Starting phenix.real_space_refine
on Sat Aug 23 08:38:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xk3_38414/08_2025/8xk3_38414.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xk3_38414/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xk3_38414/08_2025/8xk3_38414.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xk3_38414/08_2025/8xk3_38414.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xk3_38414/08_2025/8xk3_38414.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xk3_38414/08_2025/8xk3_38414.map"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1}
          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: 1.62, per 1000 atoms: 0.26
  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: 0.52
  Conformation dependent library (CDL) restraints added in 334.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.58
  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: 1.37

  Time building geometry restraints manager: 0.71 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:             1.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.840
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:8.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.170
-------------------------------------------------------------------------------
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= 0.176
  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 : 5.06
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG A  41 
 TYR   0.011   0.001   TYR A  37 
 PHE   0.019   0.002   PHE A 101 
 TRP   0.007   0.001   TRP A 282 
 HIS   0.005   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6485)
  covalent geometry    : angle       0.57060 ( 8906)
  hydrogen bonds       : bond        0.16319 (  260)
  hydrogen bonds       : angle       6.82605 (  780)

*********************** 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  : 0.189 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.5758
  time to fit residues: 68.3648
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  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 638 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.170775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.133479 restraints weight = 6261.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.42
r_work: 0.3200 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6485  Z= 0.194
  Angle     :  0.586   5.115   8906  Z= 0.324
  Chirality :  0.044   0.162    994
  Planarity :  0.004   0.035   1020
  Dihedral  : 16.532 161.977   1106
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 10.84 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.32), residues: 686
  helix:  0.72 (0.35), residues: 237
  sheet:  1.14 (0.41), residues: 152
  loop : -1.34 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  11 
 TYR   0.019   0.001   TYR A 158 
 PHE   0.017   0.002   PHE A 351 
 TRP   0.008   0.001   TRP A 599 
 HIS   0.003   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 6485)
  covalent geometry    : angle       0.58560 ( 8906)
  hydrogen bonds       : bond        0.04915 (  260)
  hydrogen bonds       : angle       4.85354 (  780)

*********************** 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
  95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   41 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7383 (mtt-85)
REVERT: A   55 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7163 (mt0)
REVERT: A  140 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8112 (pt)
REVERT: A  534 ASN cc_start: 0.7479 (m-40) cc_final: 0.7255 (m110)
  outliers start: 18
  outliers final: 4
  residues processed: 86
  average time/residue: 0.4984
  time to fit residues: 44.8904
Evaluate side-chains
  79 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   41 ARG
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  262 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.171461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.132508 restraints weight = 6236.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.51
r_work: 0.3240 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6485  Z= 0.156
  Angle     :  0.541   5.311   8906  Z= 0.299
  Chirality :  0.043   0.156    994
  Planarity :  0.004   0.034   1020
  Dihedral  : 16.532 163.631   1106
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 11.82 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.32), residues: 686
  helix:  0.95 (0.35), residues: 236
  sheet:  1.08 (0.41), residues: 152
  loop : -1.37 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  11 
 TYR   0.015   0.001   TYR A 158 
 PHE   0.012   0.002   PHE A 351 
 TRP   0.008   0.001   TRP A 599 
 HIS   0.002   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6485)
  covalent geometry    : angle       0.54123 ( 8906)
  hydrogen bonds       : bond        0.04327 (  260)
  hydrogen bonds       : angle       4.55950 (  780)

*********************** 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
  102 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  130 TYR cc_start: 0.7678 (m-80) cc_final: 0.6375 (m-80)
REVERT: A  140 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8106 (pt)
REVERT: A  534 ASN cc_start: 0.7450 (m-40) cc_final: 0.7249 (m110)
REVERT: A  653 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8118 (mt-10)
  outliers start: 21
  outliers final: 3
  residues processed: 90
  average time/residue: 0.6025
  time to fit residues: 56.7541
Evaluate side-chains
  82 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  653 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.171288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.144052 restraints weight = 6249.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.91
r_work: 0.3213 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6485  Z= 0.157
  Angle     :  0.546   6.534   8906  Z= 0.300
  Chirality :  0.043   0.154    994
  Planarity :  0.004   0.034   1020
  Dihedral  : 16.559 164.312   1106
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 14.12 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.32), residues: 686
  helix:  1.11 (0.35), residues: 238
  sheet:  0.98 (0.40), residues: 157
  loop : -1.44 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  11 
 TYR   0.010   0.001   TYR A  37 
 PHE   0.011   0.002   PHE A 351 
 TRP   0.008   0.001   TRP A 599 
 HIS   0.002   0.001   HIS A 696 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6485)
  covalent geometry    : angle       0.54603 ( 8906)
  hydrogen bonds       : bond        0.04228 (  260)
  hydrogen bonds       : angle       4.45922 (  780)

*********************** 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
  97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8136 (t80) cc_final: 0.7715 (t80)
REVERT: A   41 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7321 (mtt-85)
REVERT: A   55 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7253 (mt0)
REVERT: A  130 TYR cc_start: 0.7751 (m-80) cc_final: 0.6483 (m-80)
REVERT: A  140 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8079 (pt)
REVERT: A  653 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8131 (mt-10)
  outliers start: 20
  outliers final: 6
  residues processed: 87
  average time/residue: 0.5599
  time to fit residues: 51.1416
Evaluate side-chains
  85 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLU
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  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  653 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 467 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.172155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.145054 restraints weight = 6285.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 1.91
r_work: 0.3219 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2227

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= 0.143
  Angle     :  0.538   7.150   8906  Z= 0.294
  Chirality :  0.042   0.151    994
  Planarity :  0.004   0.037   1020
  Dihedral  : 16.524 164.384   1106
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.76 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.32), residues: 686
  helix:  1.22 (0.35), residues: 238
  sheet:  1.09 (0.41), residues: 151
  loop : -1.36 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  11 
 TYR   0.011   0.001   TYR A 158 
 PHE   0.012   0.001   PHE A 101 
 TRP   0.008   0.001   TRP A 599 
 HIS   0.002   0.000   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6485)
  covalent geometry    : angle       0.53777 ( 8906)
  hydrogen bonds       : bond        0.03941 (  260)
  hydrogen bonds       : angle       4.36375 (  780)

*********************** 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
  97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7245 (mt0)
REVERT: A  130 TYR cc_start: 0.7714 (m-80) cc_final: 0.6421 (m-80)
REVERT: A  140 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8061 (pt)
REVERT: A  653 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8108 (mt-10)
REVERT: A  680 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8602 (mp)
  outliers start: 18
  outliers final: 6
  residues processed: 87
  average time/residue: 0.5292
  time to fit residues: 48.5021
Evaluate side-chains
  85 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
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  653 GLU
Chi-restraints excluded: chain A residue  680 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 59 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0470
   chunk 37 optimal weight:    0.4980
   chunk 54 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 13 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.174487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.140633 restraints weight = 6266.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.24
r_work: 0.3275 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6485  Z= 0.111
  Angle     :  0.509   8.096   8906  Z= 0.279
  Chirality :  0.041   0.143    994
  Planarity :  0.003   0.035   1020
  Dihedral  : 16.374 164.161   1106
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.08 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.33), residues: 686
  helix:  1.37 (0.35), residues: 240
  sheet:  1.21 (0.41), residues: 151
  loop : -1.30 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  11 
 TYR   0.009   0.001   TYR A 158 
 PHE   0.014   0.001   PHE A 101 
 TRP   0.008   0.001   TRP A 282 
 HIS   0.002   0.000   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6485)
  covalent geometry    : angle       0.50908 ( 8906)
  hydrogen bonds       : bond        0.03216 (  260)
  hydrogen bonds       : angle       4.17329 (  780)

*********************** 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
  92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7198 (mt0)
  outliers start: 14
  outliers final: 3
  residues processed: 86
  average time/residue: 0.5072
  time to fit residues: 46.0351
Evaluate side-chains
  79 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  262 LEU
Chi-restraints excluded: chain A residue  384 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.166982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.139340 restraints weight = 6267.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 1.93
r_work: 0.3153 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.077   6485  Z= 0.296
  Angle     :  0.690   8.905   8906  Z= 0.370
  Chirality :  0.048   0.160    994
  Planarity :  0.005   0.040   1020
  Dihedral  : 16.864 165.778   1106
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.32), residues: 686
  helix:  0.83 (0.34), residues: 235
  sheet:  1.23 (0.43), residues: 131
  loop : -1.38 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  11 
 TYR   0.011   0.002   TYR A 158 
 PHE   0.019   0.002   PHE A 736 
 TRP   0.008   0.002   TRP A 599 
 HIS   0.004   0.001   HIS A 696 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 ( 6485)
  covalent geometry    : angle       0.69021 ( 8906)
  hydrogen bonds       : bond        0.05702 (  260)
  hydrogen bonds       : angle       4.74331 (  780)

*********************** 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
  92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7255 (mt0)
REVERT: A  680 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8711 (mp)
  outliers start: 15
  outliers final: 5
  residues processed: 85
  average time/residue: 0.6228
  time to fit residues: 55.6827
Evaluate side-chains
  81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
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  262 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  545 SER
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 10 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3965 r_free = 0.3965 target = 0.171802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.133233 restraints weight = 6265.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.48
r_work: 0.3239 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2458

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= 0.131
  Angle     :  0.550   9.172   8906  Z= 0.300
  Chirality :  0.042   0.152    994
  Planarity :  0.003   0.038   1020
  Dihedral  : 16.687 165.140   1106
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.72 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.32), residues: 686
  helix:  1.18 (0.35), residues: 237
  sheet:  1.19 (0.42), residues: 137
  loop : -1.35 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  11 
 TYR   0.011   0.001   TYR A 158 
 PHE   0.021   0.001   PHE A 397 
 TRP   0.009   0.001   TRP A 282 
 HIS   0.002   0.000   HIS A 696 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6485)
  covalent geometry    : angle       0.55019 ( 8906)
  hydrogen bonds       : bond        0.03753 (  260)
  hydrogen bonds       : angle       4.38851 (  780)

*********************** 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
  89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   41 ARG cc_start: 0.7556 (mmt90) cc_final: 0.7145 (mmt180)
REVERT: A   55 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7211 (mt0)
REVERT: A  140 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8078 (pt)
REVERT: A  680 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8565 (mp)
  outliers start: 14
  outliers final: 6
  residues processed: 83
  average time/residue: 0.5541
  time to fit residues: 48.5239
Evaluate side-chains
  80 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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  140 ILE
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  680 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.169087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.141727 restraints weight = 6305.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.89
r_work: 0.3189 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6485  Z= 0.212
  Angle     :  0.623   9.889   8906  Z= 0.336
  Chirality :  0.045   0.155    994
  Planarity :  0.004   0.039   1020
  Dihedral  : 16.842 165.850   1106
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.81 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.05 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.32), residues: 686
  helix:  1.03 (0.35), residues: 235
  sheet:  1.07 (0.42), residues: 137
  loop : -1.35 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  11 
 TYR   0.010   0.001   TYR A 158 
 PHE   0.015   0.002   PHE A 736 
 TRP   0.009   0.001   TRP A 599 
 HIS   0.003   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 6485)
  covalent geometry    : angle       0.62345 ( 8906)
  hydrogen bonds       : bond        0.04755 (  260)
  hydrogen bonds       : angle       4.57196 (  780)

*********************** 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
  87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7225 (mt0)
REVERT: A  140 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8108 (pt)
REVERT: A  680 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8674 (mp)
  outliers start: 12
  outliers final: 7
  residues processed: 81
  average time/residue: 0.5844
  time to fit residues: 49.9588
Evaluate side-chains
  83 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  140 ILE
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  605 LEU
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 50 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0070
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.6600

-------------------------------------------------------------------------------
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 = 0.172717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.134404 restraints weight = 6209.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.45
r_work: 0.3264 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6485  Z= 0.122
  Angle     :  0.549   9.956   8906  Z= 0.297
  Chirality :  0.041   0.148    994
  Planarity :  0.003   0.037   1020
  Dihedral  : 16.592 165.178   1106
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.79 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.32), residues: 686
  helix:  1.32 (0.35), residues: 236
  sheet:  1.22 (0.42), residues: 137
  loop : -1.31 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  11 
 TYR   0.009   0.001   TYR A 158 
 PHE   0.016   0.001   PHE A 101 
 TRP   0.009   0.001   TRP A 282 
 HIS   0.002   0.000   HIS A 696 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6485)
  covalent geometry    : angle       0.54891 ( 8906)
  hydrogen bonds       : bond        0.03479 (  260)
  hydrogen bonds       : angle       4.33561 (  780)

********************** 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  : 0.265 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7198 (mt0)
REVERT: A  140 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8050 (pt)
REVERT: A  680 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8528 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 78
  average time/residue: 0.5396
  time to fit residues: 44.5621
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  : 0.231 
-------------------------------------------------------------------------------
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  140 ILE
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  680 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.171806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135261 restraints weight = 6262.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.33
r_work: 0.3233 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2548

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= 0.137
  Angle     :  0.560   9.938   8906  Z= 0.302
  Chirality :  0.042   0.149    994
  Planarity :  0.004   0.037   1020
  Dihedral  : 16.582 165.540   1106
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.08 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 19.38 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.32), residues: 686
  helix:  1.34 (0.35), residues: 236
  sheet:  1.24 (0.42), residues: 137
  loop : -1.29 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  11 
 TYR   0.008   0.001   TYR A 158 
 PHE   0.015   0.001   PHE A 101 
 TRP   0.009   0.001   TRP A 599 
 HIS   0.002   0.000   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6485)
  covalent geometry    : angle       0.55983 ( 8906)
  hydrogen bonds       : bond        0.03733 (  260)
  hydrogen bonds       : angle       4.34622 (  780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2080.35 seconds
wall clock time: 36 minutes 12.89 seconds (2172.89 seconds total)