Starting phenix.real_space_refine
on Sat May 10 19:53:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxt_40858/05_2025/8sxt_40858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxt_40858/05_2025/8sxt_40858.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxt_40858/05_2025/8sxt_40858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxt_40858/05_2025/8sxt_40858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxt_40858/05_2025/8sxt_40858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxt_40858/05_2025/8sxt_40858.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      20      5.49       5
     Mg      1      5.21       5
     S      20      5.16       5
     C    4061      2.51       5
     N    1080      2.21       5
     O    1200      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6382
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 140
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 225
          Classifications: {'RNA': 11}
          Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 1, 'rna3p': 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'  U%5*END:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 5987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 726, 5987
          Classifications: {'peptide': 726}
          Link IDs: {'PTRANS': 33, 'TRANS': 692}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'TTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.57, per 1000 atoms: 0.72
  Number of scatterers: 6382
  At special positions: 0
  Unit cell: (92.02, 87.72, 110.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P      20     15.00
     Mg      1     11.99
     O    1200      8.00
     N    1080      7.00
     C    4061      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: 2.00
  Conformation dependent library (CDL) restraints added in 704.1 milliseconds
  

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      64.0% alpha, 5.1% beta
      5 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 2.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 255 through 258
    Processing helix  chain 'A' and resid 259 through 275
    Processing helix  chain 'A' and resid 283 through 310
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.644A  pdb=" N   GLN A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 435
      removed outlier: 3.685A  pdb=" N   ASP A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   THR A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   PHE A 432 " --> pdb=" O   GLU A 428 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A 435 " --> pdb=" O   THR A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 450
    Processing helix  chain 'A' and resid 455 through 463
      removed outlier: 3.749A  pdb=" N   VAL A 459 " --> pdb=" O   GLY A 455 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ILE A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 484
      removed outlier: 3.687A  pdb=" N   TYR A 481 " --> pdb=" O   THR A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 503
      removed outlier: 3.625A  pdb=" N   LEU A 488 " --> pdb=" O   TYR A 484 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL A 489 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
      Proline residue:  A 490  - end of helix
      removed outlier: 4.233A  pdb=" N   LYS A 494 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 511
      removed outlier: 3.768A  pdb=" N   TYR A 510 " --> pdb=" O   ASN A 507 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLU A 511 " --> pdb=" O   SER A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 528
      No H-bonds generated for 'chain 'A' and resid 526 through 528'
    Processing helix  chain 'A' and resid 537 through 559
      removed outlier: 4.445A  pdb=" N   HIS A 554 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   LYS A 556 " --> pdb=" O   GLN A 552 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   LYS A 557 " --> pdb=" O   GLN A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 589
      removed outlier: 3.889A  pdb=" N   ILE A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LYS A 578 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 608
      removed outlier: 3.990A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 620
    Processing helix  chain 'A' and resid 624 through 634
      removed outlier: 3.619A  pdb=" N   ALA A 632 " --> pdb=" O   LYS A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 682
      removed outlier: 3.624A  pdb=" N   VAL A 674 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU A 675 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 730
      removed outlier: 4.483A  pdb=" N   GLN A 716 " --> pdb=" O   ILE A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 757
      removed outlier: 3.741A  pdb=" N   GLU A 750 " --> pdb=" O   ASN A 746 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER A 751 " --> pdb=" O   ARG A 747 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLN A 752 " --> pdb=" O   GLN A 748 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 753 " --> pdb=" O   THR A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 778
      No H-bonds generated for 'chain 'A' and resid 776 through 778'
    Processing helix  chain 'A' and resid 779 through 785
    Processing helix  chain 'A' and resid 785 through 799
      removed outlier: 3.711A  pdb=" N   ASN A 797 " --> pdb=" O   LYS A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 817
    Processing helix  chain 'A' and resid 817 through 828
    Processing helix  chain 'A' and resid 833 through 850
      removed outlier: 4.042A  pdb=" N   PHE A 837 " --> pdb=" O   PRO A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 863
    Processing helix  chain 'A' and resid 864 through 868
    Processing helix  chain 'A' and resid 874 through 885
    Processing helix  chain 'A' and resid 885 through 893
      removed outlier: 4.249A  pdb=" N   TYR A 889 " --> pdb=" O   LYS A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 902
    Processing helix  chain 'A' and resid 911 through 915
      removed outlier: 3.646A  pdb=" N   LEU A 915 " --> pdb=" O   TYR A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 947
    Processing helix  chain 'A' and resid 961 through 966
      removed outlier: 3.870A  pdb=" N   LYS A 965 " --> pdb=" O   SER A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 981
      removed outlier: 4.126A  pdb=" N   ILE A 974 " --> pdb=" O   LYS A 970 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS A 975 " --> pdb=" O   PRO A 971 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   THR A 976 " --> pdb=" O   LYS A 972 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A 977 " --> pdb=" O   THR A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 989
      removed outlier: 4.033A  pdb=" N   ILE A 988 " --> pdb=" O   THR A 984 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLY A 989 " --> pdb=" O   ILE A 985 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 984 through 989'
    Processing helix  chain 'A' and resid 990 through 994
      removed outlier: 3.923A  pdb=" N   PHE A 994 " --> pdb=" O   GLY A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1005
    Processing helix  chain 'A' and resid 1006 through 1008
      No H-bonds generated for 'chain 'A' and resid 1006 through 1008'
    Processing helix  chain 'A' and resid 1009 through 1022
      removed outlier: 3.733A  pdb=" N   LYS A1015 " --> pdb=" O   TRP A1011 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ALA A1022 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1022 through 1030
    Processing helix  chain 'A' and resid 1034 through 1041
      removed outlier: 3.575A  pdb=" N   PHE A1040 " --> pdb=" O   TRP A1036 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1048 through 1061
    Processing sheet with id=AA1, first strand: chain 'A' and resid 530 through 535
      removed outlier: 6.050A  pdb=" N   ILE A 514 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 697 through 698
      removed outlier: 3.506A  pdb=" N   MET A 704 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLN A 739 " --> pdb=" O   SER A 598 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA A 740 " --> pdb=" O   THR A 760 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690
    Processing sheet with id=AA4, first strand: chain 'A' and resid 767 through 768

    285 hydrogen bonds defined for protein.
    816 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      13 hydrogen bonds
      26 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 2.08

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1001
        1.32 -     1.44: 1772
        1.44 -     1.57: 3710
        1.57 -     1.69: 38
        1.69 -     1.82: 34
  Bond restraints: 6555
  Sorted by residual:
  bond pdb=" C   PRO A 518 "
       pdb=" O   PRO A 518 "
    ideal  model  delta    sigma   weight residual
    1.233  1.197  0.036 1.23e-02 6.61e+03 8.78e+00
  bond pdb=" C   ILE A 517 "
       pdb=" N   PRO A 518 "
    ideal  model  delta    sigma   weight residual
    1.331  1.357 -0.026 1.20e-02 6.94e+03 4.71e+00
  bond pdb=" CA  LYS A 519 "
       pdb=" C   LYS A 519 "
    ideal  model  delta    sigma   weight residual
    1.523  1.504  0.018 1.28e-02 6.10e+03 2.08e+00
  bond pdb=" CA  LYS A 519 "
       pdb=" CB  LYS A 519 "
    ideal  model  delta    sigma   weight residual
    1.526  1.511  0.016 1.36e-02 5.41e+03 1.30e+00
  bond pdb=" N   PRO A 518 "
       pdb=" CA  PRO A 518 "
    ideal  model  delta    sigma   weight residual
    1.468  1.455  0.013 1.20e-02 6.94e+03 1.15e+00
  ... (remaining 6550 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.14: 8889
        3.14 -     6.27: 39
        6.27 -     9.41: 1
        9.41 -    12.55: 2
       12.55 -    15.68: 1
  Bond angle restraints: 8932
  Sorted by residual:
  angle pdb=" C   ILE A 517 "
        pdb=" N   PRO A 518 "
        pdb=" CA  PRO A 518 "
      ideal   model   delta    sigma   weight residual
     119.83  135.51  -15.68 1.08e+00 8.57e-01 2.11e+02
  angle pdb=" CB  MET A 625 "
        pdb=" CG  MET A 625 "
        pdb=" SD  MET A 625 "
      ideal   model   delta    sigma   weight residual
     112.70  125.03  -12.33 3.00e+00 1.11e-01 1.69e+01
  angle pdb=" O   ILE A 517 "
        pdb=" C   ILE A 517 "
        pdb=" N   PRO A 518 "
      ideal   model   delta    sigma   weight residual
     121.10  125.42   -4.32 1.14e+00 7.69e-01 1.43e+01
  angle pdb=" N   PRO A 518 "
        pdb=" CA  PRO A 518 "
        pdb=" C   PRO A 518 "
      ideal   model   delta    sigma   weight residual
     111.03  105.99    5.04 1.54e+00 4.22e-01 1.07e+01
  angle pdb=" C   LEU A 488 "
        pdb=" N   VAL A 489 "
        pdb=" CA  VAL A 489 "
      ideal   model   delta    sigma   weight residual
     120.33  122.72   -2.39 8.00e-01 1.56e+00 8.94e+00
  ... (remaining 8927 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.59: 3729
       29.59 -    59.17: 241
       59.17 -    88.76: 19
       88.76 -   118.34: 2
      118.34 -   147.93: 1
  Dihedral angle restraints: 3992
    sinusoidal: 1844
      harmonic: 2148
  Sorted by residual:
  dihedral pdb=" C2  TTP C 101 "
           pdb=" C1' TTP C 101 "
           pdb=" N1  TTP C 101 "
           pdb=" O4' TTP C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  153.76  147.93     1      2.00e+01 2.50e-03 4.43e+01
  dihedral pdb=" O5' TTP C 101 "
           pdb=" O3A TTP C 101 "
           pdb=" PA  TTP C 101 "
           pdb=" PB  TTP C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.02   95.33   84.69     1      2.00e+01 2.50e-03 2.18e+01
  dihedral pdb=" CB  GLU A 310 "
           pdb=" CG  GLU A 310 "
           pdb=" CD  GLU A 310 "
           pdb=" OE1 GLU A 310 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.01   89.01     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 3989 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 584
       0.025 -    0.051: 253
       0.051 -    0.076: 100
       0.076 -    0.102: 45
       0.102 -    0.127: 17
  Chirality restraints: 999
  Sorted by residual:
  chirality pdb=" CA  ILE A 596 "
            pdb=" N   ILE A 596 "
            pdb=" C   ILE A 596 "
            pdb=" CB  ILE A 596 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-01
  chirality pdb=" CA  SER A 664 "
            pdb=" N   SER A 664 "
            pdb=" C   SER A 664 "
            pdb=" CB  SER A 664 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.02e-01
  chirality pdb=" CA  PRO A 490 "
            pdb=" N   PRO A 490 "
            pdb=" C   PRO A 490 "
            pdb=" CB  PRO A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 996 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 908 "    0.029 5.00e-02 4.00e+02   4.35e-02 3.03e+00
        pdb=" N   PRO A 909 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 909 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 909 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 813 "   -0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" C   VAL A 813 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL A 813 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 814 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 799 "   -0.011 2.00e-02 2.50e+03   9.11e-03 2.08e+00
        pdb=" CG  TRP A 799 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 799 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 799 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 799 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 799 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 799 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 799 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 799 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 799 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 80
        2.61 -     3.18: 5443
        3.18 -     3.76: 10039
        3.76 -     4.33: 12997
        4.33 -     4.90: 21343
  Nonbonded interactions: 49902
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 601 "
            pdb="MG    MG A1301 "
     model   vdw
     2.039 2.170
  nonbonded pdb=" O   SER A 508 "
            pdb=" ND2 ASN A 537 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   GLN A 748 "
            pdb=" NE2 GLN A 752 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" O   ALA A 540 "
            pdb=" ND2 ASN A 544 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" ND2 ASN A 442 "
            pdb=" OE2 GLU A 445 "
     model   vdw
     2.313 3.120
  ... (remaining 49897 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.310
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6555  Z= 0.129
  Angle     :  0.600  15.684   8932  Z= 0.342
  Chirality :  0.038   0.127    999
  Planarity :  0.003   0.043   1050
  Dihedral  : 17.793 147.928   2596
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.74 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 27.90 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.32), residues: 722
  helix:  1.09 (0.28), residues: 376
  sheet: -0.83 (0.83), residues: 42
  loop : -0.70 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 799 
 HIS   0.004   0.001   HIS A 263 
 PHE   0.012   0.001   PHE A 496 
 TYR   0.007   0.001   TYR A 484 
 ARG   0.004   0.000   ARG A 809 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17166 (  298)
  hydrogen bonds       : angle       6.25034 (  842)
  covalent geometry    : bond        0.00266 ( 6555)
  covalent geometry    : angle       0.59989 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 211
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  286 ASN cc_start: 0.7995 (m110) cc_final: 0.7751 (p0)
REVERT: A  422 LYS cc_start: 0.8418 (tttt) cc_final: 0.7825 (ttmt)
REVERT: A  457 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7413 (mt-10)
REVERT: A  458 ILE cc_start: 0.8548 (mt) cc_final: 0.8271 (tt)
REVERT: A  468 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8396 (mmmm)
REVERT: A  494 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7975 (mtpt)
REVERT: A  495 LEU cc_start: 0.8785 (tp) cc_final: 0.8567 (tt)
REVERT: A  502 GLU cc_start: 0.7289 (tp30) cc_final: 0.6727 (tp30)
REVERT: A  555 ILE cc_start: 0.8016 (tp) cc_final: 0.7690 (tp)
REVERT: A  618 ASN cc_start: 0.8222 (t0) cc_final: 0.7921 (t0)
REVERT: A  631 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7646 (ttp80)
REVERT: A  677 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7694 (mtt-85)
REVERT: A  681 GLN cc_start: 0.7897 (mm110) cc_final: 0.7615 (mm110)
REVERT: A  686 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7811 (ttmm)
REVERT: A  704 MET cc_start: 0.7541 (ttp) cc_final: 0.7294 (ttp)
REVERT: A  720 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7629 (ptpp)
REVERT: A  761 ILE cc_start: 0.8318 (mp) cc_final: 0.7605 (mp)
REVERT: A  810 ILE cc_start: 0.8947 (mt) cc_final: 0.8650 (tt)
REVERT: A  841 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7235 (mm-30)
REVERT: A  844 THR cc_start: 0.8486 (m) cc_final: 0.8275 (m)
REVERT: A  958 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7842 (mtpp)
REVERT: A  969 VAL cc_start: 0.8041 (m) cc_final: 0.7812 (t)
REVERT: A 1002 MET cc_start: 0.7375 (mmt) cc_final: 0.7050 (mmt)
REVERT: A 1011 TRP cc_start: 0.6936 (m100) cc_final: 0.6714 (m100)
REVERT: A 1024 GLU cc_start: 0.8076 (pm20) cc_final: 0.7835 (pm20)
  outliers start: 3
  outliers final: 2
  residues processed: 213
  average time/residue: 0.2456
  time to fit residues: 64.3530
Evaluate side-chains
  187 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 263 HIS
A 581 ASN
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
A 851 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.117967 restraints weight = 10566.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.62
r_work: 0.3413 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6555  Z= 0.168
  Angle     :  0.613   6.999   8932  Z= 0.318
  Chirality :  0.043   0.160    999
  Planarity :  0.004   0.040   1050
  Dihedral  : 11.443 146.546   1027
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.46 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 23.23 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.31), residues: 722
  helix:  1.04 (0.27), residues: 385
  sheet: -0.93 (0.81), residues: 44
  loop : -0.80 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 799 
 HIS   0.009   0.002   HIS A 560 
 PHE   0.021   0.002   PHE A 668 
 TYR   0.012   0.001   TYR A 415 
 ARG   0.006   0.001   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  298)
  hydrogen bonds       : angle       4.56744 (  842)
  covalent geometry    : bond        0.00371 ( 6555)
  covalent geometry    : angle       0.61296 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 205
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7834 (ptm) cc_final: 0.7451 (ptm)
REVERT: A  277 ASN cc_start: 0.8034 (p0) cc_final: 0.7832 (p0)
REVERT: A  292 LYS cc_start: 0.8277 (mtmt) cc_final: 0.8072 (mttt)
REVERT: A  422 LYS cc_start: 0.8359 (tttt) cc_final: 0.8067 (ttmt)
REVERT: A  428 GLU cc_start: 0.6900 (tt0) cc_final: 0.6694 (tt0)
REVERT: A  444 GLU cc_start: 0.7577 (mp0) cc_final: 0.7301 (mp0)
REVERT: A  457 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: A  458 ILE cc_start: 0.8806 (mt) cc_final: 0.8603 (tt)
REVERT: A  482 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6788 (tp-100)
REVERT: A  485 LYS cc_start: 0.8479 (tttp) cc_final: 0.8267 (tptt)
REVERT: A  502 GLU cc_start: 0.7413 (tp30) cc_final: 0.6862 (tp30)
REVERT: A  505 LEU cc_start: 0.8518 (mp) cc_final: 0.8268 (mp)
REVERT: A  541 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7369 (mtmm)
REVERT: A  570 MET cc_start: 0.8289 (mmm) cc_final: 0.7499 (mmm)
REVERT: A  582 VAL cc_start: 0.8480 (m) cc_final: 0.8249 (p)
REVERT: A  591 ASP cc_start: 0.7814 (t0) cc_final: 0.7555 (t0)
REVERT: A  618 ASN cc_start: 0.8409 (t0) cc_final: 0.8122 (t0)
REVERT: A  619 LYS cc_start: 0.8890 (tptp) cc_final: 0.8607 (tptm)
REVERT: A  631 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7890 (ttp80)
REVERT: A  677 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7875 (mtt-85)
REVERT: A  681 GLN cc_start: 0.8002 (mm110) cc_final: 0.7713 (mm110)
REVERT: A  686 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8207 (ttmm)
REVERT: A  707 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8319 (m-80)
REVERT: A  735 VAL cc_start: 0.5650 (p) cc_final: 0.4718 (m)
REVERT: A  761 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8312 (mp)
REVERT: A  764 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7614 (mmmm)
REVERT: A  765 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7305 (mtm-85)
REVERT: A  776 ASP cc_start: 0.7653 (t0) cc_final: 0.7277 (t0)
REVERT: A  777 VAL cc_start: 0.8797 (p) cc_final: 0.8563 (p)
REVERT: A  783 GLU cc_start: 0.7711 (tp30) cc_final: 0.7499 (tp30)
REVERT: A  791 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7436 (tm-30)
REVERT: A  810 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8781 (tt)
REVERT: A  812 ILE cc_start: 0.8291 (mm) cc_final: 0.8086 (mm)
REVERT: A  823 TYR cc_start: 0.8429 (t80) cc_final: 0.8226 (t80)
REVERT: A  836 PHE cc_start: 0.8258 (t80) cc_final: 0.7951 (t80)
REVERT: A  841 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7260 (mm-30)
REVERT: A  897 ASP cc_start: 0.7710 (p0) cc_final: 0.7463 (p0)
REVERT: A  910 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6593 (p90)
REVERT: A  929 ASP cc_start: 0.6127 (OUTLIER) cc_final: 0.5754 (m-30)
REVERT: A  936 CYS cc_start: 0.8192 (t) cc_final: 0.7894 (t)
REVERT: A  937 TRP cc_start: 0.8652 (t-100) cc_final: 0.8294 (t-100)
REVERT: A  953 LEU cc_start: 0.7729 (tp) cc_final: 0.7349 (tp)
REVERT: A  964 ILE cc_start: 0.8425 (pt) cc_final: 0.8181 (pt)
REVERT: A  984 THR cc_start: 0.8013 (p) cc_final: 0.7703 (t)
REVERT: A 1002 MET cc_start: 0.6953 (mmt) cc_final: 0.6667 (mmt)
  outliers start: 41
  outliers final: 16
  residues processed: 230
  average time/residue: 0.2270
  time to fit residues: 65.0246
Evaluate side-chains
  222 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 198
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  482 GLN
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  761 ILE
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  805 SER
Chi-restraints excluded: chain A residue  810 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  910 HIS
Chi-restraints excluded: chain A residue  929 ASP
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 48 optimal weight:    0.0770
   chunk 36 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0470
   chunk 3 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
A 254 ASN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
A 851 GLN
** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.139086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.116426 restraints weight = 10540.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.71
r_work: 0.3405 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6555  Z= 0.124
  Angle     :  0.567   8.297   8932  Z= 0.291
  Chirality :  0.041   0.137    999
  Planarity :  0.004   0.037   1050
  Dihedral  : 11.291 145.798   1024
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.32 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 26.24 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.32), residues: 722
  helix:  1.40 (0.27), residues: 384
  sheet: -0.81 (0.81), residues: 44
  loop : -0.81 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 940 
 HIS   0.004   0.001   HIS A 560 
 PHE   0.012   0.001   PHE A 847 
 TYR   0.012   0.001   TYR A 415 
 ARG   0.004   0.000   ARG A 945 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  298)
  hydrogen bonds       : angle       4.30419 (  842)
  covalent geometry    : bond        0.00283 ( 6555)
  covalent geometry    : angle       0.56672 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7822 (ptm) cc_final: 0.7407 (ptm)
REVERT: A  422 LYS cc_start: 0.8313 (tttt) cc_final: 0.8029 (ttmt)
REVERT: A  428 GLU cc_start: 0.7168 (tt0) cc_final: 0.6967 (tt0)
REVERT: A  444 GLU cc_start: 0.7561 (mp0) cc_final: 0.7291 (mp0)
REVERT: A  485 LYS cc_start: 0.8554 (tttp) cc_final: 0.8285 (tptm)
REVERT: A  486 GLU cc_start: 0.8129 (pt0) cc_final: 0.7795 (pm20)
REVERT: A  502 GLU cc_start: 0.7464 (tp30) cc_final: 0.6933 (tp30)
REVERT: A  505 LEU cc_start: 0.8622 (mp) cc_final: 0.8340 (mp)
REVERT: A  541 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7512 (mtmm)
REVERT: A  591 ASP cc_start: 0.7799 (t0) cc_final: 0.7581 (t0)
REVERT: A  618 ASN cc_start: 0.8421 (t0) cc_final: 0.8139 (t0)
REVERT: A  631 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7870 (ttp80)
REVERT: A  677 ARG cc_start: 0.8275 (mtt90) cc_final: 0.7961 (mtt-85)
REVERT: A  681 GLN cc_start: 0.8038 (mm110) cc_final: 0.7733 (mm110)
REVERT: A  686 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8162 (ttmm)
REVERT: A  735 VAL cc_start: 0.5528 (p) cc_final: 0.4625 (m)
REVERT: A  741 PHE cc_start: 0.8368 (m-10) cc_final: 0.8145 (m-10)
REVERT: A  761 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8199 (mp)
REVERT: A  765 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7331 (mtm-85)
REVERT: A  776 ASP cc_start: 0.7544 (t0) cc_final: 0.7136 (t0)
REVERT: A  777 VAL cc_start: 0.8779 (p) cc_final: 0.8524 (p)
REVERT: A  791 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7444 (tm-30)
REVERT: A  795 ASP cc_start: 0.7905 (t0) cc_final: 0.7695 (t0)
REVERT: A  807 VAL cc_start: 0.8605 (m) cc_final: 0.8376 (p)
REVERT: A  810 ILE cc_start: 0.9024 (mt) cc_final: 0.8749 (tt)
REVERT: A  812 ILE cc_start: 0.8337 (mm) cc_final: 0.8101 (mm)
REVERT: A  841 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7349 (mm-30)
REVERT: A  846 LYS cc_start: 0.8603 (mttm) cc_final: 0.8015 (mttm)
REVERT: A  910 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6598 (p90)
REVERT: A  929 ASP cc_start: 0.6144 (OUTLIER) cc_final: 0.5766 (m-30)
REVERT: A  936 CYS cc_start: 0.8214 (t) cc_final: 0.7907 (t)
REVERT: A  953 LEU cc_start: 0.7668 (tp) cc_final: 0.7290 (tp)
REVERT: A 1002 MET cc_start: 0.6906 (mmt) cc_final: 0.6595 (mmt)
  outliers start: 27
  outliers final: 14
  residues processed: 210
  average time/residue: 0.2252
  time to fit residues: 59.1059
Evaluate side-chains
  201 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 182
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  761 ILE
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  910 HIS
Chi-restraints excluded: chain A residue  929 ASP
Chi-restraints excluded: chain A residue  963 TRP
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 744 ASN
A 939 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.136489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.113802 restraints weight = 10659.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.70
r_work: 0.3307 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6555  Z= 0.210
  Angle     :  0.611   8.228   8932  Z= 0.315
  Chirality :  0.044   0.171    999
  Planarity :  0.004   0.035   1050
  Dihedral  : 11.261 146.812   1024
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.74 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 27.90 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.32), residues: 722
  helix:  1.41 (0.27), residues: 386
  sheet: -0.89 (0.83), residues: 44
  loop : -0.91 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 573 
 HIS   0.004   0.001   HIS A 560 
 PHE   0.018   0.002   PHE A 651 
 TYR   0.011   0.001   TYR A1061 
 ARG   0.010   0.001   ARG A 483 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04587 (  298)
  hydrogen bonds       : angle       4.47110 (  842)
  covalent geometry    : bond        0.00473 ( 6555)
  covalent geometry    : angle       0.61059 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 196
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7849 (ptm) cc_final: 0.7427 (ptm)
REVERT: A  430 ASP cc_start: 0.7824 (m-30) cc_final: 0.7611 (m-30)
REVERT: A  444 GLU cc_start: 0.7673 (mp0) cc_final: 0.7413 (mp0)
REVERT: A  502 GLU cc_start: 0.7587 (tp30) cc_final: 0.7076 (tp30)
REVERT: A  505 LEU cc_start: 0.8714 (mt) cc_final: 0.8469 (mp)
REVERT: A  570 MET cc_start: 0.8387 (mmm) cc_final: 0.7634 (mmm)
REVERT: A  588 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8067 (mtp-110)
REVERT: A  672 LEU cc_start: 0.9150 (tp) cc_final: 0.8897 (tt)
REVERT: A  677 ARG cc_start: 0.8458 (mtt90) cc_final: 0.8030 (mtt-85)
REVERT: A  681 GLN cc_start: 0.8242 (mm110) cc_final: 0.7884 (mm110)
REVERT: A  735 VAL cc_start: 0.6311 (p) cc_final: 0.5502 (m)
REVERT: A  741 PHE cc_start: 0.8356 (m-10) cc_final: 0.8062 (m-10)
REVERT: A  765 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7676 (mtm-85)
REVERT: A  776 ASP cc_start: 0.7677 (t0) cc_final: 0.7259 (t0)
REVERT: A  777 VAL cc_start: 0.8801 (p) cc_final: 0.8547 (p)
REVERT: A  807 VAL cc_start: 0.8700 (m) cc_final: 0.8481 (p)
REVERT: A  810 ILE cc_start: 0.9005 (mt) cc_final: 0.8769 (tt)
REVERT: A  812 ILE cc_start: 0.8628 (mm) cc_final: 0.8349 (mm)
REVERT: A  834 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7649 (tmm)
REVERT: A  836 PHE cc_start: 0.8380 (t80) cc_final: 0.8049 (t80)
REVERT: A  841 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7511 (mm-30)
REVERT: A  910 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6691 (p90)
REVERT: A  929 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5883 (m-30)
REVERT: A  953 LEU cc_start: 0.7780 (tp) cc_final: 0.7432 (tp)
REVERT: A 1002 MET cc_start: 0.6953 (mmt) cc_final: 0.6619 (mmt)
  outliers start: 28
  outliers final: 15
  residues processed: 209
  average time/residue: 0.2224
  time to fit residues: 58.2083
Evaluate side-chains
  206 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  659 GLN
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  805 SER
Chi-restraints excluded: chain A residue  834 MET
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  910 HIS
Chi-restraints excluded: chain A residue  929 ASP
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    0.0870
   chunk 53 optimal weight:    0.5980
   chunk 43 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0370
   chunk 70 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
A 254 ASN
A 581 ASN
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.138708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.115996 restraints weight = 10453.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.67
r_work: 0.3361 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6555  Z= 0.114
  Angle     :  0.559   7.172   8932  Z= 0.292
  Chirality :  0.041   0.145    999
  Planarity :  0.004   0.032   1050
  Dihedral  : 11.074 144.922   1024
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.05 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 31.52 %
    Favored  : 64.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.32), residues: 722
  helix:  1.46 (0.27), residues: 384
  sheet: -0.95 (0.80), residues: 44
  loop : -0.75 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 940 
 HIS   0.005   0.001   HIS A 263 
 PHE   0.012   0.001   PHE A 651 
 TYR   0.009   0.001   TYR A 415 
 ARG   0.003   0.000   ARG A 945 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  298)
  hydrogen bonds       : angle       4.19117 (  842)
  covalent geometry    : bond        0.00254 ( 6555)
  covalent geometry    : angle       0.55940 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 188
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A  272 MET cc_start: 0.7840 (ptm) cc_final: 0.7396 (ptm)
REVERT: A  430 ASP cc_start: 0.7779 (m-30) cc_final: 0.7560 (m-30)
REVERT: A  444 GLU cc_start: 0.7588 (mp0) cc_final: 0.7320 (mp0)
REVERT: A  483 ARG cc_start: 0.8569 (ptm160) cc_final: 0.8319 (tmm-80)
REVERT: A  494 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7994 (ptmt)
REVERT: A  502 GLU cc_start: 0.7544 (tp30) cc_final: 0.7254 (tp30)
REVERT: A  505 LEU cc_start: 0.8703 (mt) cc_final: 0.8442 (mp)
REVERT: A  588 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8460 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8069 (t0) cc_final: 0.7594 (t0)
REVERT: A  672 LEU cc_start: 0.9116 (tp) cc_final: 0.8833 (tt)
REVERT: A  677 ARG cc_start: 0.8399 (mtt90) cc_final: 0.7963 (mtt-85)
REVERT: A  681 GLN cc_start: 0.8184 (mm110) cc_final: 0.7829 (mm110)
REVERT: A  735 VAL cc_start: 0.6015 (p) cc_final: 0.5210 (m)
REVERT: A  741 PHE cc_start: 0.8175 (m-10) cc_final: 0.7859 (m-10)
REVERT: A  765 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7362 (mtm-85)
REVERT: A  776 ASP cc_start: 0.7636 (t0) cc_final: 0.7217 (t0)
REVERT: A  777 VAL cc_start: 0.8771 (p) cc_final: 0.8519 (p)
REVERT: A  783 GLU cc_start: 0.7804 (tp30) cc_final: 0.7440 (tp30)
REVERT: A  807 VAL cc_start: 0.8657 (m) cc_final: 0.8416 (p)
REVERT: A  810 ILE cc_start: 0.8977 (mt) cc_final: 0.8746 (tt)
REVERT: A  812 ILE cc_start: 0.8590 (mm) cc_final: 0.8322 (mm)
REVERT: A  834 MET cc_start: 0.8114 (mmm) cc_final: 0.7496 (tmm)
REVERT: A  836 PHE cc_start: 0.8325 (t80) cc_final: 0.8011 (t80)
REVERT: A  841 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7441 (mm-30)
REVERT: A  910 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6626 (p90)
REVERT: A  945 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7533 (ttm-80)
REVERT: A  953 LEU cc_start: 0.7438 (tp) cc_final: 0.7102 (tp)
REVERT: A  962 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8041 (ttp80)
REVERT: A  984 THR cc_start: 0.8149 (m) cc_final: 0.7652 (t)
REVERT: A 1002 MET cc_start: 0.6975 (mmt) cc_final: 0.6610 (mmt)
  outliers start: 26
  outliers final: 17
  residues processed: 203
  average time/residue: 0.2242
  time to fit residues: 57.4122
Evaluate side-chains
  203 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  659 GLN
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  805 SER
Chi-restraints excluded: chain A residue  910 HIS
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  963 TRP
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0370
   chunk 56 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0470
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.2956

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

Flipped N/Q/H residues before XYZ refinement:
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
** A 939 ASN ** 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 = 0.3867 r_free = 0.3867 target = 0.140372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.117889 restraints weight = 10402.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.64
r_work: 0.3410 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6555  Z= 0.106
  Angle     :  0.542   7.983   8932  Z= 0.279
  Chirality :  0.041   0.153    999
  Planarity :  0.003   0.035   1050
  Dihedral  : 10.945 144.566   1024
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.32 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 30.92 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.32), residues: 722
  helix:  1.51 (0.27), residues: 384
  sheet: -0.92 (0.78), residues: 44
  loop : -0.65 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 940 
 HIS   0.006   0.001   HIS A 263 
 PHE   0.015   0.001   PHE A 781 
 TYR   0.009   0.001   TYR A 743 
 ARG   0.002   0.000   ARG A 945 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  298)
  hydrogen bonds       : angle       4.07529 (  842)
  covalent geometry    : bond        0.00236 ( 6555)
  covalent geometry    : angle       0.54166 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7740 (ptm) cc_final: 0.7306 (ptm)
REVERT: A  275 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5651 (mp0)
REVERT: A  430 ASP cc_start: 0.7774 (m-30) cc_final: 0.7533 (m-30)
REVERT: A  444 GLU cc_start: 0.7588 (mp0) cc_final: 0.7329 (mp0)
REVERT: A  483 ARG cc_start: 0.8527 (ptm160) cc_final: 0.8185 (tmm-80)
REVERT: A  487 GLU cc_start: 0.8192 (pm20) cc_final: 0.7985 (pm20)
REVERT: A  502 GLU cc_start: 0.7530 (tp30) cc_final: 0.7272 (tp30)
REVERT: A  505 LEU cc_start: 0.8702 (mt) cc_final: 0.8471 (mp)
REVERT: A  588 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.7999 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8058 (t0) cc_final: 0.7592 (t0)
REVERT: A  672 LEU cc_start: 0.9106 (tp) cc_final: 0.8804 (tt)
REVERT: A  677 ARG cc_start: 0.8402 (mtt90) cc_final: 0.8111 (mtt-85)
REVERT: A  681 GLN cc_start: 0.8197 (mm110) cc_final: 0.7829 (mm110)
REVERT: A  735 VAL cc_start: 0.5894 (p) cc_final: 0.5149 (m)
REVERT: A  741 PHE cc_start: 0.7986 (m-10) cc_final: 0.7599 (m-10)
REVERT: A  765 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7344 (mtm-85)
REVERT: A  783 GLU cc_start: 0.7751 (tp30) cc_final: 0.7373 (tp30)
REVERT: A  802 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7070 (mp)
REVERT: A  807 VAL cc_start: 0.8640 (m) cc_final: 0.8390 (p)
REVERT: A  810 ILE cc_start: 0.8981 (mt) cc_final: 0.8753 (tt)
REVERT: A  812 ILE cc_start: 0.8597 (mm) cc_final: 0.8325 (mm)
REVERT: A  834 MET cc_start: 0.8087 (mmm) cc_final: 0.7417 (tmm)
REVERT: A  836 PHE cc_start: 0.8320 (t80) cc_final: 0.8074 (t80)
REVERT: A  910 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.6631 (p90)
REVERT: A  929 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5668 (m-30)
REVERT: A  962 ARG cc_start: 0.8396 (ttp80) cc_final: 0.7987 (ttp80)
REVERT: A 1002 MET cc_start: 0.6932 (mmt) cc_final: 0.6579 (mmt)
  outliers start: 29
  outliers final: 17
  residues processed: 207
  average time/residue: 0.2306
  time to fit residues: 60.0833
Evaluate side-chains
  204 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 182
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  659 GLN
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  805 SER
Chi-restraints excluded: chain A residue  910 HIS
Chi-restraints excluded: chain A residue  929 ASP
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  963 TRP
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 4 optimal weight:    0.0470
   chunk 12 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 44 optimal weight:    0.2980
   chunk 5 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0000
   chunk 16 optimal weight:    0.0870
   overall best weight:    0.2260

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

Flipped N/Q/H residues before XYZ refinement:
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.141724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.119053 restraints weight = 10373.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.69
r_work: 0.3410 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.4233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6555  Z= 0.108
  Angle     :  0.572   9.145   8932  Z= 0.290
  Chirality :  0.040   0.157    999
  Planarity :  0.004   0.034   1050
  Dihedral  : 10.863 144.166   1024
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.91 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 32.73 %
    Favored  : 63.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.32), residues: 722
  helix:  1.58 (0.27), residues: 382
  sheet: -0.88 (0.79), residues: 44
  loop : -0.53 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 940 
 HIS   0.006   0.001   HIS A 263 
 PHE   0.015   0.001   PHE A 781 
 TYR   0.008   0.001   TYR A 891 
 ARG   0.007   0.000   ARG A 945 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03155 (  298)
  hydrogen bonds       : angle       4.02776 (  842)
  covalent geometry    : bond        0.00243 ( 6555)
  covalent geometry    : angle       0.57171 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  272 MET cc_start: 0.7754 (ptm) cc_final: 0.7318 (ptm)
REVERT: A  275 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5664 (mp0)
REVERT: A  430 ASP cc_start: 0.7776 (m-30) cc_final: 0.7533 (m-30)
REVERT: A  483 ARG cc_start: 0.8485 (ptm160) cc_final: 0.8135 (tmm-80)
REVERT: A  494 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7910 (ptmt)
REVERT: A  588 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.7989 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8028 (t0) cc_final: 0.7597 (t0)
REVERT: A  672 LEU cc_start: 0.9127 (tp) cc_final: 0.8802 (tt)
REVERT: A  735 VAL cc_start: 0.5928 (p) cc_final: 0.5206 (m)
REVERT: A  765 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7383 (mtm-85)
REVERT: A  783 GLU cc_start: 0.7738 (tp30) cc_final: 0.7382 (tp30)
REVERT: A  795 ASP cc_start: 0.7972 (t0) cc_final: 0.7709 (t0)
REVERT: A  807 VAL cc_start: 0.8641 (m) cc_final: 0.8394 (p)
REVERT: A  810 ILE cc_start: 0.9003 (mt) cc_final: 0.8780 (tt)
REVERT: A  812 ILE cc_start: 0.8604 (mm) cc_final: 0.8326 (mm)
REVERT: A  834 MET cc_start: 0.8062 (mmm) cc_final: 0.7407 (tmm)
REVERT: A  836 PHE cc_start: 0.8285 (t80) cc_final: 0.8079 (t80)
REVERT: A  913 ASN cc_start: 0.7409 (p0) cc_final: 0.6816 (p0)
REVERT: A  929 ASP cc_start: 0.5924 (OUTLIER) cc_final: 0.5563 (m-30)
REVERT: A  962 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7954 (ttp80)
REVERT: A 1002 MET cc_start: 0.6909 (mmt) cc_final: 0.6514 (mmt)
REVERT: A 1052 ARG cc_start: 0.8814 (mtp180) cc_final: 0.8583 (mtm180)
  outliers start: 23
  outliers final: 14
  residues processed: 202
  average time/residue: 0.2351
  time to fit residues: 59.7384
Evaluate side-chains
  199 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  659 GLN
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  765 ARG
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  929 ASP
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  963 TRP
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 36 optimal weight:    0.0470
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.138067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.115509 restraints weight = 10523.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.64
r_work: 0.3386 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6555  Z= 0.134
  Angle     :  0.607   8.898   8932  Z= 0.311
  Chirality :  0.042   0.159    999
  Planarity :  0.004   0.036   1050
  Dihedral  : 10.860 144.900   1024
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.60 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 32.43 %
    Favored  : 63.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.32), residues: 722
  helix:  1.46 (0.27), residues: 384
  sheet: -0.74 (0.82), residues: 44
  loop : -0.53 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 940 
 HIS   0.006   0.001   HIS A 263 
 PHE   0.047   0.002   PHE A 741 
 TYR   0.008   0.001   TYR A 914 
 ARG   0.006   0.000   ARG A 945 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  298)
  hydrogen bonds       : angle       4.09702 (  842)
  covalent geometry    : bond        0.00305 ( 6555)
  covalent geometry    : angle       0.60716 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 186
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: A  269 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7872 (tp30)
REVERT: A  272 MET cc_start: 0.7766 (ptm) cc_final: 0.7305 (ptm)
REVERT: A  275 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5654 (mp0)
REVERT: A  428 GLU cc_start: 0.7220 (tt0) cc_final: 0.6744 (tt0)
REVERT: A  430 ASP cc_start: 0.7774 (m-30) cc_final: 0.7542 (m-30)
REVERT: A  588 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.7981 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8062 (t0) cc_final: 0.7630 (t0)
REVERT: A  672 LEU cc_start: 0.9170 (tp) cc_final: 0.8857 (tt)
REVERT: A  735 VAL cc_start: 0.5866 (p) cc_final: 0.5167 (m)
REVERT: A  739 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8206 (mt0)
REVERT: A  807 VAL cc_start: 0.8656 (m) cc_final: 0.8419 (p)
REVERT: A  810 ILE cc_start: 0.9015 (mt) cc_final: 0.8783 (tt)
REVERT: A  812 ILE cc_start: 0.8640 (mm) cc_final: 0.8362 (mm)
REVERT: A  834 MET cc_start: 0.8035 (mmm) cc_final: 0.7388 (tmm)
REVERT: A  836 PHE cc_start: 0.8316 (t80) cc_final: 0.8083 (t80)
REVERT: A  846 LYS cc_start: 0.8572 (mttm) cc_final: 0.8046 (mttm)
REVERT: A  929 ASP cc_start: 0.5871 (OUTLIER) cc_final: 0.5513 (m-30)
REVERT: A 1002 MET cc_start: 0.6942 (mmt) cc_final: 0.6562 (mmt)
  outliers start: 28
  outliers final: 20
  residues processed: 202
  average time/residue: 0.2223
  time to fit residues: 56.6060
Evaluate side-chains
  202 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 GLU
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  659 GLN
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  739 GLN
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  805 SER
Chi-restraints excluded: chain A residue  929 ASP
Chi-restraints excluded: chain A residue  963 TRP
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 59 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.138338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.115984 restraints weight = 10550.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.65
r_work: 0.3371 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.4663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6555  Z= 0.141
  Angle     :  0.624  11.240   8932  Z= 0.316
  Chirality :  0.042   0.164    999
  Planarity :  0.004   0.038   1050
  Dihedral  : 10.853 145.586   1024
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.32 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 32.58 %
    Favored  : 63.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.32), residues: 722
  helix:  1.43 (0.27), residues: 382
  sheet: -0.85 (0.82), residues: 44
  loop : -0.51 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 899 
 HIS   0.006   0.001   HIS A 263 
 PHE   0.015   0.001   PHE A 781 
 TYR   0.009   0.001   TYR A 914 
 ARG   0.005   0.000   ARG A 945 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03695 (  298)
  hydrogen bonds       : angle       4.14105 (  842)
  covalent geometry    : bond        0.00319 ( 6555)
  covalent geometry    : angle       0.62410 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7779 (ptm) cc_final: 0.7292 (ptm)
REVERT: A  275 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5718 (mp0)
REVERT: A  428 GLU cc_start: 0.7262 (tt0) cc_final: 0.6741 (tt0)
REVERT: A  430 ASP cc_start: 0.7829 (m-30) cc_final: 0.7580 (m-30)
REVERT: A  588 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.7927 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8074 (t0) cc_final: 0.7670 (t0)
REVERT: A  672 LEU cc_start: 0.9181 (tp) cc_final: 0.8896 (tt)
REVERT: A  735 VAL cc_start: 0.6046 (p) cc_final: 0.5387 (m)
REVERT: A  739 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8271 (mt0)
REVERT: A  807 VAL cc_start: 0.8650 (m) cc_final: 0.8437 (p)
REVERT: A  810 ILE cc_start: 0.9013 (mt) cc_final: 0.8766 (tt)
REVERT: A  812 ILE cc_start: 0.8692 (mm) cc_final: 0.8408 (mm)
REVERT: A  834 MET cc_start: 0.8059 (mmm) cc_final: 0.7413 (tmm)
REVERT: A  836 PHE cc_start: 0.8349 (t80) cc_final: 0.8069 (t80)
REVERT: A  846 LYS cc_start: 0.8601 (mttm) cc_final: 0.8057 (mttm)
REVERT: A  929 ASP cc_start: 0.5857 (OUTLIER) cc_final: 0.5519 (m-30)
REVERT: A  953 LEU cc_start: 0.7455 (tp) cc_final: 0.7182 (tp)
REVERT: A  984 THR cc_start: 0.8038 (m) cc_final: 0.7552 (t)
REVERT: A 1002 MET cc_start: 0.6939 (mmt) cc_final: 0.6540 (mmt)
REVERT: A 1052 ARG cc_start: 0.8846 (mtp180) cc_final: 0.8625 (mtm180)
  outliers start: 25
  outliers final: 22
  residues processed: 204
  average time/residue: 0.2323
  time to fit residues: 58.9419
Evaluate side-chains
  210 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 185
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  474 ASP
Chi-restraints excluded: chain A residue  483 ARG
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  659 GLN
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  739 GLN
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  805 SER
Chi-restraints excluded: chain A residue  929 ASP
Chi-restraints excluded: chain A residue  963 TRP
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue  995 MET
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0060
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.138401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.115902 restraints weight = 10578.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.65
r_work: 0.3386 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.4821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6555  Z= 0.137
  Angle     :  0.646   9.404   8932  Z= 0.327
  Chirality :  0.042   0.171    999
  Planarity :  0.004   0.037   1050
  Dihedral  : 10.807 145.190   1024
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.60 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 32.73 %
    Favored  : 63.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.32), residues: 722
  helix:  1.38 (0.27), residues: 384
  sheet: -0.91 (0.82), residues: 44
  loop : -0.44 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 940 
 HIS   0.006   0.001   HIS A 263 
 PHE   0.013   0.001   PHE A 741 
 TYR   0.010   0.001   TYR A 914 
 ARG   0.009   0.000   ARG A 901 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03580 (  298)
  hydrogen bonds       : angle       4.12564 (  842)
  covalent geometry    : bond        0.00311 ( 6555)
  covalent geometry    : angle       0.64558 ( 8932)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 189
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7767 (ptm) cc_final: 0.7274 (ptm)
REVERT: A  275 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5720 (mp0)
REVERT: A  428 GLU cc_start: 0.7377 (tt0) cc_final: 0.6828 (tt0)
REVERT: A  430 ASP cc_start: 0.7818 (m-30) cc_final: 0.7528 (m-30)
REVERT: A  593 ASN cc_start: 0.8106 (t0) cc_final: 0.7685 (t0)
REVERT: A  672 LEU cc_start: 0.9130 (tp) cc_final: 0.8824 (tt)
REVERT: A  735 VAL cc_start: 0.5996 (p) cc_final: 0.5365 (m)
REVERT: A  739 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8266 (mt0)
REVERT: A  765 ARG cc_start: 0.8202 (mpp80) cc_final: 0.7816 (mpt-90)
REVERT: A  783 GLU cc_start: 0.7885 (tp30) cc_final: 0.7435 (tp30)
REVERT: A  807 VAL cc_start: 0.8653 (m) cc_final: 0.8441 (p)
REVERT: A  810 ILE cc_start: 0.8984 (mt) cc_final: 0.8749 (tt)
REVERT: A  812 ILE cc_start: 0.8669 (mm) cc_final: 0.8382 (mm)
REVERT: A  834 MET cc_start: 0.8040 (mmm) cc_final: 0.7378 (tmm)
REVERT: A  836 PHE cc_start: 0.8353 (t80) cc_final: 0.8136 (t80)
REVERT: A  846 LYS cc_start: 0.8610 (mttm) cc_final: 0.7947 (mttm)
REVERT: A  953 LEU cc_start: 0.7407 (tp) cc_final: 0.7142 (tp)
REVERT: A  984 THR cc_start: 0.8029 (m) cc_final: 0.7549 (t)
REVERT: A 1002 MET cc_start: 0.7067 (mmt) cc_final: 0.6689 (mmt)
REVERT: A 1052 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8601 (mtm180)
  outliers start: 25
  outliers final: 20
  residues processed: 203
  average time/residue: 0.2338
  time to fit residues: 59.1568
Evaluate side-chains
  207 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  474 ASP
Chi-restraints excluded: chain A residue  483 ARG
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  659 GLN
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  739 GLN
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  805 SER
Chi-restraints excluded: chain A residue  929 ASP
Chi-restraints excluded: chain A residue  963 TRP
Chi-restraints excluded: chain A residue  967 LEU
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue 1017 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0270
   chunk 53 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   chunk 39 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.6040

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.139268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.116712 restraints weight = 10649.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.71
r_work: 0.3366 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6555  Z= 0.135
  Angle     :  0.641   9.398   8932  Z= 0.324
  Chirality :  0.042   0.171    999
  Planarity :  0.004   0.037   1050
  Dihedral  : 10.762 144.868   1024
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 32.73 %
    Favored  : 63.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.32), residues: 722
  helix:  1.39 (0.27), residues: 383
  sheet: -0.98 (0.82), residues: 44
  loop : -0.41 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 940 
 HIS   0.006   0.001   HIS A 263 
 PHE   0.010   0.001   PHE A 741 
 TYR   0.007   0.001   TYR A1054 
 ARG   0.007   0.001   ARG A 901 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  298)
  hydrogen bonds       : angle       4.10383 (  842)
  covalent geometry    : bond        0.00308 ( 6555)
  covalent geometry    : angle       0.64121 ( 8932)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3287.36 seconds
wall clock time: 57 minutes 45.40 seconds (3465.40 seconds total)