Starting phenix.real_space_refine
on Tue Sep 24 09:02:19 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/09_2024/6xow_22282.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/09_2024/6xow_22282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/09_2024/6xow_22282.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/09_2024/6xow_22282.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/09_2024/6xow_22282.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xow_22282/09_2024/6xow_22282.cif"
  }
  resolution = 4.6
  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=   0.006
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      39      5.16       5
     C    4904      2.51       5
     N    1307      2.21       5
     O    1461      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 7711
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7711
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 966, 7697
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 4, 'PTRANS': 60, 'TRANS': 901}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 966, 7697
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 4, 'PTRANS': 60, 'TRANS': 901}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7872
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ASER A 723 " occ=0.42
      ... (10 atoms not shown)
      pdb=" OG BSER A 723 " occ=0.58
    residue:
      pdb=" N  AASN A 915 " occ=0.59
      ... (14 atoms not shown)
      pdb=" ND2BASN A 915 " occ=0.41
  Time building chain proxies: 7.61, per 1000 atoms: 0.99
  Number of scatterers: 7711
  At special positions: 0
  Unit cell: (87.21, 87.21, 97.47, 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      39     16.00
     O    1461      8.00
     N    1307      7.00
     C    4904      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.06
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      54.7% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 58 through 60
      No H-bonds generated for 'chain 'A' and resid 58 through 60'
    Processing helix  chain 'A' and resid 101 through 111
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 3.775A  pdb=" N   LYS A 125 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 200 through 210
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 229 through 233
    Processing helix  chain 'A' and resid 241 through 245
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 272 through 284
      removed outlier: 3.909A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 288
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.573A  pdb=" N   ILE A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 457
      removed outlier: 4.852A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 465
    Processing helix  chain 'A' and resid 466 through 481
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 509 through 528
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 608 through 613
      Proline residue:  A 613  - end of helix
    Processing helix  chain 'A' and resid 614 through 622
    Processing helix  chain 'A' and resid 623 through 625
      No H-bonds generated for 'chain 'A' and resid 623 through 625'
    Processing helix  chain 'A' and resid 631 through 643
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 695 through 713
    Processing helix  chain 'A' and resid 714 through 716
      No H-bonds generated for 'chain 'A' and resid 714 through 716'
    Processing helix  chain 'A' and resid 717 through 727
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 764 through 773
      removed outlier: 3.865A  pdb=" N   HIS A 771 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 787
      No H-bonds generated for 'chain 'A' and resid 785 through 787'
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 878 through 894
      removed outlier: 4.200A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 902
    Processing helix  chain 'A' and resid 928 through 945
      removed outlier: 3.512A  pdb=" N   LEU A 932 " --> pdb=" O   THR A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 964
    Processing helix  chain 'A' and resid 973 through 980
      removed outlier: 3.808A  pdb=" N   PHE A 977 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 995
      removed outlier: 3.693A  pdb=" N   LYS A 986 " --> pdb=" O   SER A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1009
    Processing helix  chain 'A' and resid 1025 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.227A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A  63 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ARG A  75 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   MET A 135 " --> pdb=" O   PRO A 147 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   SER A 149 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.227A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A  63 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ARG A  75 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 185
    Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313
      removed outlier: 6.298A  pdb=" N   ARG A 307 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   SER A 503 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   PHE A 309 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   ARG A 505 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   ILE A 311 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL A 328 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   GLN A 394 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   GLY A 392 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   PHE A 332 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   SER A 390 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   TYR A 388 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   ASP A 336 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   GLU A 386 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR A 388 " --> pdb=" O   ASN A 381 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN A 381 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER A 390 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 579
      removed outlier: 7.402A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 667 " --> pdb=" O   SER A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 576 through 579
      removed outlier: 7.402A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912
      removed outlier: 3.889A  pdb=" N   VAL A 866 " --> pdb=" O   SER A 922 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   LYS A 854 " --> pdb=" O   ILE A1035 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ARG A1037 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   HIS A 856 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1336 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: 2.93

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2455
        1.33 -     1.45: 1286
        1.45 -     1.57: 4101
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7904
  Sorted by residual:
  bond pdb=" CG  ARG A 545 "
       pdb=" CD  ARG A 545 "
    ideal  model  delta    sigma   weight residual
    1.520  1.469  0.051 3.00e-02 1.11e+03 2.86e+00
  bond pdb=" CB  GLN A  91 "
       pdb=" CG  GLN A  91 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.45e+00
  bond pdb=" N   ILE A 724 "
       pdb=" CA  ILE A 724 "
    ideal  model  delta    sigma   weight residual
    1.460  1.443  0.017 1.21e-02 6.83e+03 1.87e+00
  bond pdb=" CA  GLY A 644 "
       pdb=" C   GLY A 644 "
    ideal  model  delta    sigma   weight residual
    1.514  1.496  0.019 1.41e-02 5.03e+03 1.74e+00
  bond pdb=" CA  THR A 144 "
       pdb=" CB  THR A 144 "
    ideal  model  delta    sigma   weight residual
    1.532  1.508  0.024 1.82e-02 3.02e+03 1.69e+00
  ... (remaining 7899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 10344
        2.31 -     4.61: 306
        4.61 -     6.92: 57
        6.92 -     9.23: 10
        9.23 -    11.53: 3
  Bond angle restraints: 10720
  Sorted by residual:
  angle pdb=" C   TYR A 614 "
        pdb=" N   VAL A 615 "
        pdb=" CA  VAL A 615 "
      ideal   model   delta    sigma   weight residual
     120.24  123.48   -3.24 6.30e-01 2.52e+00 2.64e+01
  angle pdb=" C   ILE A 899 "
        pdb=" N   ARG A 900 "
        pdb=" CA  ARG A 900 "
      ideal   model   delta    sigma   weight residual
     120.88  114.63    6.25 1.62e+00 3.81e-01 1.49e+01
  angle pdb=" CB  MET A 749 "
        pdb=" CG  MET A 749 "
        pdb=" SD  MET A 749 "
      ideal   model   delta    sigma   weight residual
     112.70  101.17   11.53 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" CA  TYR A 492 "
        pdb=" CB  TYR A 492 "
        pdb=" CG  TYR A 492 "
      ideal   model   delta    sigma   weight residual
     113.90  107.22    6.68 1.80e+00 3.09e-01 1.38e+01
  angle pdb=" N   GLU A 709 "
        pdb=" CA  GLU A 709 "
        pdb=" CB  GLU A 709 "
      ideal   model   delta    sigma   weight residual
     110.16  115.32   -5.16 1.48e+00 4.57e-01 1.21e+01
  ... (remaining 10715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4413
       17.91 -    35.83: 294
       35.83 -    53.74: 46
       53.74 -    71.65: 18
       71.65 -    89.56: 10
  Dihedral angle restraints: 4781
    sinusoidal: 1955
      harmonic: 2826
  Sorted by residual:
  dihedral pdb=" CA  ALA A 319 "
           pdb=" C   ALA A 319 "
           pdb=" N   THR A 320 "
           pdb=" CA  THR A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.15  -21.85     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  GLN A 394 "
           pdb=" C   GLN A 394 "
           pdb=" N   GLY A 395 "
           pdb=" CA  GLY A 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.36   21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  ARG A 129 "
           pdb=" C   ARG A 129 "
           pdb=" N   SER A 130 "
           pdb=" CA  SER A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.50  -20.50     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 4778 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 733
       0.044 -    0.089: 324
       0.089 -    0.133: 100
       0.133 -    0.177: 15
       0.177 -    0.222: 2
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  TYR A 163 "
            pdb=" N   TYR A 163 "
            pdb=" C   TYR A 163 "
            pdb=" CB  TYR A 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CB  ILE A1020 "
            pdb=" CA  ILE A1020 "
            pdb=" CG1 ILE A1020 "
            pdb=" CG2 ILE A1020 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.17e-01
  chirality pdb=" CA  LYS A 437 "
            pdb=" N   LYS A 437 "
            pdb=" C   LYS A 437 "
            pdb=" CB  LYS A 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.10e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1401
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 303 "   -0.033 2.00e-02 2.50e+03   2.63e-02 1.73e+01
        pdb=" CG  TRP A 303 "    0.069 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 303 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 303 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 303 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 303 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 303 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 303 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 303 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 303 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 314 "   -0.065 5.00e-02 4.00e+02   9.81e-02 1.54e+01
        pdb=" N   PRO A 315 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A 315 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 315 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 242 "    0.050 5.00e-02 4.00e+02   7.58e-02 9.20e+00
        pdb=" N   PRO A 243 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 243 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 243 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1398 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 117
        2.57 -     3.15: 7115
        3.15 -     3.74: 12800
        3.74 -     4.32: 17159
        4.32 -     4.90: 26933
  Nonbonded interactions: 64124
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 872 "
            pdb=" O   GLY A 916 "
     model   vdw
     1.991 3.040
  nonbonded pdb=" O   ASP A 377 "
            pdb=" OG  SER A 390 "
     model   vdw
     2.033 3.040
  nonbonded pdb=" OD2 ASP A 336 "
            pdb=" OG1 THR A 338 "
     model   vdw
     2.060 3.040
  nonbonded pdb=" ND1 HIS A 186 "
            pdb=" O   THR A 194 "
     model   vdw
     2.070 3.120
  nonbonded pdb=" O   ILE A 803 "
            pdb=" NH1 ARG A 805 "
     model   vdw
     2.089 3.120
  ... (remaining 64119 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.41 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     25.500
  Find NCS groups from input model:        0.080
  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:   28.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
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      :  0.006   0.051   7904  Z= 0.409
  Angle     :  0.998  11.533  10720  Z= 0.543
  Chirality :  0.053   0.222   1174
  Planarity :  0.007   0.098   1401
  Dihedral  : 13.389  89.563   2953
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 24.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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: -0.98 (0.26), residues: 968
  helix: -0.40 (0.22), residues: 458
  sheet:  0.30 (0.38), residues: 176
  loop : -1.35 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.006   TRP A 303 
 HIS   0.012   0.002   HIS A 498 
 PHE   0.024   0.003   PHE A 138 
 TYR   0.032   0.003   TYR A 597 
 ARG   0.016   0.002   ARG A 410 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 PHE cc_start: 0.7623 (t80) cc_final: 0.7296 (t80)
REVERT: A  266 PHE cc_start: 0.7046 (t80) cc_final: 0.6057 (t80)
REVERT: A  436 MET cc_start: 0.9288 (mtp) cc_final: 0.8949 (mtt)
REVERT: A  454 CYS cc_start: 0.8124 (t) cc_final: 0.7782 (p)
REVERT: A  667 LEU cc_start: 0.9016 (tp) cc_final: 0.8585 (tp)
REVERT: A  702 LEU cc_start: 0.9307 (mt) cc_final: 0.9061 (pp)
REVERT: A  917 ILE cc_start: 0.7541 (mm) cc_final: 0.7304 (mm)
REVERT: A  985 MET cc_start: 0.7967 (mpp) cc_final: 0.6747 (mpp)
REVERT: A 1037 ARG cc_start: 0.7777 (mmt90) cc_final: 0.7224 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.2059
  time to fit residues: 36.9627
Evaluate side-chains
  77 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:   20.0000
   chunk 45 optimal weight:    0.1980
   chunk 56 optimal weight:    4.9990
   chunk 87 optimal weight:    9.9990
   overall best weight:    4.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN
A 495 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 536 GLN
A 976 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7904  Z= 0.253
  Angle     :  0.791   9.728  10720  Z= 0.414
  Chirality :  0.048   0.236   1174
  Planarity :  0.007   0.083   1401
  Dihedral  :  5.558  19.436   1039
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.14 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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: -0.24 (0.27), residues: 968
  helix:  0.43 (0.23), residues: 464
  sheet:  0.32 (0.38), residues: 176
  loop : -1.15 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 303 
 HIS   0.009   0.001   HIS A 276 
 PHE   0.020   0.002   PHE A 935 
 TYR   0.030   0.002   TYR A 597 
 ARG   0.007   0.001   ARG A 307 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 LEU cc_start: 0.9183 (tp) cc_final: 0.8939 (tp)
REVERT: A  454 CYS cc_start: 0.8208 (t) cc_final: 0.7935 (p)
REVERT: A  667 LEU cc_start: 0.9108 (tp) cc_final: 0.8679 (tp)
REVERT: A  702 LEU cc_start: 0.9443 (mt) cc_final: 0.9029 (pp)
REVERT: A  872 THR cc_start: 0.6170 (p) cc_final: 0.5960 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1655
  time to fit residues: 26.0533
Evaluate side-chains
  79 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 72 optimal weight:    0.4980
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    7.9990
   chunk 87 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 524 GLN
A 676 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7904  Z= 0.205
  Angle     :  0.706   7.741  10720  Z= 0.363
  Chirality :  0.046   0.219   1174
  Planarity :  0.006   0.072   1401
  Dihedral  :  5.152  18.081   1039
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.75 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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 (0.27), residues: 968
  helix:  0.57 (0.23), residues: 475
  sheet:  0.35 (0.38), residues: 176
  loop : -1.05 (0.37), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 303 
 HIS   0.008   0.001   HIS A  69 
 PHE   0.020   0.002   PHE A 935 
 TYR   0.027   0.002   TYR A 597 
 ARG   0.005   0.001   ARG A 173 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 PHE cc_start: 0.7125 (t80) cc_final: 0.6713 (t80)
REVERT: A  361 PHE cc_start: 0.8290 (m-80) cc_final: 0.7646 (m-80)
REVERT: A  667 LEU cc_start: 0.8918 (tp) cc_final: 0.8626 (tp)
REVERT: A  702 LEU cc_start: 0.9363 (mt) cc_final: 0.9047 (pp)
REVERT: A  710 LEU cc_start: 0.9354 (mt) cc_final: 0.8954 (tp)
REVERT: A  749 MET cc_start: 0.8456 (ptt) cc_final: 0.7783 (ptt)
REVERT: A  872 THR cc_start: 0.6464 (p) cc_final: 0.6251 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 96
  average time/residue: 0.1721
  time to fit residues: 23.8219
Evaluate side-chains
  73 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:   30.0000
   chunk 65 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   chunk 58 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 92 optimal weight:   20.0000
   chunk 83 optimal weight:   50.0000
   chunk 25 optimal weight:    0.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7904  Z= 0.226
  Angle     :  0.697   9.251  10720  Z= 0.358
  Chirality :  0.045   0.187   1174
  Planarity :  0.006   0.068   1401
  Dihedral  :  5.000  17.356   1039
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 17.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.98 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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:  0.04 (0.27), residues: 968
  helix:  0.64 (0.23), residues: 470
  sheet:  0.19 (0.38), residues: 174
  loop : -0.82 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 303 
 HIS   0.013   0.002   HIS A 498 
 PHE   0.016   0.002   PHE A 935 
 TYR   0.021   0.002   TYR A 492 
 ARG   0.010   0.001   ARG A 307 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 LEU cc_start: 0.8738 (tp) cc_final: 0.8535 (tp)
REVERT: A  361 PHE cc_start: 0.8247 (m-80) cc_final: 0.7596 (m-80)
REVERT: A  667 LEU cc_start: 0.8787 (tp) cc_final: 0.8428 (tp)
REVERT: A  702 LEU cc_start: 0.9546 (mt) cc_final: 0.9114 (pp)
REVERT: A 1037 ARG cc_start: 0.7743 (mmt90) cc_final: 0.7213 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1627
  time to fit residues: 21.3091
Evaluate side-chains
  64 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 79 optimal weight:   20.0000
   chunk 64 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 47 optimal weight:    7.9990
   chunk 83 optimal weight:   50.0000
   chunk 23 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 ASN
A 281 HIS
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7904  Z= 0.229
  Angle     :  0.694   8.186  10720  Z= 0.357
  Chirality :  0.045   0.161   1174
  Planarity :  0.006   0.069   1401
  Dihedral  :  4.971  17.869   1039
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.75 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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:  0.15 (0.27), residues: 968
  helix:  0.76 (0.24), residues: 465
  sheet:  0.16 (0.39), residues: 171
  loop : -0.73 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 303 
 HIS   0.010   0.001   HIS A 498 
 PHE   0.021   0.002   PHE A 124 
 TYR   0.021   0.002   TYR A 492 
 ARG   0.011   0.001   ARG A 545 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 PHE cc_start: 0.8234 (m-80) cc_final: 0.7704 (m-80)
REVERT: A  667 LEU cc_start: 0.8882 (tp) cc_final: 0.8588 (tp)
REVERT: A  702 LEU cc_start: 0.9470 (mt) cc_final: 0.9099 (pp)
REVERT: A  706 THR cc_start: 0.9070 (p) cc_final: 0.8742 (p)
REVERT: A  710 LEU cc_start: 0.9240 (mt) cc_final: 0.9000 (tt)
REVERT: A  749 MET cc_start: 0.8683 (ppp) cc_final: 0.8460 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1701
  time to fit residues: 21.6117
Evaluate side-chains
  63 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 54 optimal weight:   40.0000
   chunk 22 optimal weight:    9.9990
   chunk 92 optimal weight:    0.8980
   chunk 77 optimal weight:   20.0000
   chunk 43 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 30 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   chunk 89 optimal weight:   40.0000
   overall best weight:    4.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7904  Z= 0.222
  Angle     :  0.690   8.082  10720  Z= 0.357
  Chirality :  0.045   0.157   1174
  Planarity :  0.006   0.066   1401
  Dihedral  :  4.937  18.199   1039
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 19.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.40 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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:  0.14 (0.27), residues: 968
  helix:  0.73 (0.24), residues: 459
  sheet:  0.09 (0.39), residues: 172
  loop : -0.64 (0.37), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 684 
 HIS   0.007   0.001   HIS A 498 
 PHE   0.018   0.002   PHE A 688 
 TYR   0.020   0.001   TYR A 492 
 ARG   0.005   0.001   ARG A 173 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 PHE cc_start: 0.8240 (m-80) cc_final: 0.7670 (m-80)
REVERT: A  667 LEU cc_start: 0.8909 (tp) cc_final: 0.8547 (tp)
REVERT: A  749 MET cc_start: 0.8757 (ppp) cc_final: 0.8548 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1510
  time to fit residues: 18.2209
Evaluate side-chains
  57 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:   40.0000
   chunk 52 optimal weight:    5.9990
   chunk 67 optimal weight:   20.0000
   chunk 78 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   chunk 92 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 36 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN
A 204 ASN
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1016 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7904  Z= 0.306
  Angle     :  0.773   9.039  10720  Z= 0.405
  Chirality :  0.046   0.156   1174
  Planarity :  0.006   0.068   1401
  Dihedral  :  5.317  25.689   1039
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 26.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.81 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.27), residues: 968
  helix:  0.38 (0.24), residues: 464
  sheet: -0.34 (0.38), residues: 176
  loop : -0.65 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A 303 
 HIS   0.008   0.002   HIS A 259 
 PHE   0.022   0.002   PHE A 309 
 TYR   0.032   0.002   TYR A 492 
 ARG   0.008   0.001   ARG A 173 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 PHE cc_start: 0.8113 (m-80) cc_final: 0.7816 (m-80)
REVERT: A  667 LEU cc_start: 0.8773 (tp) cc_final: 0.8378 (tp)
REVERT: A  749 MET cc_start: 0.8918 (ppp) cc_final: 0.8386 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1701
  time to fit residues: 20.3028
Evaluate side-chains
  55 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 17 optimal weight:   50.0000
   chunk 58 optimal weight:   20.0000
   chunk 63 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 72 optimal weight:   20.0000
   chunk 84 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7904  Z= 0.245
  Angle     :  0.713   8.444  10720  Z= 0.371
  Chirality :  0.045   0.156   1174
  Planarity :  0.006   0.064   1401
  Dihedral  :  5.200  29.727   1039
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 21.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.81 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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: -0.21 (0.27), residues: 968
  helix:  0.33 (0.23), residues: 471
  sheet: -0.26 (0.39), residues: 174
  loop : -0.54 (0.38), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 303 
 HIS   0.010   0.002   HIS A  78 
 PHE   0.016   0.002   PHE A 124 
 TYR   0.023   0.002   TYR A 597 
 ARG   0.007   0.001   ARG A 173 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 PHE cc_start: 0.8106 (m-80) cc_final: 0.7753 (m-80)
REVERT: A  667 LEU cc_start: 0.8675 (tp) cc_final: 0.8365 (tp)
REVERT: A  705 MET cc_start: 0.8590 (ptp) cc_final: 0.8376 (ptp)
REVERT: A  743 MET cc_start: 0.8644 (mmm) cc_final: 0.8365 (tpt)
REVERT: A  749 MET cc_start: 0.8760 (ppp) cc_final: 0.8545 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1703
  time to fit residues: 19.5839
Evaluate side-chains
  57 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 88 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 67 optimal weight:    5.9990
   chunk 26 optimal weight:   20.0000
   chunk 77 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    5.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 GLN
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.5234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7904  Z= 0.227
  Angle     :  0.706   8.279  10720  Z= 0.365
  Chirality :  0.045   0.155   1174
  Planarity :  0.006   0.064   1401
  Dihedral  :  5.125  30.718   1039
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 21.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.12 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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: -0.12 (0.28), residues: 968
  helix:  0.42 (0.24), residues: 471
  sheet: -0.19 (0.39), residues: 171
  loop : -0.55 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 303 
 HIS   0.010   0.001   HIS A  78 
 PHE   0.016   0.002   PHE A 203 
 TYR   0.019   0.002   TYR A 492 
 ARG   0.007   0.001   ARG A 924 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  667 LEU cc_start: 0.8820 (tp) cc_final: 0.8502 (tp)
REVERT: A  743 MET cc_start: 0.8728 (mmm) cc_final: 0.8492 (tpt)
REVERT: A  749 MET cc_start: 0.8780 (ppp) cc_final: 0.8560 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1511
  time to fit residues: 17.5917
Evaluate side-chains
  55 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:   30.0000
   chunk 43 optimal weight:    0.8980
   chunk 63 optimal weight:    6.9990
   chunk 95 optimal weight:    5.9990
   chunk 88 optimal weight:   30.0000
   chunk 76 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 58 optimal weight:   20.0000
   chunk 46 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.5386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7904  Z= 0.229
  Angle     :  0.712   8.185  10720  Z= 0.366
  Chirality :  0.045   0.158   1174
  Planarity :  0.006   0.080   1401
  Dihedral  :  5.109  31.067   1039
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 21.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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: -0.14 (0.27), residues: 968
  helix:  0.42 (0.24), residues: 468
  sheet: -0.27 (0.38), residues: 169
  loop : -0.51 (0.37), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 303 
 HIS   0.009   0.001   HIS A  78 
 PHE   0.016   0.002   PHE A 124 
 TYR   0.021   0.002   TYR A 597 
 ARG   0.006   0.001   ARG A 173 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  667 LEU cc_start: 0.8812 (tp) cc_final: 0.8508 (tp)
REVERT: A  749 MET cc_start: 0.8834 (ppp) cc_final: 0.8388 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1581
  time to fit residues: 17.8949
Evaluate side-chains
  56 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 70 optimal weight:   30.0000
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 381 ASN
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.041664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.029089 restraints weight = 252432.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.030715 restraints weight = 130325.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.031964 restraints weight = 86620.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.2607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.5594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7904  Z= 0.224
  Angle     :  0.701   8.217  10720  Z= 0.361
  Chirality :  0.045   0.171   1174
  Planarity :  0.006   0.075   1401
  Dihedral  :  5.092  32.124   1039
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 22.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.12 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    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: -0.08 (0.28), residues: 968
  helix:  0.44 (0.24), residues: 473
  sheet: -0.41 (0.37), residues: 175
  loop : -0.33 (0.39), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 303 
 HIS   0.008   0.002   HIS A  78 
 PHE   0.013   0.002   PHE A 124 
 TYR   0.021   0.002   TYR A 597 
 ARG   0.006   0.001   ARG A 173 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1409.81 seconds
wall clock time: 26 minutes 32.47 seconds (1592.47 seconds total)