Starting phenix.real_space_refine
on Tue Mar 11 22:54:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxt_40858/03_2025/8sxt_40858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxt_40858/03_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_40858/03_2025/8sxt_40858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxt_40858/03_2025/8sxt_40858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxt_40858/03_2025/8sxt_40858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxt_40858/03_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-5624/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: 4.63, per 1000 atoms: 0.73
  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: 1.98
  Conformation dependent library (CDL) restraints added in 697.2 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: 2.07
  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: 1.94

  Time building geometry restraints manager: 2.28 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:             0.580
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.720
  Find NCS groups from input model:        0.060
  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:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.480
-------------------------------------------------------------------------------
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= 0.167
  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 

*********************** 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  : 0.822 
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: 0.2533
  time to fit residues: 66.4978
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  : 1.035 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   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
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 = 0.3872 r_free = 0.3872 target = 0.138474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.115854 restraints weight = 10628.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.62
r_work: 0.3422 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6555  Z= 0.222
  Angle     :  0.602   6.931   8932  Z= 0.311
  Chirality :  0.043   0.160    999
  Planarity :  0.004   0.040   1050
  Dihedral  : 11.399 146.401   1027
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.32 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 23.23 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.31), residues: 722
  helix:  1.11 (0.27), residues: 385
  sheet: -0.73 (0.83), residues: 42
  loop : -0.78 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   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   0.005   0.001   ARG A 550 

*********************** 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: 39
    poor density    : 207
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7772 (ptm) cc_final: 0.7402 (ptm)
REVERT: A  422 LYS cc_start: 0.8359 (tttt) cc_final: 0.8044 (ttmt)
REVERT: A  428 GLU cc_start: 0.6933 (tt0) cc_final: 0.6714 (tt0)
REVERT: A  444 GLU cc_start: 0.7530 (mp0) cc_final: 0.7251 (mp0)
REVERT: A  457 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7491 (mt-10)
REVERT: A  458 ILE cc_start: 0.8792 (mt) cc_final: 0.8592 (tt)
REVERT: A  482 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6771 (tp-100)
REVERT: A  485 LYS cc_start: 0.8449 (tttp) cc_final: 0.8224 (tptt)
REVERT: A  502 GLU cc_start: 0.7367 (tp30) cc_final: 0.6844 (tp30)
REVERT: A  505 LEU cc_start: 0.8473 (mp) cc_final: 0.8210 (mp)
REVERT: A  516 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5365 (mt)
REVERT: A  541 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7320 (mtmm)
REVERT: A  582 VAL cc_start: 0.8450 (m) cc_final: 0.8215 (p)
REVERT: A  618 ASN cc_start: 0.8382 (t0) cc_final: 0.8080 (t0)
REVERT: A  631 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7877 (ttp80)
REVERT: A  677 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7885 (mtt-85)
REVERT: A  681 GLN cc_start: 0.7990 (mm110) cc_final: 0.7699 (mm110)
REVERT: A  686 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8154 (ttmm)
REVERT: A  707 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8396 (m-80)
REVERT: A  720 LYS cc_start: 0.8332 (ptmm) cc_final: 0.8002 (ptpp)
REVERT: A  735 VAL cc_start: 0.5594 (p) cc_final: 0.4649 (m)
REVERT: A  761 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8219 (mp)
REVERT: A  765 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7392 (mtm-85)
REVERT: A  776 ASP cc_start: 0.7623 (t0) cc_final: 0.7243 (t0)
REVERT: A  777 VAL cc_start: 0.8786 (p) cc_final: 0.8550 (p)
REVERT: A  791 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: A  810 ILE cc_start: 0.9050 (mt) cc_final: 0.8775 (tt)
REVERT: A  836 PHE cc_start: 0.8226 (t80) cc_final: 0.7940 (t80)
REVERT: A  841 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7348 (mm-30)
REVERT: A  897 ASP cc_start: 0.7649 (p0) cc_final: 0.7433 (p0)
REVERT: A  910 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.6609 (p90)
REVERT: A  929 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5726 (m-30)
REVERT: A  936 CYS cc_start: 0.8219 (t) cc_final: 0.7918 (t)
REVERT: A  964 ILE cc_start: 0.8332 (pt) cc_final: 0.8107 (pt)
REVERT: A  984 THR cc_start: 0.8016 (p) cc_final: 0.7717 (t)
REVERT: A 1002 MET cc_start: 0.7018 (mmt) cc_final: 0.6723 (mmt)
  outliers start: 39
  outliers final: 16
  residues processed: 231
  average time/residue: 0.2332
  time to fit residues: 67.1455
Evaluate side-chains
  216 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 192
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
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  516 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  614 LEU
Chi-restraints excluded: chain A residue  666 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  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:    0.0040
   chunk 36 optimal weight:    0.3980
   chunk 53 optimal weight:    0.7980
   chunk 14 optimal weight:    0.2980
   chunk 3 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0970
   chunk 26 optimal weight:    0.8980
   chunk 46 optimal weight:    0.3980
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.2390

-------------------------------------------------------------------------------
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 851 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.139961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.117273 restraints weight = 10549.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.67
r_work: 0.3433 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6555  Z= 0.164
  Angle     :  0.577   8.127   8932  Z= 0.297
  Chirality :  0.040   0.138    999
  Planarity :  0.004   0.036   1050
  Dihedral  : 11.274 144.903   1024
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.32 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 27.60 %
    Favored  : 68.78 %
  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:  0.63 (0.32), residues: 722
  helix:  1.49 (0.27), residues: 378
  sheet: -0.73 (0.80), residues: 44
  loop : -0.77 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 940 
 HIS   0.010   0.002   HIS A 263 
 PHE   0.010   0.001   PHE A 725 
 TYR   0.013   0.001   TYR A 743 
 ARG   0.004   0.000   ARG A 901 

*********************** 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
  223 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 199
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7811 (ptm) cc_final: 0.7397 (ptm)
REVERT: A  422 LYS cc_start: 0.8322 (tttt) cc_final: 0.8023 (ttmt)
REVERT: A  428 GLU cc_start: 0.7118 (tt0) cc_final: 0.6910 (tt0)
REVERT: A  444 GLU cc_start: 0.7510 (mp0) cc_final: 0.7249 (mp0)
REVERT: A  457 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7615 (mt-10)
REVERT: A  485 LYS cc_start: 0.8456 (tttp) cc_final: 0.8221 (tptm)
REVERT: A  486 GLU cc_start: 0.8100 (pt0) cc_final: 0.7824 (pm20)
REVERT: A  502 GLU cc_start: 0.7431 (tp30) cc_final: 0.6886 (tp30)
REVERT: A  505 LEU cc_start: 0.8552 (mp) cc_final: 0.8267 (mp)
REVERT: A  618 ASN cc_start: 0.8397 (t0) cc_final: 0.8098 (t0)
REVERT: A  619 LYS cc_start: 0.8906 (tptp) cc_final: 0.8629 (tptm)
REVERT: A  631 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7759 (ttp80)
REVERT: A  636 LYS cc_start: 0.8639 (ptpp) cc_final: 0.8430 (ptpp)
REVERT: A  677 ARG cc_start: 0.8189 (mtt90) cc_final: 0.7896 (mtt-85)
REVERT: A  681 GLN cc_start: 0.7990 (mm110) cc_final: 0.7663 (mm110)
REVERT: A  686 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8117 (ttmm)
REVERT: A  707 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8189 (m-80)
REVERT: A  735 VAL cc_start: 0.5505 (p) cc_final: 0.4626 (m)
REVERT: A  741 PHE cc_start: 0.8408 (m-10) cc_final: 0.8188 (m-10)
REVERT: A  761 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7966 (mp)
REVERT: A  765 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7283 (mtm-85)
REVERT: A  776 ASP cc_start: 0.7562 (t0) cc_final: 0.7145 (t0)
REVERT: A  777 VAL cc_start: 0.8760 (p) cc_final: 0.8503 (p)
REVERT: A  783 GLU cc_start: 0.7606 (tp30) cc_final: 0.7393 (tp30)
REVERT: A  807 VAL cc_start: 0.8590 (m) cc_final: 0.8347 (p)
REVERT: A  810 ILE cc_start: 0.9021 (mt) cc_final: 0.8749 (tt)
REVERT: A  841 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7372 (mm-30)
REVERT: A  846 LYS cc_start: 0.8570 (mttm) cc_final: 0.7984 (mttm)
REVERT: A  910 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6526 (p90)
REVERT: A  929 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5771 (m-30)
REVERT: A  936 CYS cc_start: 0.8189 (t) cc_final: 0.7940 (t)
REVERT: A  953 LEU cc_start: 0.7783 (tp) cc_final: 0.7470 (tp)
REVERT: A  964 ILE cc_start: 0.8224 (pt) cc_final: 0.7950 (pt)
REVERT: A 1002 MET cc_start: 0.6906 (mmt) cc_final: 0.6584 (mmt)
  outliers start: 24
  outliers final: 13
  residues processed: 212
  average time/residue: 0.2410
  time to fit residues: 63.1991
Evaluate side-chains
  203 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 185
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
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  474 ASP
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  688 ILE
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:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 744 ASN
A 851 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.134974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112453 restraints weight = 10701.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.70
r_work: 0.3323 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6555  Z= 0.337
  Angle     :  0.655   8.628   8932  Z= 0.340
  Chirality :  0.046   0.161    999
  Planarity :  0.004   0.037   1050
  Dihedral  : 11.377 147.164   1024
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.74 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 28.21 %
    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:  0.44 (0.32), residues: 722
  helix:  1.35 (0.27), residues: 384
  sheet: -0.96 (0.83), residues: 44
  loop : -0.90 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 940 
 HIS   0.009   0.002   HIS A 263 
 PHE   0.019   0.002   PHE A 875 
 TYR   0.013   0.002   TYR A1061 
 ARG   0.005   0.001   ARG A 483 

*********************** 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
  233 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7863 (ptm) cc_final: 0.7437 (ptm)
REVERT: A  430 ASP cc_start: 0.7869 (m-30) cc_final: 0.7659 (m-30)
REVERT: A  444 GLU cc_start: 0.7688 (mp0) cc_final: 0.7438 (mp0)
REVERT: A  468 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8681 (mtmm)
REVERT: A  502 GLU cc_start: 0.7602 (tp30) cc_final: 0.7100 (tp30)
REVERT: A  505 LEU cc_start: 0.8745 (mt) cc_final: 0.8518 (mp)
REVERT: A  570 MET cc_start: 0.8386 (mmm) cc_final: 0.7662 (mmm)
REVERT: A  588 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8059 (mtp-110)
REVERT: A  672 LEU cc_start: 0.9150 (tp) cc_final: 0.8892 (tt)
REVERT: A  677 ARG cc_start: 0.8476 (mtt90) cc_final: 0.8076 (mtt-85)
REVERT: A  681 GLN cc_start: 0.8218 (mm110) cc_final: 0.7866 (mm110)
REVERT: A  735 VAL cc_start: 0.6460 (p) cc_final: 0.5634 (m)
REVERT: A  741 PHE cc_start: 0.8495 (m-10) cc_final: 0.8081 (m-10)
REVERT: A  764 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7778 (mmmm)
REVERT: A  765 ARG cc_start: 0.8151 (mpp80) cc_final: 0.7588 (mtm-85)
REVERT: A  776 ASP cc_start: 0.7694 (t0) cc_final: 0.7286 (t0)
REVERT: A  777 VAL cc_start: 0.8806 (p) cc_final: 0.8562 (p)
REVERT: A  791 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: A  807 VAL cc_start: 0.8633 (m) cc_final: 0.8425 (p)
REVERT: A  810 ILE cc_start: 0.9041 (mt) cc_final: 0.8784 (tt)
REVERT: A  834 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7656 (tmm)
REVERT: A  836 PHE cc_start: 0.8415 (t80) cc_final: 0.8088 (t80)
REVERT: A  841 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: A  910 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6653 (p90)
REVERT: A  929 ASP cc_start: 0.6226 (OUTLIER) cc_final: 0.5915 (m-30)
REVERT: A  953 LEU cc_start: 0.7851 (tp) cc_final: 0.7447 (tp)
REVERT: A  962 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8154 (ttp80)
REVERT: A  967 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7957 (pp)
REVERT: A 1002 MET cc_start: 0.6942 (mmt) cc_final: 0.6616 (mmt)
  outliers start: 26
  outliers final: 18
  residues processed: 218
  average time/residue: 0.2251
  time to fit residues: 61.6189
Evaluate side-chains
  225 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 203
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
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  474 ASP
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  697 LEU
Chi-restraints excluded: chain A residue  702 ASP
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  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:    0.5980
   chunk 53 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
** 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 = 0.3842 r_free = 0.3842 target = 0.138304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.115742 restraints weight = 10507.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.67
r_work: 0.3357 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.4081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6555  Z= 0.185
  Angle     :  0.583   6.946   8932  Z= 0.305
  Chirality :  0.042   0.147    999
  Planarity :  0.004   0.032   1050
  Dihedral  : 11.090 145.579   1024
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.32 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 31.07 %
    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:  0.51 (0.32), residues: 722
  helix:  1.35 (0.27), residues: 388
  sheet: -0.97 (0.82), residues: 44
  loop : -0.81 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 940 
 HIS   0.009   0.001   HIS A 263 
 PHE   0.012   0.001   PHE A 847 
 TYR   0.010   0.001   TYR A 284 
 ARG   0.005   0.000   ARG A 945 

*********************** 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
  225 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7844 (ptm) cc_final: 0.7410 (ptm)
REVERT: A  275 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5772 (mp0)
REVERT: A  428 GLU cc_start: 0.7285 (tt0) cc_final: 0.6755 (tt0)
REVERT: A  430 ASP cc_start: 0.7826 (m-30) cc_final: 0.7596 (m-30)
REVERT: A  444 GLU cc_start: 0.7618 (mp0) cc_final: 0.7364 (mp0)
REVERT: A  468 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8667 (mtmm)
REVERT: A  502 GLU cc_start: 0.7542 (tp30) cc_final: 0.7258 (tp30)
REVERT: A  505 LEU cc_start: 0.8740 (mt) cc_final: 0.8497 (mp)
REVERT: A  516 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5829 (mt)
REVERT: A  570 MET cc_start: 0.8392 (mmm) cc_final: 0.7601 (mmm)
REVERT: A  588 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8486 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8090 (t0) cc_final: 0.7641 (t0)
REVERT: A  672 LEU cc_start: 0.9145 (tp) cc_final: 0.8877 (tt)
REVERT: A  677 ARG cc_start: 0.8443 (mtt90) cc_final: 0.8182 (ttm-80)
REVERT: A  681 GLN cc_start: 0.8196 (mm110) cc_final: 0.7827 (mm110)
REVERT: A  707 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7904 (m-80)
REVERT: A  735 VAL cc_start: 0.6107 (p) cc_final: 0.5320 (m)
REVERT: A  741 PHE cc_start: 0.8321 (m-10) cc_final: 0.8102 (m-10)
REVERT: A  764 LYS cc_start: 0.8086 (mmmm) cc_final: 0.7675 (mmmm)
REVERT: A  765 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7604 (mtm-85)
REVERT: A  807 VAL cc_start: 0.8572 (m) cc_final: 0.8345 (p)
REVERT: A  810 ILE cc_start: 0.9004 (mt) cc_final: 0.8766 (tt)
REVERT: A  834 MET cc_start: 0.8107 (mmm) cc_final: 0.7528 (tmm)
REVERT: A  836 PHE cc_start: 0.8362 (t80) cc_final: 0.8023 (t80)
REVERT: A  841 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7496 (mm-30)
REVERT: A  897 ASP cc_start: 0.7878 (p0) cc_final: 0.7605 (p0)
REVERT: A  910 HIS cc_start: 0.6966 (OUTLIER) cc_final: 0.6607 (p90)
REVERT: A  953 LEU cc_start: 0.7641 (tp) cc_final: 0.7324 (tp)
REVERT: A  962 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8053 (ttp80)
REVERT: A  984 THR cc_start: 0.8092 (m) cc_final: 0.7601 (t)
REVERT: A 1002 MET cc_start: 0.6964 (mmt) cc_final: 0.6606 (mmt)
  outliers start: 28
  outliers final: 18
  residues processed: 213
  average time/residue: 0.2322
  time to fit residues: 61.8259
Evaluate side-chains
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 GLU
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  474 ASP
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  516 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  754 MET
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  967 LEU
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:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 15 optimal weight:    0.1980
   chunk 56 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 40 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0020
   overall best weight:    0.3388

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.139028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.116626 restraints weight = 10432.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.63
r_work: 0.3402 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.4244

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= 0.155
  Angle     :  0.561   7.287   8932  Z= 0.291
  Chirality :  0.041   0.152    999
  Planarity :  0.004   0.035   1050
  Dihedral  : 10.944 144.928   1024
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.32 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 30.47 %
    Favored  : 65.01 %
  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:  0.68 (0.32), residues: 722
  helix:  1.48 (0.27), residues: 374
  sheet: -0.97 (0.80), residues: 44
  loop : -0.59 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 940 
 HIS   0.007   0.001   HIS A 263 
 PHE   0.014   0.001   PHE A 781 
 TYR   0.008   0.001   TYR A 743 
 ARG   0.006   0.000   ARG A 945 

*********************** 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
  222 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 MET cc_start: 0.8290 (tpp) cc_final: 0.7958 (tpp)
REVERT: A  269 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7892 (tp30)
REVERT: A  272 MET cc_start: 0.7769 (ptm) cc_final: 0.7294 (ptm)
REVERT: A  275 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5667 (mp0)
REVERT: A  428 GLU cc_start: 0.7289 (tt0) cc_final: 0.6763 (tt0)
REVERT: A  430 ASP cc_start: 0.7777 (m-30) cc_final: 0.7537 (m-30)
REVERT: A  468 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8679 (mtmm)
REVERT: A  487 GLU cc_start: 0.8127 (pm20) cc_final: 0.7914 (pm20)
REVERT: A  502 GLU cc_start: 0.7491 (tp30) cc_final: 0.7273 (tp30)
REVERT: A  505 LEU cc_start: 0.8748 (mt) cc_final: 0.8530 (mp)
REVERT: A  516 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5848 (mt)
REVERT: A  588 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8003 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8058 (t0) cc_final: 0.7626 (t0)
REVERT: A  619 LYS cc_start: 0.8971 (tptp) cc_final: 0.8762 (tptp)
REVERT: A  672 LEU cc_start: 0.9104 (tp) cc_final: 0.8795 (tt)
REVERT: A  677 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8191 (mtt-85)
REVERT: A  735 VAL cc_start: 0.5947 (p) cc_final: 0.5207 (m)
REVERT: A  741 PHE cc_start: 0.8091 (m-10) cc_final: 0.7849 (m-10)
REVERT: A  764 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7778 (mmmt)
REVERT: A  765 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7721 (mtm-85)
REVERT: A  807 VAL cc_start: 0.8550 (m) cc_final: 0.8268 (p)
REVERT: A  810 ILE cc_start: 0.8992 (mt) cc_final: 0.8760 (tt)
REVERT: A  834 MET cc_start: 0.8097 (mmm) cc_final: 0.7443 (tmm)
REVERT: A  836 PHE cc_start: 0.8315 (t80) cc_final: 0.8027 (t80)
REVERT: A  910 HIS cc_start: 0.6890 (OUTLIER) cc_final: 0.6581 (p90)
REVERT: A  929 ASP cc_start: 0.6053 (OUTLIER) cc_final: 0.5707 (m-30)
REVERT: A  962 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8048 (ttp80)
REVERT: A  984 THR cc_start: 0.8082 (m) cc_final: 0.7596 (t)
REVERT: A 1002 MET cc_start: 0.6936 (mmt) cc_final: 0.6592 (mmt)
  outliers start: 30
  outliers final: 17
  residues processed: 210
  average time/residue: 0.2235
  time to fit residues: 58.6913
Evaluate side-chains
  209 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
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  443 GLN
Chi-restraints excluded: chain A residue  474 ASP
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  516 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  613 MET
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  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  974 ILE
Chi-restraints excluded: chain A residue  988 ILE
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:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0000
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0010
   chunk 5 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.4990

-------------------------------------------------------------------------------
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 = 0.3863 r_free = 0.3863 target = 0.139823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.117377 restraints weight = 10415.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.70
r_work: 0.3390 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.4380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6555  Z= 0.176
  Angle     :  0.585   8.069   8932  Z= 0.300
  Chirality :  0.042   0.157    999
  Planarity :  0.004   0.035   1050
  Dihedral  : 10.890 145.459   1024
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.60 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 31.22 %
    Favored  : 64.10 %
  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:  0.69 (0.32), residues: 722
  helix:  1.47 (0.27), residues: 374
  sheet: -0.91 (0.81), residues: 44
  loop : -0.56 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 940 
 HIS   0.007   0.001   HIS A 263 
 PHE   0.015   0.001   PHE A 781 
 TYR   0.007   0.001   TYR A 891 
 ARG   0.003   0.000   ARG A 483 

*********************** 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
  219 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 188
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 MET cc_start: 0.8208 (tpp) cc_final: 0.7981 (tpp)
REVERT: A  272 MET cc_start: 0.7778 (ptm) cc_final: 0.7356 (ptm)
REVERT: A  275 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5714 (mp0)
REVERT: A  428 GLU cc_start: 0.7322 (tt0) cc_final: 0.6808 (tt0)
REVERT: A  430 ASP cc_start: 0.7808 (m-30) cc_final: 0.7555 (m-30)
REVERT: A  468 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8708 (mtmm)
REVERT: A  516 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5905 (mt)
REVERT: A  588 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8014 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8071 (t0) cc_final: 0.7642 (t0)
REVERT: A  672 LEU cc_start: 0.9130 (tp) cc_final: 0.8832 (tt)
REVERT: A  677 ARG cc_start: 0.8453 (mtt90) cc_final: 0.8237 (mtt-85)
REVERT: A  735 VAL cc_start: 0.5918 (p) cc_final: 0.5176 (m)
REVERT: A  764 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7822 (mmmm)
REVERT: A  783 GLU cc_start: 0.7807 (tp30) cc_final: 0.7535 (tp30)
REVERT: A  807 VAL cc_start: 0.8547 (m) cc_final: 0.8279 (p)
REVERT: A  810 ILE cc_start: 0.8996 (mt) cc_final: 0.8771 (tt)
REVERT: A  834 MET cc_start: 0.8144 (mmm) cc_final: 0.7477 (tmm)
REVERT: A  836 PHE cc_start: 0.8332 (t80) cc_final: 0.8045 (t80)
REVERT: A  913 ASN cc_start: 0.7447 (p0) cc_final: 0.6532 (p0)
REVERT: A  929 ASP cc_start: 0.6000 (OUTLIER) cc_final: 0.5649 (m-30)
REVERT: A  962 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8046 (ttp80)
REVERT: A 1002 MET cc_start: 0.6983 (mmt) cc_final: 0.6585 (mmt)
  outliers start: 31
  outliers final: 22
  residues processed: 203
  average time/residue: 0.2307
  time to fit residues: 58.9514
Evaluate side-chains
  205 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 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  443 GLN
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  474 ASP
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  516 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  754 MET
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  995 MET
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:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0270
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5838

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.139485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.117262 restraints weight = 10501.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.62
r_work: 0.3379 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.4548

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= 0.186
  Angle     :  0.608   8.249   8932  Z= 0.315
  Chirality :  0.042   0.158    999
  Planarity :  0.004   0.036   1050
  Dihedral  : 10.881 145.841   1024
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.74 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 32.43 %
    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:  0.62 (0.32), residues: 722
  helix:  1.46 (0.28), residues: 367
  sheet: -0.93 (0.81), residues: 44
  loop : -0.62 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 940 
 HIS   0.006   0.001   HIS A 263 
 PHE   0.016   0.001   PHE A 781 
 TYR   0.007   0.001   TYR A 891 
 ARG   0.003   0.000   ARG A 483 

*********************** 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: 26
    poor density    : 188
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 MET cc_start: 0.8233 (tpp) cc_final: 0.7987 (tpp)
REVERT: A  269 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7880 (tp30)
REVERT: A  272 MET cc_start: 0.7789 (ptm) cc_final: 0.7318 (ptm)
REVERT: A  275 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5743 (mp0)
REVERT: A  428 GLU cc_start: 0.7258 (tt0) cc_final: 0.6752 (tt0)
REVERT: A  430 ASP cc_start: 0.7777 (m-30) cc_final: 0.7548 (m-30)
REVERT: A  468 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8702 (mtmm)
REVERT: A  516 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5968 (mt)
REVERT: A  588 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8436 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8088 (t0) cc_final: 0.7664 (t0)
REVERT: A  672 LEU cc_start: 0.9171 (tp) cc_final: 0.8856 (tt)
REVERT: A  677 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8221 (mtt-85)
REVERT: A  735 VAL cc_start: 0.5935 (p) cc_final: 0.5221 (m)
REVERT: A  739 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8284 (mt0)
REVERT: A  764 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7767 (mmmt)
REVERT: A  783 GLU cc_start: 0.7822 (tp30) cc_final: 0.7575 (tp30)
REVERT: A  810 ILE cc_start: 0.9018 (mt) cc_final: 0.8781 (tt)
REVERT: A  834 MET cc_start: 0.8078 (mmm) cc_final: 0.7450 (tmm)
REVERT: A  836 PHE cc_start: 0.8323 (t80) cc_final: 0.8040 (t80)
REVERT: A  984 THR cc_start: 0.8056 (m) cc_final: 0.7582 (t)
REVERT: A 1002 MET cc_start: 0.6957 (mmt) cc_final: 0.6557 (mmt)
  outliers start: 26
  outliers final: 19
  residues processed: 204
  average time/residue: 0.2493
  time to fit residues: 62.8307
Evaluate side-chains
  208 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 185
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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  286 ASN
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  474 ASP
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  516 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  739 GLN
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  802 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0670
   chunk 58 optimal weight:    0.0980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 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 = 0.3853 r_free = 0.3853 target = 0.139314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.116682 restraints weight = 10521.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.72
r_work: 0.3388 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4719

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= 0.181
  Angle     :  0.602   8.280   8932  Z= 0.312
  Chirality :  0.042   0.165    999
  Planarity :  0.004   0.037   1050
  Dihedral  : 10.836 145.934   1024
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.60 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 31.98 %
    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:  0.65 (0.32), residues: 722
  helix:  1.46 (0.27), residues: 368
  sheet: -1.02 (0.82), residues: 44
  loop : -0.55 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 940 
 HIS   0.007   0.001   HIS A 263 
 PHE   0.017   0.001   PHE A 781 
 TYR   0.008   0.001   TYR A 891 
 ARG   0.007   0.000   ARG A 945 

*********************** 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
  223 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 194
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 MET cc_start: 0.8254 (tpp) cc_final: 0.8017 (tpp)
REVERT: A  272 MET cc_start: 0.7761 (ptm) cc_final: 0.7320 (ptm)
REVERT: A  275 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5823 (mp0)
REVERT: A  428 GLU cc_start: 0.7377 (tt0) cc_final: 0.6856 (tt0)
REVERT: A  430 ASP cc_start: 0.7835 (m-30) cc_final: 0.7554 (m-30)
REVERT: A  516 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6023 (mt)
REVERT: A  588 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.7991 (mtp-110)
REVERT: A  593 ASN cc_start: 0.8110 (t0) cc_final: 0.7705 (t0)
REVERT: A  672 LEU cc_start: 0.9146 (tp) cc_final: 0.8843 (tt)
REVERT: A  677 ARG cc_start: 0.8465 (mtt90) cc_final: 0.8225 (mtt-85)
REVERT: A  735 VAL cc_start: 0.6084 (p) cc_final: 0.5411 (m)
REVERT: A  739 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8280 (mt0)
REVERT: A  810 ILE cc_start: 0.8997 (mt) cc_final: 0.8761 (tt)
REVERT: A  834 MET cc_start: 0.8099 (mmm) cc_final: 0.7449 (tmm)
REVERT: A  836 PHE cc_start: 0.8326 (t80) cc_final: 0.8052 (t80)
REVERT: A  846 LYS cc_start: 0.8595 (mttm) cc_final: 0.7961 (mttm)
REVERT: A  929 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5606 (m-30)
REVERT: A  984 THR cc_start: 0.8025 (m) cc_final: 0.7548 (t)
REVERT: A  995 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7392 (ptp)
REVERT: A 1002 MET cc_start: 0.7030 (mmt) cc_final: 0.6632 (mmt)
  outliers start: 29
  outliers final: 22
  residues processed: 210
  average time/residue: 0.2272
  time to fit residues: 59.6537
Evaluate side-chains
  214 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 187
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
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  286 ASN
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  474 ASP
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  516 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  590 LYS
Chi-restraints excluded: chain A residue  659 GLN
Chi-restraints excluded: chain A residue  707 TYR
Chi-restraints excluded: chain A residue  739 GLN
Chi-restraints excluded: chain A residue  754 MET
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  766 ILE
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  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:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0870
   chunk 48 optimal weight:    0.0870
   chunk 54 optimal weight:   10.0000
   chunk 52 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.5936

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.138103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.115471 restraints weight = 10549.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.66
r_work: 0.3342 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.4865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6555  Z= 0.197
  Angle     :  0.647  11.210   8932  Z= 0.329
  Chirality :  0.042   0.163    999
  Planarity :  0.004   0.036   1050
  Dihedral  : 10.828 145.773   1024
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.88 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 32.88 %
    Favored  : 63.20 %
  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:  0.62 (0.32), residues: 722
  helix:  1.36 (0.27), residues: 373
  sheet: -1.09 (0.82), residues: 44
  loop : -0.48 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 940 
 HIS   0.008   0.001   HIS A 263 
 PHE   0.021   0.001   PHE A 741 
 TYR   0.007   0.001   TYR A 743 
 ARG   0.006   0.000   ARG A 945 

********************** 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
  209 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7742 (ptm) cc_final: 0.7295 (ptm)
REVERT: A  275 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5782 (mp0)
REVERT: A  428 GLU cc_start: 0.7350 (tt0) cc_final: 0.6817 (tt0)
REVERT: A  430 ASP cc_start: 0.7795 (m-30) cc_final: 0.7523 (m-30)
REVERT: A  516 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6097 (mt)
REVERT: A  672 LEU cc_start: 0.9166 (tp) cc_final: 0.8856 (tt)
REVERT: A  677 ARG cc_start: 0.8428 (mtt90) cc_final: 0.8205 (mtt-85)
REVERT: A  735 VAL cc_start: 0.6129 (p) cc_final: 0.5494 (m)
REVERT: A  810 ILE cc_start: 0.9022 (mt) cc_final: 0.8787 (tt)
REVERT: A  834 MET cc_start: 0.8116 (mmm) cc_final: 0.7462 (tmm)
REVERT: A  836 PHE cc_start: 0.8338 (t80) cc_final: 0.8070 (t80)
REVERT: A  846 LYS cc_start: 0.8571 (mttm) cc_final: 0.7950 (mttm)
REVERT: A  984 THR cc_start: 0.8055 (m) cc_final: 0.7574 (t)
REVERT: A 1002 MET cc_start: 0.7086 (mmt) cc_final: 0.6696 (mmt)
  outliers start: 26
  outliers final: 23
  residues processed: 197
  average time/residue: 0.2406
  time to fit residues: 59.1229
Evaluate side-chains
  207 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 182
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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  286 ASN
Chi-restraints excluded: chain A residue  443 GLN
Chi-restraints excluded: chain A residue  474 ASP
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  516 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  613 MET
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    0.1980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.139427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.116851 restraints weight = 10650.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.65
r_work: 0.3383 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4972

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= 0.209
  Angle     :  0.646  10.211   8932  Z= 0.331
  Chirality :  0.043   0.174    999
  Planarity :  0.004   0.037   1050
  Dihedral  : 10.805 145.705   1024
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 32.58 %
    Favored  : 62.90 %
  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:  0.49 (0.32), residues: 722
  helix:  1.31 (0.27), residues: 373
  sheet: -1.25 (0.80), residues: 44
  loop : -0.61 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 940 
 HIS   0.007   0.001   HIS A 263 
 PHE   0.018   0.001   PHE A 741 
 TYR   0.007   0.001   TYR A1054 
 ARG   0.006   0.000   ARG A 945 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3308.31 seconds
wall clock time: 57 minutes 37.37 seconds (3457.37 seconds total)