP cc_start: 0.6920 (t0) cc_final: 0.6418 (t0)
REVERT: A  825 ARG cc_start: 0.8408 (mtt180) cc_final: 0.8184 (mtt180)
REVERT: A  886 LEU cc_start: 0.8636 (pp) cc_final: 0.8431 (pp)
REVERT: A  887 PHE cc_start: 0.6895 (m-80) cc_final: 0.6658 (m-80)
REVERT: B  137 ARG cc_start: 0.8937 (mtp180) cc_final: 0.8116 (mtm-85)
REVERT: B  197 MET cc_start: 0.4449 (tmm) cc_final: 0.4147 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 205
  average time/residue: 0.2115
  time to fit residues: 59.4112
Evaluate side-chains
  147 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0970
   chunk 78 optimal weight:    2.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 343 GLN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 GLN
A 967 GLN
B 225 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8709  Z= 0.283
  Angle     :  0.657   7.581  11786  Z= 0.343
  Chirality :  0.043   0.171   1413
  Planarity :  0.004   0.055   1484
  Dihedral  :  4.834  19.872   1133
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.67 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.16 (0.25), residues: 1057
  helix:  0.58 (0.18), residues: 733
  sheet: -1.22 (0.68), residues: 47
  loop : -0.67 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 127 
 HIS   0.002   0.001   HIS B 179 
 PHE   0.021   0.002   PHE B  99 
 TYR   0.017   0.002   TYR B 139 
 ARG   0.008   0.001   ARG A 720 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 189
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.8872 (mt) cc_final: 0.8537 (mt)
REVERT: A  135 TYR cc_start: 0.8568 (m-80) cc_final: 0.8253 (m-80)
REVERT: A  163 PHE cc_start: 0.7698 (t80) cc_final: 0.7296 (t80)
REVERT: A  255 GLU cc_start: 0.8091 (pp20) cc_final: 0.7717 (pp20)
REVERT: A  887 PHE cc_start: 0.6876 (m-80) cc_final: 0.6615 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2068
  time to fit residues: 54.2735
Evaluate side-chains
  133 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 ASN
A 490 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8709  Z= 0.224
  Angle     :  0.624   9.255  11786  Z= 0.322
  Chirality :  0.043   0.164   1413
  Planarity :  0.004   0.055   1484
  Dihedral  :  4.738  20.732   1133
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 18.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.29 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.42 (0.25), residues: 1057
  helix:  0.83 (0.19), residues: 731
  sheet: -1.00 (0.77), residues: 37
  loop : -0.76 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 127 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.023   0.002   PHE B 177 
 TYR   0.014   0.002   TYR A 154 
 ARG   0.008   0.001   ARG A 720 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 196
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.8863 (mt) cc_final: 0.8507 (mt)
REVERT: A  135 TYR cc_start: 0.8643 (m-80) cc_final: 0.8328 (m-80)
REVERT: A  163 PHE cc_start: 0.7557 (t80) cc_final: 0.7067 (t80)
REVERT: A  200 CYS cc_start: 0.8407 (t) cc_final: 0.8104 (t)
REVERT: A  255 GLU cc_start: 0.8003 (pp20) cc_final: 0.7726 (pp20)
REVERT: A  262 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7534 (m110)
REVERT: A  601 CYS cc_start: 0.7570 (m) cc_final: 0.7355 (m)
REVERT: A  886 LEU cc_start: 0.8680 (pp) cc_final: 0.8452 (pp)
REVERT: A  887 PHE cc_start: 0.6930 (m-80) cc_final: 0.6673 (m-80)
REVERT: B   66 THR cc_start: 0.8590 (m) cc_final: 0.8389 (m)
  outliers start: 3
  outliers final: 0
  residues processed: 198
  average time/residue: 0.2130
  time to fit residues: 57.5248
Evaluate side-chains
  142 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 88 optimal weight:   30.0000
   chunk 71 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 568 HIS
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8709  Z= 0.246
  Angle     :  0.624   6.800  11786  Z= 0.324
  Chirality :  0.042   0.169   1413
  Planarity :  0.005   0.075   1484
  Dihedral  :  4.759  20.110   1133
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.24 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.17 (0.25), residues: 1057
  helix:  0.76 (0.19), residues: 732
  sheet: -1.90 (0.56), residues: 63
  loop : -0.97 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 127 
 HIS   0.003   0.001   HIS A 308 
 PHE   0.028   0.002   PHE A 218 
 TYR   0.013   0.001   TYR A 154 
 ARG   0.014   0.001   ARG B 107 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.9335 (mt) cc_final: 0.9114 (pp)
REVERT: A  131 LEU cc_start: 0.8857 (mt) cc_final: 0.8515 (mt)
REVERT: A  135 TYR cc_start: 0.8671 (m-10) cc_final: 0.8348 (m-80)
REVERT: A  163 PHE cc_start: 0.7523 (t80) cc_final: 0.7045 (t80)
REVERT: A  200 CYS cc_start: 0.8408 (t) cc_final: 0.8015 (t)
REVERT: A  255 GLU cc_start: 0.8030 (pp20) cc_final: 0.7697 (pp20)
REVERT: A  290 HIS cc_start: 0.8255 (m-70) cc_final: 0.8043 (m-70)
REVERT: A  815 GLU cc_start: 0.8604 (mp0) cc_final: 0.8244 (mp0)
REVERT: A  825 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8215 (mtt180)
REVERT: A  886 LEU cc_start: 0.8664 (pp) cc_final: 0.8464 (pp)
REVERT: A  887 PHE cc_start: 0.6961 (m-80) cc_final: 0.6723 (m-80)
REVERT: B   84 THR cc_start: 0.8855 (p) cc_final: 0.8530 (p)
REVERT: B  137 ARG cc_start: 0.8972 (mtm-85) cc_final: 0.7973 (mtm-85)
  outliers start: 1
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2082
  time to fit residues: 54.3669
Evaluate side-chains
  142 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0970
   chunk 20 optimal weight:    3.9990
   chunk 60 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8709  Z= 0.212
  Angle     :  0.613   7.395  11786  Z= 0.315
  Chirality :  0.042   0.165   1413
  Planarity :  0.004   0.055   1484
  Dihedral  :  4.622  17.735   1133
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.44 (0.26), residues: 1057
  helix:  0.93 (0.19), residues: 732
  sheet: -1.76 (0.58), residues: 60
  loop : -0.80 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 127 
 HIS   0.004   0.001   HIS B  88 
 PHE   0.023   0.002   PHE A 177 
 TYR   0.013   0.001   TYR A 939 
 ARG   0.007   0.001   ARG B 107 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.9355 (mt) cc_final: 0.9127 (pp)
REVERT: A  135 TYR cc_start: 0.8691 (m-10) cc_final: 0.8358 (m-80)
REVERT: A  234 LEU cc_start: 0.8217 (mt) cc_final: 0.7891 (mt)
REVERT: A  255 GLU cc_start: 0.7970 (pp20) cc_final: 0.7643 (pp20)
REVERT: A  280 MET cc_start: 0.8557 (ptp) cc_final: 0.8000 (ppp)
REVERT: A  601 CYS cc_start: 0.7556 (m) cc_final: 0.7266 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2023
  time to fit residues: 53.6402
Evaluate side-chains
  145 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 58 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 103 optimal weight:   20.0000
   chunk 64 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.7162

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8709  Z= 0.184
  Angle     :  0.593   7.628  11786  Z= 0.303
  Chirality :  0.041   0.164   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.499  17.916   1133
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 17.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.61 (0.26), residues: 1057
  helix:  1.10 (0.19), residues: 728
  sheet: -1.72 (0.58), residues: 62
  loop : -0.79 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 127 
 HIS   0.004   0.001   HIS A 290 
 PHE   0.022   0.002   PHE A 249 
 TYR   0.016   0.001   TYR A 370 
 ARG   0.010   0.001   ARG A 755 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.9332 (mt) cc_final: 0.9125 (pp)
REVERT: A  131 LEU cc_start: 0.8839 (mt) cc_final: 0.8488 (mt)
REVERT: A  135 TYR cc_start: 0.8677 (m-10) cc_final: 0.8334 (m-80)
REVERT: A  163 PHE cc_start: 0.7043 (t80) cc_final: 0.6588 (t80)
REVERT: A  280 MET cc_start: 0.8530 (ptp) cc_final: 0.8011 (ppp)
REVERT: A  290 HIS cc_start: 0.8290 (m-70) cc_final: 0.8024 (m90)
REVERT: A  601 CYS cc_start: 0.7434 (m) cc_final: 0.7143 (m)
REVERT: A  689 GLN cc_start: 0.9008 (tt0) cc_final: 0.8415 (mt0)
REVERT: A  825 ARG cc_start: 0.8534 (mtt180) cc_final: 0.8258 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1990
  time to fit residues: 53.3200
Evaluate side-chains
  144 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 81 optimal weight:   20.0000
   chunk 93 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 733 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8709  Z= 0.194
  Angle     :  0.603   7.331  11786  Z= 0.311
  Chirality :  0.041   0.161   1413
  Planarity :  0.004   0.051   1484
  Dihedral  :  4.458  18.197   1133
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 17.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.59 (0.26), residues: 1057
  helix:  1.07 (0.19), residues: 728
  sheet: -1.45 (0.58), residues: 62
  loop : -0.85 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 290 
 PHE   0.032   0.002   PHE A 177 
 TYR   0.014   0.001   TYR A 210 
 ARG   0.011   0.001   ARG A 755 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8654 (m-10) cc_final: 0.8328 (m-80)
REVERT: A  163 PHE cc_start: 0.7049 (t80) cc_final: 0.6586 (t80)
REVERT: A  290 HIS cc_start: 0.8293 (m-70) cc_final: 0.8034 (m90)
REVERT: A  601 CYS cc_start: 0.7445 (m) cc_final: 0.7080 (m)
REVERT: A  825 ARG cc_start: 0.8521 (mtt180) cc_final: 0.8222 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.2096
  time to fit residues: 55.0676
Evaluate side-chains
  139 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 86 optimal weight:    0.6980
   chunk 95 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 101 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8709  Z= 0.219
  Angle     :  0.635  13.113  11786  Z= 0.323
  Chirality :  0.042   0.185   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.494  18.370   1133
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 19.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.58 (0.26), residues: 1057
  helix:  1.04 (0.19), residues: 729
  sheet: -1.25 (0.62), residues: 59
  loop : -0.86 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 127 
 HIS   0.004   0.001   HIS A 290 
 PHE   0.031   0.002   PHE A 177 
 TYR   0.012   0.001   TYR A 210 
 ARG   0.013   0.001   ARG A 755 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 TYR cc_start: 0.8685 (m-10) cc_final: 0.8356 (m-80)
REVERT: A  163 PHE cc_start: 0.7182 (t80) cc_final: 0.6712 (t80)
REVERT: A  290 HIS cc_start: 0.8297 (m-70) cc_final: 0.8056 (m90)
REVERT: A  601 CYS cc_start: 0.7419 (m) cc_final: 0.7110 (m)
REVERT: B   84 THR cc_start: 0.8715 (p) cc_final: 0.8501 (p)
REVERT: B  197 MET cc_start: 0.4136 (tmm) cc_final: 0.3931 (tmm)
REVERT: B  215 THR cc_start: 0.8433 (t) cc_final: 0.8067 (p)
REVERT: B  219 GLN cc_start: 0.8087 (mp10) cc_final: 0.7860 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2064
  time to fit residues: 51.5008
Evaluate side-chains
  139 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    0.0070
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 829 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8709  Z= 0.191
  Angle     :  0.623  11.377  11786  Z= 0.319
  Chirality :  0.042   0.167   1413
  Planarity :  0.004   0.051   1484
  Dihedral  :  4.402  17.655   1133
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 (0.26), residues: 1057
  helix:  1.14 (0.19), residues: 727
  sheet: -1.03 (0.65), residues: 59
  loop : -0.88 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 352 
 HIS   0.004   0.001   HIS A 290 
 PHE   0.030   0.002   PHE A 177 
 TYR   0.015   0.001   TYR A 254 
 ARG   0.012   0.001   ARG A 755 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.9016 (ptpt) cc_final: 0.8741 (ptmt)
REVERT: A  135 TYR cc_start: 0.8670 (m-10) cc_final: 0.8331 (m-80)
REVERT: A  163 PHE cc_start: 0.7044 (t80) cc_final: 0.6666 (t80)
REVERT: A  255 GLU cc_start: 0.7861 (pp20) cc_final: 0.7458 (pp20)
REVERT: A  290 HIS cc_start: 0.8285 (m-70) cc_final: 0.8052 (m90)
REVERT: A  601 CYS cc_start: 0.7389 (m) cc_final: 0.7016 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2088
  time to fit residues: 52.7688
Evaluate side-chains
  136 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   chunk 4 optimal weight:    0.3980
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 GLN ** 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 = 0.4474 r_free = 0.4474 target = 0.137803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.109057 restraints weight = 26577.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.110680 restraints weight = 15281.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.111275 restraints weight = 11347.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8709  Z= 0.252
  Angle     :  0.646   9.436  11786  Z= 0.331
  Chirality :  0.042   0.174   1413
  Planarity :  0.004   0.052   1484
  Dihedral  :  4.490  17.548   1133
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 21.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.54 (0.26), residues: 1057
  helix:  0.98 (0.19), residues: 729
  sheet: -0.96 (0.66), residues: 56
  loop : -0.85 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 127 
 HIS   0.003   0.001   HIS A 290 
 PHE   0.026   0.002   PHE A 794 
 TYR   0.017   0.002   TYR A 370 
 ARG   0.007   0.001   ARG A 720 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2053.54 seconds
wall clock time: 38 minutes 2.30 seconds (2282.30 seconds total)