Starting phenix.real_space_refine
on Tue Mar 19 08:29:40 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/03_2024/8foz_29357_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/03_2024/8foz_29357.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/03_2024/8foz_29357.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/03_2024/8foz_29357.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/03_2024/8foz_29357_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foz_29357/03_2024/8foz_29357_updated.pdb"
  }
  resolution = 2.0
  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=   0.227
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      24      5.49       5
     S     144      5.16       5
     C   14832      2.51       5
     N    4040      2.21       5
     O    4608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   16": "OD1" <-> "OD2"
    Residue "A ASP   28": "OD1" <-> "OD2"
    Residue "A ASP   43": "OD1" <-> "OD2"
    Residue "A ASP   50": "OD1" <-> "OD2"
    Residue "A PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  239": "OD1" <-> "OD2"
    Residue "A GLU  254": "OE1" <-> "OE2"
    Residue "A ASP  255": "OD1" <-> "OD2"
    Residue "A ASP  256": "OD1" <-> "OD2"
    Residue "A ASP  269": "OD1" <-> "OD2"
    Residue "A ASP  315": "OD1" <-> "OD2"
    Residue "A ASP  319": "OD1" <-> "OD2"
    Residue "A ARG  356": "NH1" <-> "NH2"
    Residue "A ASP  364": "OD1" <-> "OD2"
    Residue "A GLU  395": "OE1" <-> "OE2"
    Residue "A GLU  399": "OE1" <-> "OE2"
    Residue "A ARG  407": "NH1" <-> "NH2"
    Residue "A ARG  412": "NH1" <-> "NH2"
    Residue "A ASP  418": "OD1" <-> "OD2"
    Residue "A ASP  421": "OD1" <-> "OD2"
    Residue "A ASP  435": "OD1" <-> "OD2"
    Residue "A GLU  487": "OE1" <-> "OE2"
    Residue "A GLU  500": "OE1" <-> "OE2"
    Residue "B ASP   15": "OD1" <-> "OD2"
    Residue "B ASP   16": "OD1" <-> "OD2"
    Residue "B ASP   28": "OD1" <-> "OD2"
    Residue "B ASP   43": "OD1" <-> "OD2"
    Residue "B ASP   50": "OD1" <-> "OD2"
    Residue "B PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  239": "OD1" <-> "OD2"
    Residue "B ASP  255": "OD1" <-> "OD2"
    Residue "B ASP  256": "OD1" <-> "OD2"
    Residue "B ASP  269": "OD1" <-> "OD2"
    Residue "B ASP  315": "OD1" <-> "OD2"
    Residue "B ASP  319": "OD1" <-> "OD2"
    Residue "B ARG  356": "NH1" <-> "NH2"
    Residue "B ASP  364": "OD1" <-> "OD2"
    Residue "B GLU  399": "OE1" <-> "OE2"
    Residue "B ARG  407": "NH1" <-> "NH2"
    Residue "B ARG  412": "NH1" <-> "NH2"
    Residue "B ASP  418": "OD1" <-> "OD2"
    Residue "B ASP  421": "OD1" <-> "OD2"
    Residue "B ASP  435": "OD1" <-> "OD2"
    Residue "B GLU  487": "OE1" <-> "OE2"
    Residue "C ASP   16": "OD1" <-> "OD2"
    Residue "C ASP   28": "OD1" <-> "OD2"
    Residue "C ASP   43": "OD1" <-> "OD2"
    Residue "C ASP   50": "OD1" <-> "OD2"
    Residue "C PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  239": "OD1" <-> "OD2"
    Residue "C GLU  254": "OE1" <-> "OE2"
    Residue "C ASP  255": "OD1" <-> "OD2"
    Residue "C ASP  256": "OD1" <-> "OD2"
    Residue "C ASP  315": "OD1" <-> "OD2"
    Residue "C ASP  319": "OD1" <-> "OD2"
    Residue "C ARG  356": "NH1" <-> "NH2"
    Residue "C ASP  364": "OD1" <-> "OD2"
    Residue "C ARG  407": "NH1" <-> "NH2"
    Residue "C ARG  412": "NH1" <-> "NH2"
    Residue "C ASP  418": "OD1" <-> "OD2"
    Residue "C ASP  421": "OD1" <-> "OD2"
    Residue "C ASP  435": "OD1" <-> "OD2"
    Residue "C GLU  487": "OE1" <-> "OE2"
    Residue "D ASP   15": "OD1" <-> "OD2"
    Residue "D ASP   16": "OD1" <-> "OD2"
    Residue "D ASP   28": "OD1" <-> "OD2"
    Residue "D ASP   43": "OD1" <-> "OD2"
    Residue "D ASP   50": "OD1" <-> "OD2"
    Residue "D PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  103": "OE1" <-> "OE2"
    Residue "D TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  239": "OD1" <-> "OD2"
    Residue "D GLU  254": "OE1" <-> "OE2"
    Residue "D ASP  255": "OD1" <-> "OD2"
    Residue "D ASP  256": "OD1" <-> "OD2"
    Residue "D ASP  269": "OD1" <-> "OD2"
    Residue "D ASP  315": "OD1" <-> "OD2"
    Residue "D ASP  319": "OD1" <-> "OD2"
    Residue "D GLU  335": "OE1" <-> "OE2"
    Residue "D ARG  356": "NH1" <-> "NH2"
    Residue "D ASP  364": "OD1" <-> "OD2"
    Residue "D GLU  399": "OE1" <-> "OE2"
    Residue "D ARG  407": "NH1" <-> "NH2"
    Residue "D ARG  412": "NH1" <-> "NH2"
    Residue "D ASP  418": "OD1" <-> "OD2"
    Residue "D ASP  421": "OD1" <-> "OD2"
    Residue "D ASP  435": "OD1" <-> "OD2"
    Residue "D GLU  487": "OE1" <-> "OE2"
    Residue "D GLU  491": "OE1" <-> "OE2"
    Residue "E ASP   15": "OD1" <-> "OD2"
    Residue "E ASP   16": "OD1" <-> "OD2"
    Residue "E ASP   28": "OD1" <-> "OD2"
    Residue "E ASP   34": "OD1" <-> "OD2"
    Residue "E ASP   43": "OD1" <-> "OD2"
    Residue "E ASP   50": "OD1" <-> "OD2"
    Residue "E GLU   75": "OE1" <-> "OE2"
    Residue "E PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU   98": "OE1" <-> "OE2"
    Residue "E TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  239": "OD1" <-> "OD2"
    Residue "E GLU  254": "OE1" <-> "OE2"
    Residue "E ASP  255": "OD1" <-> "OD2"
    Residue "E ASP  256": "OD1" <-> "OD2"
    Residue "E ASP  269": "OD1" <-> "OD2"
    Residue "E ASP  315": "OD1" <-> "OD2"
    Residue "E ASP  319": "OD1" <-> "OD2"
    Residue "E ARG  356": "NH1" <-> "NH2"
    Residue "E ASP  364": "OD1" <-> "OD2"
    Residue "E GLU  395": "OE1" <-> "OE2"
    Residue "E ARG  407": "NH1" <-> "NH2"
    Residue "E ARG  412": "NH1" <-> "NH2"
    Residue "E ASP  418": "OD1" <-> "OD2"
    Residue "E ASP  421": "OD1" <-> "OD2"
    Residue "E ASP  435": "OD1" <-> "OD2"
    Residue "E GLU  487": "OE1" <-> "OE2"
    Residue "F ASP   16": "OD1" <-> "OD2"
    Residue "F ASP   28": "OD1" <-> "OD2"
    Residue "F ASP   43": "OD1" <-> "OD2"
    Residue "F ASP   50": "OD1" <-> "OD2"
    Residue "F PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  239": "OD1" <-> "OD2"
    Residue "F GLU  254": "OE1" <-> "OE2"
    Residue "F ASP  255": "OD1" <-> "OD2"
    Residue "F ASP  256": "OD1" <-> "OD2"
    Residue "F ASP  269": "OD1" <-> "OD2"
    Residue "F ASP  315": "OD1" <-> "OD2"
    Residue "F ASP  319": "OD1" <-> "OD2"
    Residue "F ARG  356": "NH1" <-> "NH2"
    Residue "F ASP  364": "OD1" <-> "OD2"
    Residue "F GLU  399": "OE1" <-> "OE2"
    Residue "F ARG  407": "NH1" <-> "NH2"
    Residue "F ARG  412": "NH1" <-> "NH2"
    Residue "F ASP  418": "OD1" <-> "OD2"
    Residue "F ASP  421": "OD1" <-> "OD2"
    Residue "F ASP  435": "OD1" <-> "OD2"
    Residue "F GLU  487": "OE1" <-> "OE2"
    Residue "G ASP   15": "OD1" <-> "OD2"
    Residue "G ASP   16": "OD1" <-> "OD2"
    Residue "G ASP   28": "OD1" <-> "OD2"
    Residue "G ASP   43": "OD1" <-> "OD2"
    Residue "G ASP   50": "OD1" <-> "OD2"
    Residue "G PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  103": "OE1" <-> "OE2"
    Residue "G TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP  239": "OD1" <-> "OD2"
    Residue "G GLU  254": "OE1" <-> "OE2"
    Residue "G ASP  255": "OD1" <-> "OD2"
    Residue "G ASP  256": "OD1" <-> "OD2"
    Residue "G ASP  269": "OD1" <-> "OD2"
    Residue "G ASP  292": "OD1" <-> "OD2"
    Residue "G ASP  315": "OD1" <-> "OD2"
    Residue "G ASP  319": "OD1" <-> "OD2"
    Residue "G ARG  356": "NH1" <-> "NH2"
    Residue "G ASP  364": "OD1" <-> "OD2"
    Residue "G GLU  399": "OE1" <-> "OE2"
    Residue "G ARG  407": "NH1" <-> "NH2"
    Residue "G ARG  412": "NH1" <-> "NH2"
    Residue "G ASP  421": "OD1" <-> "OD2"
    Residue "G ASP  435": "OD1" <-> "OD2"
    Residue "G GLU  487": "OE1" <-> "OE2"
    Residue "H ASP   16": "OD1" <-> "OD2"
    Residue "H ASP   28": "OD1" <-> "OD2"
    Residue "H ASP   34": "OD1" <-> "OD2"
    Residue "H ASP   43": "OD1" <-> "OD2"
    Residue "H ASP   50": "OD1" <-> "OD2"
    Residue "H GLU   75": "OE1" <-> "OE2"
    Residue "H PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP  239": "OD1" <-> "OD2"
    Residue "H ASP  255": "OD1" <-> "OD2"
    Residue "H ASP  256": "OD1" <-> "OD2"
    Residue "H ASP  269": "OD1" <-> "OD2"
    Residue "H ASP  315": "OD1" <-> "OD2"
    Residue "H ASP  319": "OD1" <-> "OD2"
    Residue "H ARG  356": "NH1" <-> "NH2"
    Residue "H ASP  364": "OD1" <-> "OD2"
    Residue "H GLU  395": "OE1" <-> "OE2"
    Residue "H GLU  399": "OE1" <-> "OE2"
    Residue "H ARG  407": "NH1" <-> "NH2"
    Residue "H ARG  412": "NH1" <-> "NH2"
    Residue "H ASP  418": "OD1" <-> "OD2"
    Residue "H ASP  421": "OD1" <-> "OD2"
    Residue "H ASP  435": "OD1" <-> "OD2"
    Residue "H GLU  487": "OE1" <-> "OE2"
    Residue "H GLU  500": "OE1" <-> "OE2"
  Time to flip residues: 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 23648
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 2889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2889
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2889
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2889
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2889
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 2889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2889
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 2889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2889
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 2889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2889
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 2889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2889
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'NAD': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'NAD': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'NAD': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'NAD': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'NAD': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'NAD': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'NAD': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 1}
    Chain: "H"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'NAD': 1}
          Classifications: {'RNA': 1, 'undetermined': 1}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 12.29, per 1000 atoms: 0.52
  Number of scatterers: 23648
  At special positions: 0
  Unit cell: (122.235, 122.235, 120.549, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     144     16.00
     P      24     15.00
     O    4608      8.00
     N    4040      7.00
     C   14832      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  - 3.50
        Amino acid           : False - 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=8, symmetry=0
  Number of additional bonds: simple=8, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 9.74
  Conformation dependent library (CDL) restraints added in 4.1 seconds
  

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5520

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      130 helices and 32 sheets defined
      37.7% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 4.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 5
      No H-bonds generated for 'chain 'A' and resid 2 through 5'
    Processing helix  chain 'A' and resid 20 through 25
    Processing helix  chain 'A' and resid 32 through 34
      No H-bonds generated for 'chain 'A' and resid 32 through 34'
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 76 through 84
    Processing helix  chain 'A' and resid 97 through 109
    Processing helix  chain 'A' and resid 254 through 266
    Processing helix  chain 'A' and resid 281 through 293
    Processing helix  chain 'A' and resid 307 through 316
      removed outlier: 3.534A  pdb=" N   ASN A 312 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 337
    Processing helix  chain 'A' and resid 343 through 357
      removed outlier: 4.026A  pdb=" N   ARG A 356 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   PHE A 357 " --> pdb=" O   TYR A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 378
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 453 through 471
      Proline residue:  A 458  - end of helix
    Processing helix  chain 'A' and resid 476 through 484
    Processing helix  chain 'A' and resid 495 through 501
    Processing helix  chain 'B' and resid 2 through 5
      No H-bonds generated for 'chain 'B' and resid 2 through 5'
    Processing helix  chain 'B' and resid 20 through 25
    Processing helix  chain 'B' and resid 32 through 34
      No H-bonds generated for 'chain 'B' and resid 32 through 34'
    Processing helix  chain 'B' and resid 46 through 48
      No H-bonds generated for 'chain 'B' and resid 46 through 48'
    Processing helix  chain 'B' and resid 76 through 84
    Processing helix  chain 'B' and resid 97 through 109
    Processing helix  chain 'B' and resid 254 through 266
    Processing helix  chain 'B' and resid 281 through 293
    Processing helix  chain 'B' and resid 307 through 316
      removed outlier: 3.542A  pdb=" N   ASN B 312 " --> pdb=" O   ALA B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 337
    Processing helix  chain 'B' and resid 343 through 357
      removed outlier: 4.026A  pdb=" N   ARG B 356 " --> pdb=" O   GLU B 352 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE B 357 " --> pdb=" O   TYR B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 378
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 453 through 471
      Proline residue:  B 458  - end of helix
    Processing helix  chain 'B' and resid 476 through 484
    Processing helix  chain 'B' and resid 495 through 501
    Processing helix  chain 'C' and resid 2 through 5
      No H-bonds generated for 'chain 'C' and resid 2 through 5'
    Processing helix  chain 'C' and resid 20 through 25
    Processing helix  chain 'C' and resid 32 through 34
      No H-bonds generated for 'chain 'C' and resid 32 through 34'
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'C' and resid 76 through 84
    Processing helix  chain 'C' and resid 97 through 109
    Processing helix  chain 'C' and resid 254 through 266
    Processing helix  chain 'C' and resid 281 through 293
    Processing helix  chain 'C' and resid 307 through 316
      removed outlier: 3.538A  pdb=" N   ASN C 312 " --> pdb=" O   ALA C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 337
    Processing helix  chain 'C' and resid 343 through 357
      removed outlier: 4.026A  pdb=" N   ARG C 356 " --> pdb=" O   GLU C 352 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   PHE C 357 " --> pdb=" O   TYR C 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 370 through 378
    Processing helix  chain 'C' and resid 417 through 422
    Processing helix  chain 'C' and resid 453 through 471
      Proline residue:  C 458  - end of helix
    Processing helix  chain 'C' and resid 476 through 484
    Processing helix  chain 'C' and resid 495 through 501
    Processing helix  chain 'D' and resid 2 through 5
      No H-bonds generated for 'chain 'D' and resid 2 through 5'
    Processing helix  chain 'D' and resid 20 through 25
    Processing helix  chain 'D' and resid 32 through 34
      No H-bonds generated for 'chain 'D' and resid 32 through 34'
    Processing helix  chain 'D' and resid 46 through 48
      No H-bonds generated for 'chain 'D' and resid 46 through 48'
    Processing helix  chain 'D' and resid 76 through 84
    Processing helix  chain 'D' and resid 97 through 109
    Processing helix  chain 'D' and resid 254 through 266
    Processing helix  chain 'D' and resid 281 through 293
    Processing helix  chain 'D' and resid 307 through 316
      removed outlier: 3.539A  pdb=" N   ASN D 312 " --> pdb=" O   ALA D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 333 through 337
    Processing helix  chain 'D' and resid 343 through 357
      removed outlier: 4.025A  pdb=" N   ARG D 356 " --> pdb=" O   GLU D 352 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE D 357 " --> pdb=" O   TYR D 353 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 370 through 378
    Processing helix  chain 'D' and resid 388 through 390
      No H-bonds generated for 'chain 'D' and resid 388 through 390'
    Processing helix  chain 'D' and resid 417 through 422
    Processing helix  chain 'D' and resid 453 through 471
      Proline residue:  D 458  - end of helix
    Processing helix  chain 'D' and resid 476 through 484
    Processing helix  chain 'D' and resid 495 through 501
    Processing helix  chain 'E' and resid 2 through 5
      No H-bonds generated for 'chain 'E' and resid 2 through 5'
    Processing helix  chain 'E' and resid 20 through 25
    Processing helix  chain 'E' and resid 32 through 34
      No H-bonds generated for 'chain 'E' and resid 32 through 34'
    Processing helix  chain 'E' and resid 46 through 48
      No H-bonds generated for 'chain 'E' and resid 46 through 48'
    Processing helix  chain 'E' and resid 76 through 84
    Processing helix  chain 'E' and resid 97 through 109
    Processing helix  chain 'E' and resid 254 through 266
    Processing helix  chain 'E' and resid 281 through 293
    Processing helix  chain 'E' and resid 307 through 316
      removed outlier: 3.535A  pdb=" N   ASN E 312 " --> pdb=" O   ALA E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 333 through 337
    Processing helix  chain 'E' and resid 343 through 357
      removed outlier: 4.026A  pdb=" N   ARG E 356 " --> pdb=" O   GLU E 352 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE E 357 " --> pdb=" O   TYR E 353 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 370 through 378
    Processing helix  chain 'E' and resid 417 through 422
    Processing helix  chain 'E' and resid 453 through 471
      Proline residue:  E 458  - end of helix
    Processing helix  chain 'E' and resid 476 through 484
    Processing helix  chain 'E' and resid 495 through 501
    Processing helix  chain 'F' and resid 2 through 5
      No H-bonds generated for 'chain 'F' and resid 2 through 5'
    Processing helix  chain 'F' and resid 20 through 25
    Processing helix  chain 'F' and resid 32 through 34
      No H-bonds generated for 'chain 'F' and resid 32 through 34'
    Processing helix  chain 'F' and resid 46 through 48
      No H-bonds generated for 'chain 'F' and resid 46 through 48'
    Processing helix  chain 'F' and resid 76 through 84
    Processing helix  chain 'F' and resid 97 through 109
    Processing helix  chain 'F' and resid 254 through 266
    Processing helix  chain 'F' and resid 281 through 293
    Processing helix  chain 'F' and resid 307 through 316
      removed outlier: 3.537A  pdb=" N   ASN F 312 " --> pdb=" O   ALA F 308 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 333 through 337
    Processing helix  chain 'F' and resid 343 through 357
      removed outlier: 4.026A  pdb=" N   ARG F 356 " --> pdb=" O   GLU F 352 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   PHE F 357 " --> pdb=" O   TYR F 353 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 370 through 378
    Processing helix  chain 'F' and resid 388 through 390
      No H-bonds generated for 'chain 'F' and resid 388 through 390'
    Processing helix  chain 'F' and resid 417 through 422
    Processing helix  chain 'F' and resid 453 through 471
      Proline residue:  F 458  - end of helix
    Processing helix  chain 'F' and resid 476 through 484
    Processing helix  chain 'F' and resid 495 through 501
    Processing helix  chain 'G' and resid 2 through 5
      No H-bonds generated for 'chain 'G' and resid 2 through 5'
    Processing helix  chain 'G' and resid 20 through 25
    Processing helix  chain 'G' and resid 32 through 34
      No H-bonds generated for 'chain 'G' and resid 32 through 34'
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'G' and resid 76 through 84
    Processing helix  chain 'G' and resid 97 through 109
    Processing helix  chain 'G' and resid 254 through 266
    Processing helix  chain 'G' and resid 281 through 293
    Processing helix  chain 'G' and resid 307 through 316
      removed outlier: 3.541A  pdb=" N   ASN G 312 " --> pdb=" O   ALA G 308 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 333 through 337
    Processing helix  chain 'G' and resid 343 through 357
      removed outlier: 4.025A  pdb=" N   ARG G 356 " --> pdb=" O   GLU G 352 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   PHE G 357 " --> pdb=" O   TYR G 353 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 370 through 378
    Processing helix  chain 'G' and resid 417 through 422
    Processing helix  chain 'G' and resid 453 through 471
      Proline residue:  G 458  - end of helix
    Processing helix  chain 'G' and resid 476 through 484
    Processing helix  chain 'G' and resid 495 through 501
    Processing helix  chain 'H' and resid 2 through 5
      No H-bonds generated for 'chain 'H' and resid 2 through 5'
    Processing helix  chain 'H' and resid 20 through 25
    Processing helix  chain 'H' and resid 32 through 34
      No H-bonds generated for 'chain 'H' and resid 32 through 34'
    Processing helix  chain 'H' and resid 46 through 48
      No H-bonds generated for 'chain 'H' and resid 46 through 48'
    Processing helix  chain 'H' and resid 76 through 84
    Processing helix  chain 'H' and resid 97 through 109
    Processing helix  chain 'H' and resid 254 through 266
    Processing helix  chain 'H' and resid 281 through 293
    Processing helix  chain 'H' and resid 307 through 316
      removed outlier: 3.533A  pdb=" N   ASN H 312 " --> pdb=" O   ALA H 308 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 333 through 337
    Processing helix  chain 'H' and resid 343 through 357
      removed outlier: 4.026A  pdb=" N   ARG H 356 " --> pdb=" O   GLU H 352 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   PHE H 357 " --> pdb=" O   TYR H 353 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 370 through 378
    Processing helix  chain 'H' and resid 417 through 422
    Processing helix  chain 'H' and resid 453 through 471
      Proline residue:  H 458  - end of helix
    Processing helix  chain 'H' and resid 476 through 484
    Processing helix  chain 'H' and resid 495 through 501
    Processing sheet with id=  A, first strand: chain 'A' and resid 35 through 37
    Processing sheet with id=  B, first strand: chain 'A' and resid 65 through 67
      removed outlier: 6.245A  pdb=" N   VAL A 384 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 247 through 250
      removed outlier: 6.586A  pdb=" N   VAL A 270 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   ILE A 250 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   VAL A 272 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   GLN A 298 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   LEU A 273 " --> pdb=" O   GLN A 298 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   ILE A 300 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'A' and resid 401 through 403
      removed outlier: 3.511A  pdb=" N   ILE A 406 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 35 through 37
    Processing sheet with id=  F, first strand: chain 'B' and resid 65 through 67
      removed outlier: 6.246A  pdb=" N   VAL B 384 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 247 through 250
      removed outlier: 6.584A  pdb=" N   VAL B 270 " --> pdb=" O   ALA B 248 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   ILE B 250 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   VAL B 272 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   GLN B 298 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LEU B 273 " --> pdb=" O   GLN B 298 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ILE B 300 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  G
    Processing sheet with id=  H, first strand: chain 'B' and resid 401 through 403
    Processing sheet with id=  I, first strand: chain 'C' and resid 35 through 37
    Processing sheet with id=  J, first strand: chain 'C' and resid 65 through 67
      removed outlier: 6.245A  pdb=" N   VAL C 384 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'C' and resid 247 through 250
      removed outlier: 6.584A  pdb=" N   VAL C 270 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   ILE C 250 " --> pdb=" O   VAL C 270 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL C 272 " --> pdb=" O   ILE C 250 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   GLN C 298 " --> pdb=" O   VAL C 271 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   LEU C 273 " --> pdb=" O   GLN C 298 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ILE C 300 " --> pdb=" O   LEU C 273 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'C' and resid 401 through 403
    Processing sheet with id=  M, first strand: chain 'D' and resid 35 through 37
    Processing sheet with id=  N, first strand: chain 'D' and resid 65 through 67
      removed outlier: 6.245A  pdb=" N   VAL D 384 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'D' and resid 247 through 250
      removed outlier: 6.586A  pdb=" N   VAL D 270 " --> pdb=" O   ALA D 248 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   ILE D 250 " --> pdb=" O   VAL D 270 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL D 272 " --> pdb=" O   ILE D 250 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   GLN D 298 " --> pdb=" O   VAL D 271 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   LEU D 273 " --> pdb=" O   GLN D 298 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ILE D 300 " --> pdb=" O   LEU D 273 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  O
    Processing sheet with id=  P, first strand: chain 'D' and resid 401 through 403
    Processing sheet with id=  Q, first strand: chain 'E' and resid 35 through 37
    Processing sheet with id=  R, first strand: chain 'E' and resid 65 through 67
      removed outlier: 6.245A  pdb=" N   VAL E 384 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'E' and resid 247 through 250
      removed outlier: 6.588A  pdb=" N   VAL E 270 " --> pdb=" O   ALA E 248 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   ILE E 250 " --> pdb=" O   VAL E 270 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL E 272 " --> pdb=" O   ILE E 250 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   GLN E 298 " --> pdb=" O   VAL E 271 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   LEU E 273 " --> pdb=" O   GLN E 298 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ILE E 300 " --> pdb=" O   LEU E 273 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  S
    Processing sheet with id=  T, first strand: chain 'E' and resid 401 through 403
    Processing sheet with id=  U, first strand: chain 'F' and resid 35 through 37
    Processing sheet with id=  V, first strand: chain 'F' and resid 65 through 67
      removed outlier: 6.245A  pdb=" N   VAL F 384 " --> pdb=" O   VAL F  66 " (cutoff:3.500A)
    Processing sheet with id=  W, first strand: chain 'F' and resid 247 through 250
      removed outlier: 6.584A  pdb=" N   VAL F 270 " --> pdb=" O   ALA F 248 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   ILE F 250 " --> pdb=" O   VAL F 270 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL F 272 " --> pdb=" O   ILE F 250 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   GLN F 298 " --> pdb=" O   VAL F 271 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   LEU F 273 " --> pdb=" O   GLN F 298 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ILE F 300 " --> pdb=" O   LEU F 273 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  W
    Processing sheet with id=  X, first strand: chain 'F' and resid 401 through 403
    Processing sheet with id=  Y, first strand: chain 'G' and resid 35 through 37
    Processing sheet with id=  Z, first strand: chain 'G' and resid 65 through 67
      removed outlier: 6.246A  pdb=" N   VAL G 384 " --> pdb=" O   VAL G  66 " (cutoff:3.500A)
    Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 250
      removed outlier: 6.582A  pdb=" N   VAL G 270 " --> pdb=" O   ALA G 248 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   ILE G 250 " --> pdb=" O   VAL G 270 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL G 272 " --> pdb=" O   ILE G 250 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   GLN G 298 " --> pdb=" O   VAL G 271 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   LEU G 273 " --> pdb=" O   GLN G 298 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ILE G 300 " --> pdb=" O   LEU G 273 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AA
    Processing sheet with id= AB, first strand: chain 'G' and resid 401 through 403
    Processing sheet with id= AC, first strand: chain 'H' and resid 35 through 37
    Processing sheet with id= AD, first strand: chain 'H' and resid 65 through 67
      removed outlier: 6.244A  pdb=" N   VAL H 384 " --> pdb=" O   VAL H  66 " (cutoff:3.500A)
    Processing sheet with id= AE, first strand: chain 'H' and resid 247 through 250
      removed outlier: 6.586A  pdb=" N   VAL H 270 " --> pdb=" O   ALA H 248 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   ILE H 250 " --> pdb=" O   VAL H 270 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL H 272 " --> pdb=" O   ILE H 250 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLN H 298 " --> pdb=" O   VAL H 271 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LEU H 273 " --> pdb=" O   GLN H 298 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ILE H 300 " --> pdb=" O   LEU H 273 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AE
    Processing sheet with id= AF, first strand: chain 'H' and resid 401 through 403

    751 hydrogen bonds defined for protein.
    1944 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 7.03

  Time building geometry restraints manager: 10.43 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 3952
        1.30 -     1.43: 5962
        1.43 -     1.56: 13870
        1.56 -     1.69: 40
        1.69 -     1.82: 240
  Bond restraints: 24064
  Sorted by residual:
  bond pdb=" C5  IMP A 601 "
       pdb=" C6  IMP A 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.529 -0.139 2.00e-02 2.50e+03 4.80e+01
  bond pdb=" C5  IMP E 601 "
       pdb=" C6  IMP E 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.528 -0.138 2.00e-02 2.50e+03 4.76e+01
  bond pdb=" C5  IMP H 601 "
       pdb=" C6  IMP H 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.528 -0.138 2.00e-02 2.50e+03 4.76e+01
  bond pdb=" C5  IMP G 601 "
       pdb=" C6  IMP G 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.528 -0.138 2.00e-02 2.50e+03 4.76e+01
  bond pdb=" C5  IMP D 601 "
       pdb=" C6  IMP D 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.528 -0.138 2.00e-02 2.50e+03 4.74e+01
  ... (remaining 24059 not shown)

  Histogram of bond angle deviations from ideal:
       97.12 -   104.89: 475
      104.89 -   112.65: 12504
      112.65 -   120.42: 10300
      120.42 -   128.19: 9155
      128.19 -   135.95: 134
  Bond angle restraints: 32568
  Sorted by residual:
  angle pdb=" N   GLY G   9 "
        pdb=" CA  GLY G   9 "
        pdb=" C   GLY G   9 "
      ideal   model   delta    sigma   weight residual
     110.77  104.64    6.13 1.93e+00 2.68e-01 1.01e+01
  angle pdb=" N   GLY D   9 "
        pdb=" CA  GLY D   9 "
        pdb=" C   GLY D   9 "
      ideal   model   delta    sigma   weight residual
     110.77  104.68    6.09 1.93e+00 2.68e-01 9.97e+00
  angle pdb=" N   GLY H   9 "
        pdb=" CA  GLY H   9 "
        pdb=" C   GLY H   9 "
      ideal   model   delta    sigma   weight residual
     110.77  104.70    6.07 1.93e+00 2.68e-01 9.90e+00
  angle pdb=" N   GLY A   9 "
        pdb=" CA  GLY A   9 "
        pdb=" C   GLY A   9 "
      ideal   model   delta    sigma   weight residual
     110.77  104.76    6.01 1.93e+00 2.68e-01 9.69e+00
  angle pdb=" N   GLY C   9 "
        pdb=" CA  GLY C   9 "
        pdb=" C   GLY C   9 "
      ideal   model   delta    sigma   weight residual
     110.77  104.78    5.99 1.93e+00 2.68e-01 9.64e+00
  ... (remaining 32563 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.09: 13768
       26.09 -    52.18: 757
       52.18 -    78.27: 80
       78.27 -   104.36: 31
      104.36 -   130.45: 4
  Dihedral angle restraints: 14640
    sinusoidal: 5944
      harmonic: 8696
  Sorted by residual:
  dihedral pdb=" C5' IMP H 601 "
           pdb=" O5' IMP H 601 "
           pdb=" P   IMP H 601 "
           pdb=" O2P IMP H 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     191.93   61.48  130.45     1      2.00e+01 2.50e-03 3.96e+01
  dihedral pdb=" C5' IMP F 601 "
           pdb=" O5' IMP F 601 "
           pdb=" P   IMP F 601 "
           pdb=" O2P IMP F 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     191.93   61.65  130.28     1      2.00e+01 2.50e-03 3.95e+01
  dihedral pdb=" C5' IMP G 601 "
           pdb=" O5' IMP G 601 "
           pdb=" P   IMP G 601 "
           pdb=" O2P IMP G 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     191.93   61.69  130.24     1      2.00e+01 2.50e-03 3.95e+01
  ... (remaining 14637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 2735
       0.064 -    0.127: 884
       0.127 -    0.191: 70
       0.191 -    0.254: 15
       0.254 -    0.318: 8
  Chirality restraints: 3712
  Sorted by residual:
  chirality pdb=" CB  VAL E 361 "
            pdb=" CA  VAL E 361 "
            pdb=" CG1 VAL E 361 "
            pdb=" CG2 VAL E 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CB  VAL H 361 "
            pdb=" CA  VAL H 361 "
            pdb=" CG1 VAL H 361 "
            pdb=" CG2 VAL H 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CB  VAL A 361 "
            pdb=" CA  VAL A 361 "
            pdb=" CG1 VAL A 361 "
            pdb=" CG2 VAL A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.46e+00
  ... (remaining 3709 not shown)

  Planarity restraints: 4120
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E   4 "    0.021 2.00e-02 2.50e+03   1.61e-02 5.19e+00
        pdb=" CG  TYR E   4 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR E   4 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR E   4 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR E   4 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR E   4 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR E   4 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR E   4 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D   4 "   -0.021 2.00e-02 2.50e+03   1.60e-02 5.14e+00
        pdb=" CG  TYR D   4 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR D   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR D   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR D   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR D   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR D   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR D   4 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A   4 "   -0.021 2.00e-02 2.50e+03   1.60e-02 5.11e+00
        pdb=" CG  TYR A   4 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR A   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A   4 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 4117 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 4508
        2.77 -     3.30: 22877
        3.30 -     3.84: 41688
        3.84 -     4.37: 51211
        4.37 -     4.90: 83932
  Nonbonded interactions: 204216
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 418 "
            pdb=" NH1 ARG D 512 "
     model   vdw
     2.238 2.520
  nonbonded pdb=" NH1 ARG G 512 "
            pdb=" OD1 ASP H 418 "
     model   vdw
     2.240 2.520
  nonbonded pdb=" NH1 ARG A 512 "
            pdb=" OD1 ASP B 418 "
     model   vdw
     2.251 2.520
  nonbonded pdb=" OD1 ASP E 418 "
            pdb=" NH1 ARG H 512 "
     model   vdw
     2.260 2.520
  nonbonded pdb=" NH1 ARG E 512 "
            pdb=" OD1 ASP F 418 "
     model   vdw
     2.268 2.520
  ... (remaining 204211 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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:             3.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          13.930
  Check model and map are aligned:         0.340
  Set scattering table:                    0.200
  Process input model:                     62.410
  Find NCS groups from input model:        1.580
  Set up NCS constraints:                  0.170
  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:12.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   94.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
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      :  0.009   0.139  24064  Z= 0.586
  Angle     :  0.907   9.180  32568  Z= 0.481
  Chirality :  0.059   0.318   3712
  Planarity :  0.005   0.040   4120
  Dihedral  : 15.789 130.450   9120
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.91 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    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:  0.22 (0.15), residues: 3024
  helix:  0.71 (0.14), residues: 1232
  sheet: -0.42 (0.24), residues: 384
  loop : -0.05 (0.16), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS E 466 
 PHE   0.019   0.004   PHE G  24 
 TYR   0.039   0.004   TYR E   4 
 ARG   0.005   0.001   ARG D 412 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 369
  time to evaluate  : 2.773 
Fit side-chains
REVERT: D   98 GLU cc_start: 0.8112 (mp0) cc_final: 0.7893 (mp0)
REVERT: G   62 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8239 (mttt)
REVERT: G   98 GLU cc_start: 0.8114 (mp0) cc_final: 0.7900 (mp0)
REVERT: G  437 ILE cc_start: 0.8384 (mm) cc_final: 0.8176 (mp)
  outliers start: 32
  outliers final: 24
  residues processed: 397
  average time/residue: 1.6923
  time to fit residues: 749.6607
Evaluate side-chains
  389 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 364
  time to evaluate  : 2.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain G residue   62 LYS
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  361 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 256 optimal weight:    2.9990
   chunk 230 optimal weight:    0.7980
   chunk 127 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 155 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9980
   chunk 238 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 144 optimal weight:    0.9980
   chunk 177 optimal weight:    0.8980
   chunk 276 optimal weight:    2.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.0705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  24064  Z= 0.155
  Angle     :  0.491   4.441  32568  Z= 0.274
  Chirality :  0.042   0.167   3712
  Planarity :  0.004   0.030   4120
  Dihedral  : 10.442 109.819   3844
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  8.54 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    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:  0.59 (0.15), residues: 3024
  helix:  1.09 (0.15), residues: 1232
  sheet: -0.44 (0.24), residues: 384
  loop :  0.16 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 466 
 PHE   0.011   0.002   PHE D 401 
 TYR   0.012   0.001   TYR G   4 
 ARG   0.002   0.000   ARG B 480 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 359
  time to evaluate  : 2.748 
Fit side-chains
REVERT: A  283 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9055 (tt0)
REVERT: B  283 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.9060 (tt0)
REVERT: C  283 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9060 (tt0)
REVERT: D  283 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.9063 (tt0)
REVERT: D  399 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7270 (tp30)
REVERT: E  283 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.9069 (tt0)
REVERT: F  283 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.9068 (tt0)
REVERT: G   98 GLU cc_start: 0.8076 (mp0) cc_final: 0.7875 (mp0)
REVERT: G  283 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9072 (tt0)
REVERT: H  283 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.9063 (tt0)
  outliers start: 50
  outliers final: 31
  residues processed: 403
  average time/residue: 1.6981
  time to fit residues: 763.0861
Evaluate side-chains
  384 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 345
  time to evaluate  : 2.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  283 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  491 GLU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  283 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  491 GLU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  283 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  491 GLU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  283 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain D residue  491 GLU
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  283 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain E residue  491 GLU
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  283 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  491 GLU
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  283 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  283 GLN
Chi-restraints excluded: chain H residue  361 VAL
Chi-restraints excluded: chain H residue  491 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 153 optimal weight:    0.0470
   chunk 85 optimal weight:    0.8980
   chunk 229 optimal weight:    0.0070
   chunk 187 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   chunk 276 optimal weight:    0.5980
   chunk 298 optimal weight:    1.9990
   chunk 246 optimal weight:    3.9990
   chunk 274 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 221 optimal weight:    8.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
A 498 GLN
C 448 GLN
D  21 GLN
F 448 GLN
G  21 GLN
G 498 GLN
H 498 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  24064  Z= 0.136
  Angle     :  0.460   4.452  32568  Z= 0.254
  Chirality :  0.041   0.160   3712
  Planarity :  0.004   0.029   4120
  Dihedral  :  9.785  99.526   3840
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  8.99 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    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:  0.79 (0.15), residues: 3024
  helix:  1.27 (0.15), residues: 1232
  sheet: -0.34 (0.24), residues: 384
  loop :  0.26 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 466 
 PHE   0.009   0.002   PHE D 401 
 TYR   0.010   0.001   TYR A 353 
 ARG   0.002   0.000   ARG E 480 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 358
  time to evaluate  : 2.668 
Fit side-chains
REVERT: A  283 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.9046 (tt0)
REVERT: B  283 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9051 (tt0)
REVERT: C  283 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9051 (tt0)
REVERT: D  283 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.9057 (tt0)
REVERT: D  399 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7246 (tp30)
REVERT: E  283 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.9060 (tt0)
REVERT: F  283 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.9063 (tt0)
REVERT: G  283 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.9064 (tt0)
REVERT: H  283 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9056 (tt0)
  outliers start: 43
  outliers final: 32
  residues processed: 397
  average time/residue: 1.7507
  time to fit residues: 773.1694
Evaluate side-chains
  398 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 358
  time to evaluate  : 2.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  283 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  491 GLU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  283 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  491 GLU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  283 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  491 GLU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  283 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain D residue  491 GLU
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  283 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain E residue  491 GLU
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   75 GLU
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  283 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  491 GLU
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  283 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  283 GLN
Chi-restraints excluded: chain H residue  361 VAL
Chi-restraints excluded: chain H residue  491 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 273 optimal weight:    4.9990
   chunk 207 optimal weight:    6.9990
   chunk 143 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 131 optimal weight:    6.9990
   chunk 185 optimal weight:    4.9990
   chunk 277 optimal weight:    6.9990
   chunk 293 optimal weight:    3.9990
   chunk 145 optimal weight:    0.4980
   chunk 263 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0970
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 498 GLN
C 448 GLN
C 498 GLN
D  21 GLN
D 498 GLN
E 243 GLN
E 498 GLN
F 448 GLN
F 498 GLN
G  21 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.0709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  24064  Z= 0.274
  Angle     :  0.593   4.772  32568  Z= 0.329
  Chirality :  0.047   0.229   3712
  Planarity :  0.004   0.029   4120
  Dihedral  : 10.373 118.515   3840
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.68 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    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:  0.48 (0.15), residues: 3024
  helix:  0.95 (0.15), residues: 1232
  sheet: -0.46 (0.24), residues: 384
  loop :  0.14 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 466 
 PHE   0.014   0.003   PHE F  24 
 TYR   0.015   0.002   TYR E   4 
 ARG   0.004   0.001   ARG D 341 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 370
  time to evaluate  : 2.777 
Fit side-chains
REVERT: D  399 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7249 (tp30)
  outliers start: 33
  outliers final: 32
  residues processed: 399
  average time/residue: 1.7201
  time to fit residues: 763.5980
Evaluate side-chains
  399 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 367
  time to evaluate  : 2.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  491 GLU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  491 GLU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  491 GLU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain D residue  491 GLU
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain E residue  491 GLU
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  474 LYS
Chi-restraints excluded: chain F residue  491 GLU
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  361 VAL
Chi-restraints excluded: chain H residue  491 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 244 optimal weight:    2.9990
   chunk 166 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 218 optimal weight:    0.7980
   chunk 121 optimal weight:    3.9990
   chunk 250 optimal weight:    7.9990
   chunk 203 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 150 optimal weight:    1.9990
   chunk 263 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
C 448 GLN
D  21 GLN
E 243 GLN
F 448 GLN
G  21 GLN
H  21 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.0769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  24064  Z= 0.254
  Angle     :  0.571   4.622  32568  Z= 0.318
  Chirality :  0.046   0.209   3712
  Planarity :  0.004   0.030   4120
  Dihedral  : 10.323 117.940   3840
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.52 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    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:  0.46 (0.15), residues: 3024
  helix:  0.92 (0.15), residues: 1232
  sheet: -0.48 (0.25), residues: 384
  loop :  0.14 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 466 
 PHE   0.014   0.003   PHE G 401 
 TYR   0.014   0.002   TYR G   4 
 ARG   0.003   0.001   ARG C 341 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  410 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 369
  time to evaluate  : 2.621 
Fit side-chains
REVERT: D  399 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7240 (tp30)
  outliers start: 41
  outliers final: 32
  residues processed: 405
  average time/residue: 1.7425
  time to fit residues: 785.7715
Evaluate side-chains
  402 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 370
  time to evaluate  : 2.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  491 GLU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  491 GLU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  491 GLU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain D residue  491 GLU
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain E residue  491 GLU
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  474 LYS
Chi-restraints excluded: chain F residue  491 GLU
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  361 VAL
Chi-restraints excluded: chain H residue  491 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 264 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 172 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 294 optimal weight:    1.9990
   chunk 244 optimal weight:    2.9990
   chunk 136 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 154 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 441 GLN
B 441 GLN
C 448 GLN
D  21 GLN
D 441 GLN
E 243 GLN
E 441 GLN
F 448 GLN
G  21 GLN
H 441 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.0715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  24064  Z= 0.329
  Angle     :  0.638   5.009  32568  Z= 0.355
  Chirality :  0.050   0.265   3712
  Planarity :  0.005   0.030   4120
  Dihedral  : 10.491 119.884   3840
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.11 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.15), residues: 3024
  helix:  0.75 (0.14), residues: 1232
  sheet: -0.47 (0.25), residues: 384
  loop :  0.08 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H 466 
 PHE   0.016   0.003   PHE F  24 
 TYR   0.017   0.002   TYR H   4 
 ARG   0.004   0.001   ARG A 341 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 373
  time to evaluate  : 2.491 
Fit side-chains
REVERT: D  399 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7248 (tp30)
  outliers start: 43
  outliers final: 32
  residues processed: 410
  average time/residue: 1.7324
  time to fit residues: 789.9551
Evaluate side-chains
  404 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 372
  time to evaluate  : 2.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  491 GLU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  491 GLU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  491 GLU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain D residue  491 GLU
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain E residue  491 GLU
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  474 LYS
Chi-restraints excluded: chain F residue  491 GLU
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  361 VAL
Chi-restraints excluded: chain H residue  491 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 283 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 167 optimal weight:    3.9990
   chunk 214 optimal weight:    2.9990
   chunk 166 optimal weight:    0.9980
   chunk 247 optimal weight:    0.5980
   chunk 164 optimal weight:    1.9990
   chunk 293 optimal weight:    8.9990
   chunk 183 optimal weight:    3.9990
   chunk 178 optimal weight:    5.9990
   chunk 135 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
C 448 GLN
D  21 GLN
E 243 GLN
F 448 GLN
G  21 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.0930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  24064  Z= 0.169
  Angle     :  0.494   4.309  32568  Z= 0.275
  Chirality :  0.043   0.162   3712
  Planarity :  0.004   0.031   4120
  Dihedral  :  9.992 107.001   3840
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  9.44 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.15), residues: 3024
  helix:  1.09 (0.15), residues: 1232
  sheet: -0.47 (0.24), residues: 384
  loop :  0.20 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 466 
 PHE   0.011   0.002   PHE H 401 
 TYR   0.010   0.001   TYR G 348 
 ARG   0.002   0.000   ARG C 480 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 364
  time to evaluate  : 2.660 
Fit side-chains
REVERT: C  103 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8009 (mm-30)
REVERT: D  399 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7235 (tp30)
  outliers start: 38
  outliers final: 37
  residues processed: 390
  average time/residue: 1.7699
  time to fit residues: 776.9879
Evaluate side-chains
  400 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 363
  time to evaluate  : 2.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  491 GLU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  491 GLU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  491 GLU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain D residue  491 GLU
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain E residue  491 GLU
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   75 GLU
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  474 LYS
Chi-restraints excluded: chain F residue  491 GLU
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  361 VAL
Chi-restraints excluded: chain H residue  491 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 181 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 174 optimal weight:    2.9990
   chunk 88 optimal weight:    0.3980
   chunk 57 optimal weight:    6.9990
   chunk 56 optimal weight:    0.5980
   chunk 186 optimal weight:    0.6980
   chunk 199 optimal weight:    0.6980
   chunk 144 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 230 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 448 GLN
D  21 GLN
E 243 GLN
F 448 GLN
G  21 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  24064  Z= 0.132
  Angle     :  0.450   4.278  32568  Z= 0.250
  Chirality :  0.041   0.158   3712
  Planarity :  0.004   0.032   4120
  Dihedral  :  9.596  98.167   3840
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  8.74 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    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:  0.83 (0.16), residues: 3024
  helix:  1.27 (0.15), residues: 1232
  sheet: -0.29 (0.24), residues: 384
  loop :  0.29 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 466 
 PHE   0.010   0.002   PHE A 514 
 TYR   0.009   0.001   TYR H 353 
 ARG   0.001   0.000   ARG H 355 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  419 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 365
  time to evaluate  : 2.831 
Fit side-chains
REVERT: D  399 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7207 (tp30)
  outliers start: 54
  outliers final: 30
  residues processed: 406
  average time/residue: 1.7240
  time to fit residues: 778.6433
Evaluate side-chains
  390 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 360
  time to evaluate  : 2.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   75 GLU
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  474 LYS
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  361 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 266 optimal weight:    3.9990
   chunk 280 optimal weight:    1.9990
   chunk 256 optimal weight:    0.5980
   chunk 273 optimal weight:    4.9990
   chunk 164 optimal weight:    0.9980
   chunk 118 optimal weight:    6.9990
   chunk 214 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 246 optimal weight:    0.0980
   chunk 258 optimal weight:    5.9990
   chunk 272 optimal weight:    4.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
C 448 GLN
E 243 GLN
F 243 GLN
F 448 GLN
G 243 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  24064  Z= 0.166
  Angle     :  0.495   4.310  32568  Z= 0.275
  Chirality :  0.042   0.162   3712
  Planarity :  0.004   0.032   4120
  Dihedral  :  9.757 105.483   3840
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.42 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    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:  0.74 (0.15), residues: 3024
  helix:  1.17 (0.15), residues: 1232
  sheet: -0.36 (0.24), residues: 384
  loop :  0.29 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 466 
 PHE   0.011   0.002   PHE H 401 
 TYR   0.011   0.001   TYR B 353 
 ARG   0.002   0.000   ARG A 480 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  394 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 364
  time to evaluate  : 2.848 
Fit side-chains
REVERT: D  399 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7209 (tp30)
REVERT: H  103 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8118 (mm-30)
  outliers start: 30
  outliers final: 30
  residues processed: 389
  average time/residue: 1.7648
  time to fit residues: 761.9707
Evaluate side-chains
  389 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 359
  time to evaluate  : 2.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   75 GLU
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  474 LYS
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  361 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 179 optimal weight:    5.9990
   chunk 288 optimal weight:    8.9990
   chunk 176 optimal weight:    4.9990
   chunk 136 optimal weight:    0.9980
   chunk 200 optimal weight:    1.9990
   chunk 302 optimal weight:    4.9990
   chunk 278 optimal weight:    4.9990
   chunk 241 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 186 optimal weight:    0.9980
   chunk 147 optimal weight:    5.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
B 243 GLN
C 448 GLN
E 243 GLN
F 243 GLN
F 448 GLN
G 243 GLN
G 441 GLN
H  21 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.0856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  24064  Z= 0.261
  Angle     :  0.587   4.734  32568  Z= 0.327
  Chirality :  0.047   0.219   3712
  Planarity :  0.004   0.030   4120
  Dihedral  : 10.204 117.280   3840
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.78 %
    Favored  : 88.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.15), residues: 3024
  helix:  0.97 (0.15), residues: 1232
  sheet: -0.49 (0.24), residues: 384
  loop :  0.16 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 466 
 PHE   0.014   0.003   PHE F 401 
 TYR   0.014   0.002   TYR F 348 
 ARG   0.004   0.001   ARG F 341 

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 365
  time to evaluate  : 2.787 
Fit side-chains
REVERT: C  103 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: D  399 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7230 (tp30)
  outliers start: 25
  outliers final: 25
  residues processed: 390
  average time/residue: 1.7210
  time to fit residues: 748.4388
Evaluate side-chains
  394 residues out of total 2448 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 369
  time to evaluate  : 2.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  277 GLN
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  277 GLN
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  277 GLN
Chi-restraints excluded: chain D residue  361 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue  277 GLN
Chi-restraints excluded: chain E residue  361 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  277 GLN
Chi-restraints excluded: chain F residue  361 VAL
Chi-restraints excluded: chain F residue  474 LYS
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue  277 GLN
Chi-restraints excluded: chain G residue  361 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  277 GLN
Chi-restraints excluded: chain H residue  361 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 191 optimal weight:    0.8980
   chunk 256 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 222 optimal weight:    0.0970
   chunk 35 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 241 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 248 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0370
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN
B 368 GLN
C 243 GLN
C 448 GLN
D  21 GLN
D 243 GLN
E 243 GLN
F 448 GLN
G  21 GLN
G 243 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.123081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.099884 restraints weight = 20240.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.18
r_work: 0.2977 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 2.36 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  24064  Z= 0.139
  Angle     :  0.470   4.275  32568  Z= 0.261
  Chirality :  0.041   0.159   3712
  Planarity :  0.004   0.031   4120
  Dihedral  :  9.659 101.226   3840
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.99 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    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:  0.78 (0.16), residues: 3024
  helix:  1.24 (0.15), residues: 1232
  sheet: -0.34 (0.24), residues: 384
  loop :  0.27 (0.17), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 466 
 PHE   0.011   0.002   PHE A 514 
 TYR   0.010   0.001   TYR C 353 
 ARG   0.001   0.000   ARG F 355 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11008.32 seconds
wall clock time: 194 minutes 18.34 seconds (11658.34 seconds total)