Starting phenix.real_space_refine
on Fri Jan 17 14:21:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xk3_38414/01_2025/8xk3_38414.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xk3_38414/01_2025/8xk3_38414.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xk3_38414/01_2025/8xk3_38414.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xk3_38414/01_2025/8xk3_38414.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xk3_38414/01_2025/8xk3_38414.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xk3_38414/01_2025/8xk3_38414.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.078
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5719 atoms to isotropic.
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
     Mn      3      7.51       5
     P      32      5.49       5
     S      29      5.16       5
     C    3910      2.51       5
     N    1115      2.21       5
     O    1220      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6309
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 5621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 692, 5621
          Classifications: {'peptide': 692}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 23, 'TRANS': 668}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 358
          Classifications: {'DNA': 17}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 16}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {' DG:plan2': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "C"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 179
          Classifications: {'DNA': 9}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 8}
    Chain: "c"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 119
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "c"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 4.37, per 1000 atoms: 0.69
  Number of scatterers: 6309
  At special positions: 0
  Unit cell: (74.037, 89.355, 107.226, 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)
     Mn      3     24.99
     S      29     16.00
     P      32     15.00
     O    1220      8.00
     N    1115      7.00
     C    3910      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: 1.75
  Conformation dependent library (CDL) restraints added in 766.8 milliseconds
  

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
Warning! O2 atom is missing from residue   DC c   6  
  Was trying to link:   DC c   6 O2 with   DG B  11 N2, Saenger class: 19
Warning! O2 atom is missing from residue   DC c   6  
  Was trying to link:   DC c   6 O2 with   DG B  11 N1, Saenger class: 22
Warning! O2 atom is missing from residue   DC c   6  
  Was trying to link:   DC c   6 O2 with   DG B  11 N2, Saenger class: 19
Warning! O2 atom is missing from residue   DC c   6  
  Was trying to link:   DC c   6 O2 with   DG B  11 N1, Saenger class: 22
Warning! O2 atom is missing from residue   DC c   6  
  Was trying to link:   DC c   6 O2 with   DG B  11 N2, Saenger class: 19
Warning! O2 atom is missing from residue   DC c   6  
  Was trying to link:   DC c   6 O2 with   DG B  11 N1, Saenger class: 22
Warning! N2 atom is missing from residue   DG B  12  
  Was trying to link:   DC c   5 O2 with   DG B  12 N2, Saenger class: 19
Warning! N2 atom is missing from residue   DG B  12  
  Was trying to link:   DC c   5 N3 with   DG B  12 N2, Saenger class: 22
    Secondary structure from input PDB file:
      22 helices and 8 sheets defined
      36.7% alpha, 26.4% beta
      11 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 2.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 17
      No H-bonds generated for 'chain 'A' and resid 15 through 17'
    Processing helix  chain 'A' and resid 36 through 48
    Processing helix  chain 'A' and resid 84 through 108
      removed outlier: 3.699A  pdb=" N   HIS A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 165
      removed outlier: 3.535A  pdb=" N   MET A 163 " --> pdb=" O   THR A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 269
      removed outlier: 3.981A  pdb=" N   LYS A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   CYS A 267 " --> pdb=" O   ASN A 263 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 288
      removed outlier: 3.520A  pdb=" N   TRP A 282 " --> pdb=" O   CYS A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 333
      removed outlier: 3.547A  pdb=" N   GLY A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 358 through 373
    Processing helix  chain 'A' and resid 394 through 400
    Processing helix  chain 'A' and resid 400 through 405
    Processing helix  chain 'A' and resid 408 through 413
    Processing helix  chain 'A' and resid 422 through 428
    Processing helix  chain 'A' and resid 432 through 444
    Processing helix  chain 'A' and resid 453 through 468
      removed outlier: 3.828A  pdb=" N   ILE A 457 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 488
    Processing helix  chain 'A' and resid 491 through 508
      removed outlier: 4.077A  pdb=" N   THR A 495 " --> pdb=" O   SER A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 585
    Processing helix  chain 'A' and resid 602 through 613
      removed outlier: 3.865A  pdb=" N   VAL A 606 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLU A 607 " --> pdb=" O   THR A 603 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   HIS A 612 " --> pdb=" O   LYS A 608 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   TYR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 692
    Processing helix  chain 'A' and resid 693 through 695
      No H-bonds generated for 'chain 'A' and resid 693 through 695'
    Processing helix  chain 'A' and resid 706 through 721
      removed outlier: 3.681A  pdb=" N   LEU A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13
      removed outlier: 5.430A  pdb=" N   ILE A 144 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL A 127 " --> pdb=" O   GLN A 122 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLN A 122 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   ILE A 129 " --> pdb=" O   GLN A 120 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN A 120 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   GLU A 131 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54
      removed outlier: 3.700A  pdb=" N   GLU A  74 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 187
    Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311
      removed outlier: 3.712A  pdb=" N   GLU A 653 " --> pdb=" O   ARG A 650 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE A 591 " --> pdb=" O   ASP A 618 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   VAL A 620 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE A 593 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   ILE A 622 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ARG A 595 " --> pdb=" O   ILE A 622 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   LYS A 624 " --> pdb=" O   ARG A 595 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   CYS A 522 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   HIS A 594 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ILE A 524 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   ASP A 596 " --> pdb=" O   ILE A 524 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ILE A 526 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY A 525 " --> pdb=" O   MET A 540 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311
      removed outlier: 3.712A  pdb=" N   GLU A 653 " --> pdb=" O   ARG A 650 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE A 591 " --> pdb=" O   ASP A 618 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   VAL A 620 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE A 593 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   ILE A 622 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ARG A 595 " --> pdb=" O   ILE A 622 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   LYS A 624 " --> pdb=" O   ARG A 595 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   CYS A 522 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   HIS A 594 " --> pdb=" O   CYS A 522 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ILE A 524 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   ASP A 596 " --> pdb=" O   ILE A 524 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ILE A 526 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY A 525 " --> pdb=" O   MET A 540 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   SER A 535 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 559 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323
    Processing sheet with id=AA8, first strand: chain 'A' and resid 379 through 382
      removed outlier: 8.752A  pdb=" N   THR A 416 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   LYS A 342 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   LEU A 418 " --> pdb=" O   LYS A 342 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   SER A 344 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   PHE A 420 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   LEU A 346 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    732 hydrogen bond angles defined for protein.
NA hbond rejected because one of the atoms is absent
    Restraints generated for nucleic acids:
      24 hydrogen bonds
      48 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 2.63

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1589
        1.33 -     1.45: 1367
        1.45 -     1.57: 3415
        1.57 -     1.69: 63
        1.69 -     1.81: 51
  Bond restraints: 6485
  Sorted by residual:
  bond pdb=" P    DT C   7 "
       pdb=" OP3  DT C   7 "
    ideal  model  delta    sigma   weight residual
    1.480  1.601 -0.121 2.00e-02 2.50e+03 3.66e+01
  bond pdb=" P    DT B   1 "
       pdb=" OP3  DT B   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.598 -0.118 2.00e-02 2.50e+03 3.45e+01
  bond pdb=" N   ARG A  41 "
       pdb=" CA  ARG A  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.480 -0.021 1.23e-02 6.61e+03 2.94e+00
  bond pdb=" P    DT C   7 "
       pdb=" OP2  DT C   7 "
    ideal  model  delta    sigma   weight residual
    1.480  1.513 -0.033 2.00e-02 2.50e+03 2.78e+00
  bond pdb=" C3'  DT B  13 "
       pdb=" O3'  DT B  13 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.57e+00
  ... (remaining 6480 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 8753
        1.89 -     3.78: 137
        3.78 -     5.67: 10
        5.67 -     7.55: 2
        7.55 -     9.44: 4
  Bond angle restraints: 8906
  Sorted by residual:
  angle pdb=" N   PRO A 474 "
        pdb=" CA  PRO A 474 "
        pdb=" CB  PRO A 474 "
      ideal   model   delta    sigma   weight residual
     103.25  110.99   -7.74 1.05e+00 9.07e-01 5.43e+01
  angle pdb=" C   ARG A  41 "
        pdb=" CA  ARG A  41 "
        pdb=" CB  ARG A  41 "
      ideal   model   delta    sigma   weight residual
     110.85  118.75   -7.90 1.70e+00 3.46e-01 2.16e+01
  angle pdb=" N   ARG A  41 "
        pdb=" CA  ARG A  41 "
        pdb=" CB  ARG A  41 "
      ideal   model   delta    sigma   weight residual
     110.16  103.75    6.41 1.48e+00 4.57e-01 1.87e+01
  angle pdb=" O5'  DT C   7 "
        pdb=" P    DT C   7 "
        pdb=" OP3  DT C   7 "
      ideal   model   delta    sigma   weight residual
     109.47  100.03    9.44 3.00e+00 1.11e-01 9.91e+00
  angle pdb=" C   HIS A 400 "
        pdb=" N   PHE A 401 "
        pdb=" CA  PHE A 401 "
      ideal   model   delta    sigma   weight residual
     120.82  124.96   -4.14 1.50e+00 4.44e-01 7.61e+00
  ... (remaining 8901 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.90: 3617
       31.90 -    63.81: 160
       63.81 -    95.71: 10
       95.71 -   127.62: 0
      127.62 -   159.52: 2
  Dihedral angle restraints: 3789
    sinusoidal: 1747
      harmonic: 2042
  Sorted by residual:
  dihedral pdb=" C4'  DT B  13 "
           pdb=" C3'  DT B  13 "
           pdb=" O3'  DT B  13 "
           pdb=" P    DT B  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   60.48  159.52     1      3.50e+01 8.16e-04 1.52e+01
  dihedral pdb=" CA  VAL A 157 "
           pdb=" C   VAL A 157 "
           pdb=" N   TYR A 158 "
           pdb=" CA  TYR A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.54   18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" C4'  DT B  16 "
           pdb=" C3'  DT B  16 "
           pdb=" O3'  DT B  16 "
           pdb=" P    DA B  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   84.98  135.02     1      3.50e+01 8.16e-04 1.34e+01
  ... (remaining 3786 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 931
       0.092 -    0.184: 60
       0.184 -    0.275: 1
       0.275 -    0.367: 1
       0.367 -    0.459: 1
  Chirality restraints: 994
  Sorted by residual:
  chirality pdb=" P    DT C   7 "
            pdb=" OP1  DT C   7 "
            pdb=" OP2  DT C   7 "
            pdb=" O5'  DT C   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.80   -0.46 2.00e-01 2.50e+01 5.26e+00
  chirality pdb=" P    DT B   1 "
            pdb=" OP1  DT B   1 "
            pdb=" OP2  DT B   1 "
            pdb=" O5'  DT B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.66   -0.32 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CA  PRO A 474 "
            pdb=" N   PRO A 474 "
            pdb=" C   PRO A 474 "
            pdb=" CB  PRO A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.35e-01
  ... (remaining 991 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT B   1 "    0.025 2.00e-02 2.50e+03   1.30e-02 4.26e+00
        pdb=" N1   DT B   1 "   -0.029 2.00e-02 2.50e+03
        pdb=" C2   DT B   1 "    0.009 2.00e-02 2.50e+03
        pdb=" O2   DT B   1 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DT B   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DT B   1 "    0.001 2.00e-02 2.50e+03
        pdb=" O4   DT B   1 "    0.009 2.00e-02 2.50e+03
        pdb=" C5   DT B   1 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT B   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT B   1 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  41 "   -0.148 9.50e-02 1.11e+02   6.62e-02 2.74e+00
        pdb=" NE  ARG A  41 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  41 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  41 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  41 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C   7 "    0.017 2.00e-02 2.50e+03   9.52e-03 2.27e+00
        pdb=" N1   DT C   7 "   -0.023 2.00e-02 2.50e+03
        pdb=" C2   DT C   7 "    0.006 2.00e-02 2.50e+03
        pdb=" O2   DT C   7 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DT C   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DT C   7 "    0.001 2.00e-02 2.50e+03
        pdb=" O4   DT C   7 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DT C   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT C   7 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DT C   7 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 9
        2.39 -     3.01: 3197
        3.01 -     3.64: 8881
        3.64 -     4.27: 14645
        4.27 -     4.90: 24375
  Nonbonded interactions: 51107
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 713 "
            pdb="MN    MN A 802 "
     model   vdw
     1.758 2.320
  nonbonded pdb=" OP2  DT C   7 "
            pdb="MN    MN A 802 "
     model   vdw
     2.085 2.320
  nonbonded pdb=" OP1  DA B   3 "
            pdb="MN    MN B 101 "
     model   vdw
     2.232 2.320
  nonbonded pdb=" O   GLN A 669 "
            pdb=" O   HOH A 901 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD1 ASP A 618 "
            pdb=" OG1 THR A 677 "
     model   vdw
     2.291 3.040
  ... (remaining 51102 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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.440
  Find NCS groups from input model:        0.050
  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:13.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
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      :  0.004   0.121   6485  Z= 0.219
  Angle     :  0.571   9.442   8906  Z= 0.323
  Chirality :  0.046   0.459    994
  Planarity :  0.004   0.066   1020
  Dihedral  : 16.629 159.524   2469
  Min Nonbonded Distance : 1.758

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.23 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.31), residues: 686
  helix:  0.55 (0.34), residues: 239
  sheet:  1.25 (0.41), residues: 151
  loop : -1.42 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 282 
 HIS   0.005   0.001   HIS A 612 
 PHE   0.019   0.002   PHE A 101 
 TYR   0.011   0.001   TYR A  37 
 ARG   0.004   0.000   ARG A  41 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.679 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 1.3930
  time to fit residues: 165.8696
Evaluate side-chains
  81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0020
   overall best weight:    0.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 GLN
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 534 ASN
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 HIS
A 638 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.175093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.140577 restraints weight = 6203.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.25
r_work: 0.3259 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6485  Z= 0.171
  Angle     :  0.509   4.714   8906  Z= 0.285
  Chirality :  0.042   0.152    994
  Planarity :  0.004   0.035   1020
  Dihedral  : 16.338 158.901   1106
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 10.02 %
    Favored  : 87.36 %
  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:  0.12 (0.32), residues: 686
  helix:  0.91 (0.35), residues: 237
  sheet:  1.26 (0.40), residues: 152
  loop : -1.28 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 282 
 HIS   0.003   0.000   HIS A 320 
 PHE   0.011   0.001   PHE A 351 
 TYR   0.013   0.001   TYR A 158 
 ARG   0.008   0.000   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8285 (mm)
REVERT: A  330 MET cc_start: 0.8561 (mmp) cc_final: 0.8176 (mmt)
REVERT: A  534 ASN cc_start: 0.7429 (m-40) cc_final: 0.7194 (m110)
  outliers start: 16
  outliers final: 3
  residues processed: 89
  average time/residue: 1.2830
  time to fit residues: 119.9606
Evaluate side-chains
  78 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  140 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0870
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0770
   chunk 42 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.3720

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.171658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.132687 restraints weight = 6225.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.45
r_work: 0.3235 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6485  Z= 0.242
  Angle     :  0.543   5.255   8906  Z= 0.301
  Chirality :  0.043   0.157    994
  Planarity :  0.004   0.033   1020
  Dihedral  : 16.461 163.257   1106
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.15 %
    Favored  : 85.22 %
  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:  0.10 (0.32), residues: 686
  helix:  0.96 (0.35), residues: 238
  sheet:  1.15 (0.41), residues: 151
  loop : -1.27 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 599 
 HIS   0.003   0.001   HIS A 320 
 PHE   0.014   0.002   PHE A 351 
 TYR   0.016   0.001   TYR A 158 
 ARG   0.008   0.000   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.517 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7231 (mt0)
REVERT: A  140 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8121 (pt)
REVERT: A  534 ASN cc_start: 0.7465 (m-40) cc_final: 0.7252 (m110)
REVERT: A  653 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8144 (mt-10)
  outliers start: 16
  outliers final: 4
  residues processed: 89
  average time/residue: 1.2406
  time to fit residues: 116.0801
Evaluate side-chains
  84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  653 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0070
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.7802

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.173605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.135351 restraints weight = 6346.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.43
r_work: 0.3265 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6485  Z= 0.172
  Angle     :  0.507   5.470   8906  Z= 0.279
  Chirality :  0.041   0.147    994
  Planarity :  0.003   0.032   1020
  Dihedral  : 16.418 163.272   1106
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.12 %
    Favored  : 83.09 %
  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:  0.28 (0.33), residues: 686
  helix:  1.20 (0.35), residues: 240
  sheet:  1.21 (0.41), residues: 151
  loop : -1.25 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 282 
 HIS   0.002   0.000   HIS A 320 
 PHE   0.011   0.001   PHE A 101 
 TYR   0.011   0.001   TYR A  37 
 ARG   0.009   0.000   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7251 (mt0)
REVERT: A  174 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6593 (ttm)
REVERT: A  534 ASN cc_start: 0.7458 (m-40) cc_final: 0.7250 (m110)
REVERT: A  653 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7986 (mt-10)
  outliers start: 17
  outliers final: 4
  residues processed: 86
  average time/residue: 1.2969
  time to fit residues: 117.5568
Evaluate side-chains
  82 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  653 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** 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 = 0.3925 r_free = 0.3925 target = 0.168101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.140059 restraints weight = 6273.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.97
r_work: 0.3159 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   6485  Z= 0.407
  Angle     :  0.651   7.254   8906  Z= 0.352
  Chirality :  0.047   0.155    994
  Planarity :  0.004   0.037   1020
  Dihedral  : 16.761 165.183   1106
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 14.29 %
    Favored  : 81.94 %
  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: -0.06 (0.32), residues: 686
  helix:  0.82 (0.34), residues: 235
  sheet:  1.23 (0.42), residues: 137
  loop : -1.33 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 599 
 HIS   0.004   0.001   HIS A 320 
 PHE   0.017   0.002   PHE A 351 
 TYR   0.010   0.002   TYR A 158 
 ARG   0.008   0.001   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7227 (mt0)
REVERT: A   80 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7608 (tt)
REVERT: A  140 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8091 (pt)
REVERT: A  638 ASN cc_start: 0.8544 (m-40) cc_final: 0.8275 (m110)
REVERT: A  653 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8289 (mt-10)
  outliers start: 23
  outliers final: 8
  residues processed: 87
  average time/residue: 1.2065
  time to fit residues: 110.4302
Evaluate side-chains
  86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  653 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0170
   chunk 37 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.8620

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.172145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.133908 restraints weight = 6224.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.40
r_work: 0.3271 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6485  Z= 0.184
  Angle     :  0.528   7.878   8906  Z= 0.290
  Chirality :  0.042   0.150    994
  Planarity :  0.003   0.036   1020
  Dihedral  : 16.557 164.503   1106
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.75 %
    Favored  : 80.62 %
  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:  0.21 (0.32), residues: 686
  helix:  1.22 (0.35), residues: 237
  sheet:  1.10 (0.40), residues: 152
  loop : -1.31 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 282 
 HIS   0.002   0.000   HIS A 696 
 PHE   0.014   0.001   PHE A 101 
 TYR   0.012   0.001   TYR A 158 
 ARG   0.010   0.000   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7318 (mt0)
REVERT: A  653 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8142 (mt-10)
  outliers start: 16
  outliers final: 4
  residues processed: 88
  average time/residue: 1.2661
  time to fit residues: 117.3720
Evaluate side-chains
  81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  653 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 68 optimal weight:    0.3980
   chunk 65 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.170010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.131052 restraints weight = 6217.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.55
r_work: 0.3208 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6485  Z= 0.275
  Angle     :  0.591   8.602   8906  Z= 0.320
  Chirality :  0.043   0.155    994
  Planarity :  0.004   0.038   1020
  Dihedral  : 16.658 165.474   1106
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.24 %
    Favored  : 80.30 %
  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:  0.11 (0.32), residues: 686
  helix:  1.12 (0.35), residues: 235
  sheet:  1.24 (0.42), residues: 137
  loop : -1.32 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 599 
 HIS   0.003   0.001   HIS A 320 
 PHE   0.013   0.002   PHE A 736 
 TYR   0.009   0.001   TYR A 158 
 ARG   0.009   0.000   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7181 (mt0)
REVERT: A  140 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8117 (pt)
REVERT: A  653 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8175 (mt-10)
REVERT: A  680 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8641 (mp)
  outliers start: 15
  outliers final: 7
  residues processed: 84
  average time/residue: 1.1691
  time to fit residues: 103.7025
Evaluate side-chains
  84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  680 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0670
   chunk 50 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0570
   overall best weight:    0.7838

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

Flipped N/Q/H residues before XYZ refinement:
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.172870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.134536 restraints weight = 6240.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.40
r_work: 0.3273 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6485  Z= 0.178
  Angle     :  0.540   9.330   8906  Z= 0.293
  Chirality :  0.041   0.147    994
  Planarity :  0.003   0.036   1020
  Dihedral  : 16.556 164.777   1106
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 18.56 %
    Favored  : 79.64 %
  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:  0.25 (0.32), residues: 686
  helix:  1.29 (0.36), residues: 237
  sheet:  1.32 (0.42), residues: 137
  loop : -1.31 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 282 
 HIS   0.002   0.000   HIS A 696 
 PHE   0.013   0.001   PHE A 101 
 TYR   0.009   0.001   TYR A 158 
 ARG   0.009   0.000   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7327 (mt0)
REVERT: A  174 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.5825 (tpt)
REVERT: A  653 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8166 (mt-10)
REVERT: A  680 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8603 (mp)
  outliers start: 11
  outliers final: 5
  residues processed: 83
  average time/residue: 1.1286
  time to fit residues: 98.8410
Evaluate side-chains
  84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  680 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 61 optimal weight:    0.5980
   chunk 51 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0570
   overall best weight:    0.9304

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

Flipped N/Q/H residues before XYZ refinement:
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.171657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145239 restraints weight = 6212.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 1.85
r_work: 0.3233 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6485  Z= 0.193
  Angle     :  0.552   9.519   8906  Z= 0.297
  Chirality :  0.042   0.149    994
  Planarity :  0.003   0.037   1020
  Dihedral  : 16.564 165.063   1106
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.23 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.32), residues: 686
  helix:  1.31 (0.35), residues: 237
  sheet:  1.32 (0.42), residues: 137
  loop : -1.29 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 599 
 HIS   0.002   0.000   HIS A 696 
 PHE   0.013   0.001   PHE A 101 
 TYR   0.008   0.001   TYR A 158 
 ARG   0.010   0.000   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7201 (mt0)
REVERT: A  174 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.5969 (tpt)
REVERT: A  653 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8090 (mt-10)
REVERT: A  680 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8598 (mp)
  outliers start: 15
  outliers final: 8
  residues processed: 83
  average time/residue: 1.0909
  time to fit residues: 95.8737
Evaluate side-chains
  85 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  156 TYR
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  680 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0570
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.184306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.159485 restraints weight = 6621.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 1.78
r_work: 0.3381 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6485  Z= 0.177
  Angle     :  0.550   9.957   8906  Z= 0.295
  Chirality :  0.041   0.146    994
  Planarity :  0.003   0.036   1020
  Dihedral  : 16.456 164.944   1106
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.38 %
    Favored  : 79.15 %
  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:  0.34 (0.32), residues: 686
  helix:  1.38 (0.36), residues: 237
  sheet:  1.35 (0.42), residues: 137
  loop : -1.25 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 282 
 HIS   0.002   0.000   HIS A 320 
 PHE   0.013   0.001   PHE A 101 
 TYR   0.008   0.001   TYR A 352 
 ARG   0.010   0.000   ARG A  11 

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

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

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1372 Ramachandran restraints generated.
    686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.663 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7232 (mt0)
REVERT: A  174 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6017 (tpt)
REVERT: A  653 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7961 (mt-10)
REVERT: A  680 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8537 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 77
  average time/residue: 1.1531
  time to fit residues: 94.0457
Evaluate side-chains
  83 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  680 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.171043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.143977 restraints weight = 6352.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.91
r_work: 0.3210 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6485  Z= 0.257
  Angle     :  0.593   9.942   8906  Z= 0.318
  Chirality :  0.043   0.153    994
  Planarity :  0.004   0.037   1020
  Dihedral  : 16.594 165.460   1106
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.72 %
    Favored  : 79.15 %
  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:  0.21 (0.32), residues: 686
  helix:  1.22 (0.35), residues: 236
  sheet:  1.28 (0.42), residues: 137
  loop : -1.27 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 599 
 HIS   0.002   0.001   HIS A 320 
 PHE   0.012   0.002   PHE A 736 
 TYR   0.007   0.001   TYR A 440 
 ARG   0.009   0.000   ARG A  11 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4419.58 seconds
wall clock time: 78 minutes 49.26 seconds (4729.26 seconds total)