Starting phenix.real_space_refine
on Thu Feb 15 21:50:10 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld5_23282/02_2024/7ld5_23282.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld5_23282/02_2024/7ld5_23282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld5_23282/02_2024/7ld5_23282.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld5_23282/02_2024/7ld5_23282.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld5_23282/02_2024/7ld5_23282.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld5_23282/02_2024/7ld5_23282.pdb"
  }
  resolution = 3.07
  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=  -0.001 sd=   0.110
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      6      5.21       5
     S      54      5.16       5
     C    8451      2.51       5
     N    2358      2.21       5
     O    2664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   11": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU   30": "OE1" <-> "OE2"
    Residue "A PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP   99": "OD1" <-> "OD2"
    Residue "A ASP  108": "OD1" <-> "OD2"
    Residue "A PHE  115": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  180": "OE1" <-> "OE2"
    Residue "A ASP  188": "OD1" <-> "OD2"
    Residue "A GLU  219": "OE1" <-> "OE2"
    Residue "A ASP  256": "OD1" <-> "OD2"
    Residue "A GLU  264": "OE1" <-> "OE2"
    Residue "A PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  272": "OE1" <-> "OE2"
    Residue "A ASP  274": "OD1" <-> "OD2"
    Residue "A GLU  285": "OE1" <-> "OE2"
    Residue "A GLU  298": "OE1" <-> "OE2"
    Residue "A ASP  301": "OD1" <-> "OD2"
    Residue "A GLU  312": "OE1" <-> "OE2"
    Residue "A TYR  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  344": "OD1" <-> "OD2"
    Residue "A ASP  349": "OD1" <-> "OD2"
    Residue "A GLU  362": "OE1" <-> "OE2"
    Residue "A GLU  376": "OE1" <-> "OE2"
    Residue "A ASP  398": "OD1" <-> "OD2"
    Residue "A GLU  403": "OE1" <-> "OE2"
    Residue "A TYR  412": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  421": "OE1" <-> "OE2"
    Residue "A GLU  440": "OE1" <-> "OE2"
    Residue "A GLU  451": "OE1" <-> "OE2"
    Residue "A TYR  455": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  506": "OD1" <-> "OD2"
    Residue "A ASP  520": "OD1" <-> "OD2"
    Residue "A PHE  528": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  530": "OD1" <-> "OD2"
    Residue "A ASP  532": "OD1" <-> "OD2"
    Residue "A PHE  541": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  548": "OD1" <-> "OD2"
    Residue "A ASP  575": "OD1" <-> "OD2"
    Residue "A ASP  582": "OD1" <-> "OD2"
    Residue "A GLU  586": "OE1" <-> "OE2"
    Residue "A TYR  590": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   11": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU   30": "OE1" <-> "OE2"
    Residue "B PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   99": "OD1" <-> "OD2"
    Residue "B ASP  108": "OD1" <-> "OD2"
    Residue "B PHE  115": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  180": "OE1" <-> "OE2"
    Residue "B ASP  188": "OD1" <-> "OD2"
    Residue "B GLU  219": "OE1" <-> "OE2"
    Residue "B ASP  256": "OD1" <-> "OD2"
    Residue "B GLU  264": "OE1" <-> "OE2"
    Residue "B PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  272": "OE1" <-> "OE2"
    Residue "B ASP  274": "OD1" <-> "OD2"
    Residue "B GLU  285": "OE1" <-> "OE2"
    Residue "B GLU  298": "OE1" <-> "OE2"
    Residue "B ASP  301": "OD1" <-> "OD2"
    Residue "B GLU  312": "OE1" <-> "OE2"
    Residue "B TYR  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  344": "OD1" <-> "OD2"
    Residue "B ASP  349": "OD1" <-> "OD2"
    Residue "B GLU  362": "OE1" <-> "OE2"
    Residue "B GLU  376": "OE1" <-> "OE2"
    Residue "B ASP  398": "OD1" <-> "OD2"
    Residue "B GLU  403": "OE1" <-> "OE2"
    Residue "B TYR  412": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  421": "OE1" <-> "OE2"
    Residue "B GLU  440": "OE1" <-> "OE2"
    Residue "B GLU  451": "OE1" <-> "OE2"
    Residue "B TYR  455": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  506": "OD1" <-> "OD2"
    Residue "B ASP  520": "OD1" <-> "OD2"
    Residue "B PHE  528": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  530": "OD1" <-> "OD2"
    Residue "B ASP  532": "OD1" <-> "OD2"
    Residue "B PHE  541": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  548": "OD1" <-> "OD2"
    Residue "B ASP  575": "OD1" <-> "OD2"
    Residue "B ASP  582": "OD1" <-> "OD2"
    Residue "B GLU  586": "OE1" <-> "OE2"
    Residue "B TYR  590": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   11": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   30": "OE1" <-> "OE2"
    Residue "C PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP   99": "OD1" <-> "OD2"
    Residue "C ASP  108": "OD1" <-> "OD2"
    Residue "C PHE  115": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  180": "OE1" <-> "OE2"
    Residue "C ASP  188": "OD1" <-> "OD2"
    Residue "C GLU  219": "OE1" <-> "OE2"
    Residue "C ASP  256": "OD1" <-> "OD2"
    Residue "C GLU  264": "OE1" <-> "OE2"
    Residue "C PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  272": "OE1" <-> "OE2"
    Residue "C ASP  274": "OD1" <-> "OD2"
    Residue "C GLU  285": "OE1" <-> "OE2"
    Residue "C GLU  298": "OE1" <-> "OE2"
    Residue "C ASP  301": "OD1" <-> "OD2"
    Residue "C GLU  312": "OE1" <-> "OE2"
    Residue "C TYR  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  344": "OD1" <-> "OD2"
    Residue "C ASP  349": "OD1" <-> "OD2"
    Residue "C GLU  362": "OE1" <-> "OE2"
    Residue "C GLU  376": "OE1" <-> "OE2"
    Residue "C ASP  398": "OD1" <-> "OD2"
    Residue "C GLU  403": "OE1" <-> "OE2"
    Residue "C TYR  412": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  421": "OE1" <-> "OE2"
    Residue "C GLU  440": "OE1" <-> "OE2"
    Residue "C GLU  451": "OE1" <-> "OE2"
    Residue "C TYR  455": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  506": "OD1" <-> "OD2"
    Residue "C ASP  520": "OD1" <-> "OD2"
    Residue "C PHE  528": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  530": "OD1" <-> "OD2"
    Residue "C ASP  532": "OD1" <-> "OD2"
    Residue "C PHE  541": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  548": "OD1" <-> "OD2"
    Residue "C ASP  575": "OD1" <-> "OD2"
    Residue "C ASP  582": "OD1" <-> "OD2"
    Residue "C GLU  586": "OE1" <-> "OE2"
    Residue "C TYR  590": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 13542
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 4416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4416
          Classifications: {'peptide': 587}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4416
          Classifications: {'peptide': 587}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 555}
    Chain: "C"
      Number of atoms: 4416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4416
          Classifications: {'peptide': 587}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 555}
    Chain: "D"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 96
          Classifications: {'DNA': 1, 'RNA': 4}
          Modifications used: {'5*END': 2, 'rna3p_pur': 4}
          Link IDs: {'rna3p': 4}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 96
          Classifications: {'DNA': 1, 'RNA': 4}
          Modifications used: {'5*END': 2, 'rna3p_pur': 4}
          Link IDs: {'rna3p': 4}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 96
          Classifications: {'DNA': 1, 'RNA': 4}
          Modifications used: {'5*END': 2, 'rna3p_pur': 4}
          Link IDs: {'rna3p': 4}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 15
    residue:
      pdb=" O5'   A D   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A D   1 " occ=0.30
    residue:
      pdb=" P     A D   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   2 " occ=0.30
    residue:
      pdb=" P     A D   3 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   3 " occ=0.30
    residue:
      pdb=" P     A D   4 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   4 " occ=0.30
    residue:
      pdb=" C1'   A D   9 " occ=0.30
      ... (9 atoms not shown)
      pdb=" C4    A D   9 " occ=0.30
    residue:
      pdb=" O5'   A E   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A E   1 " occ=0.30
    residue:
      pdb=" P     A E   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   2 " occ=0.30
    residue:
      pdb=" P     A E   3 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   3 " occ=0.30
    residue:
      pdb=" P     A E   4 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   4 " occ=0.30
    residue:
      pdb=" C1'   A E   9 " occ=0.30
      ... (9 atoms not shown)
      pdb=" C4    A E   9 " occ=0.30
    residue:
      pdb=" O5'   A F   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A F   1 " occ=0.30
    residue:
      pdb=" P     A F   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A F   2 " occ=0.30
    ... (remaining 3 not shown)
  Time building chain proxies: 7.06, per 1000 atoms: 0.52
  Number of scatterers: 13542
  At special positions: 0
  Unit cell: (114.912, 122.36, 89.376, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P       9     15.00
     Mg      6     11.99
     O    2664      8.00
     N    2358      7.00
     C    8451      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=0, symmetry=0
  Time building additional restraints: 4.78
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 12 sheets defined
      37.8% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 97 through 112
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 138 through 153
      removed outlier: 4.043A  pdb=" N   ASN A 144 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A 153 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 224
    Processing helix  chain 'A' and resid 229 through 240
    Processing helix  chain 'A' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 314
    Processing helix  chain 'A' and resid 321 through 345
    Processing helix  chain 'A' and resid 390 through 394
    Processing helix  chain 'A' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 441
      removed outlier: 3.587A  pdb=" N   ILE A 433 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 447
    Processing helix  chain 'A' and resid 470 through 485
    Processing helix  chain 'A' and resid 523 through 527
      removed outlier: 3.594A  pdb=" N   ASP A 526 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 581
      removed outlier: 4.005A  pdb=" N   GLU A 579 " --> pdb=" O   ASP A 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA A 580 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE A 581 " --> pdb=" O   MET A 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 97 through 112
      Proline residue:  B 110  - end of helix
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 138 through 153
      removed outlier: 4.044A  pdb=" N   ASN B 144 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA B 153 " --> pdb=" O   SER B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 229 through 240
    Processing helix  chain 'B' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE B 244 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR B 276 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA B 286 " --> pdb=" O   VAL B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 314
    Processing helix  chain 'B' and resid 321 through 345
    Processing helix  chain 'B' and resid 390 through 394
    Processing helix  chain 'B' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 441
      removed outlier: 3.588A  pdb=" N   ILE B 433 " --> pdb=" O   LYS B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 447
    Processing helix  chain 'B' and resid 470 through 485
    Processing helix  chain 'B' and resid 523 through 527
      removed outlier: 3.595A  pdb=" N   ASP B 526 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 581
      removed outlier: 4.005A  pdb=" N   GLU B 579 " --> pdb=" O   ASP B 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA B 580 " --> pdb=" O   VAL B 576 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE B 581 " --> pdb=" O   MET B 577 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 83
    Processing helix  chain 'C' and resid 97 through 112
      Proline residue:  C 110  - end of helix
    Processing helix  chain 'C' and resid 113 through 115
      No H-bonds generated for 'chain 'C' and resid 113 through 115'
    Processing helix  chain 'C' and resid 138 through 153
      removed outlier: 4.043A  pdb=" N   ASN C 144 " --> pdb=" O   VAL C 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA C 153 " --> pdb=" O   SER C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 224
    Processing helix  chain 'C' and resid 229 through 240
    Processing helix  chain 'C' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE C 244 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR C 276 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA C 286 " --> pdb=" O   VAL C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 314
    Processing helix  chain 'C' and resid 321 through 345
    Processing helix  chain 'C' and resid 390 through 394
    Processing helix  chain 'C' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR C 419 " --> pdb=" O   PRO C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 441
      removed outlier: 3.588A  pdb=" N   ILE C 433 " --> pdb=" O   LYS C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 447
    Processing helix  chain 'C' and resid 470 through 485
    Processing helix  chain 'C' and resid 523 through 527
      removed outlier: 3.594A  pdb=" N   ASP C 526 " --> pdb=" O   GLY C 523 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 581
      removed outlier: 4.004A  pdb=" N   GLU C 579 " --> pdb=" O   ASP C 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA C 580 " --> pdb=" O   VAL C 576 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE C 581 " --> pdb=" O   MET C 577 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET A  51 " --> pdb=" O   MET A 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175
      removed outlier: 4.424A  pdb=" N   PHE A 187 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   VAL A 186 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   ALA A 213 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP A 188 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA A 211 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 190 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL A 209 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA A 192 " --> pdb=" O   MET A 207 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   MET A 207 " --> pdb=" O   THR A 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR A 543 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363
      removed outlier: 6.303A  pdb=" N   GLN A 381 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET A 409 " --> pdb=" O   GLN A 459 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   SER A 461 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS A 411 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ALA A 463 " --> pdb=" O   HIS A 411 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ASN A 413 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLY A 465 " --> pdb=" O   ASN A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET B  51 " --> pdb=" O   MET B 130 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175
      removed outlier: 4.425A  pdb=" N   PHE B 187 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   VAL B 186 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ALA B 213 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP B 188 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA B 211 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 190 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL B 209 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA B 192 " --> pdb=" O   MET B 207 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   MET B 207 " --> pdb=" O   THR B 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR B 543 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 363
      removed outlier: 6.303A  pdb=" N   GLN B 381 " --> pdb=" O   LEU B 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET B 409 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   SER B 461 " --> pdb=" O   MET B 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS B 411 " --> pdb=" O   SER B 461 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   ALA B 463 " --> pdb=" O   HIS B 411 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   ASN B 413 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLY B 465 " --> pdb=" O   ASN B 413 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 396
    Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET C  51 " --> pdb=" O   MET C 130 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 175
      removed outlier: 4.425A  pdb=" N   PHE C 187 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL C 186 " --> pdb=" O   ALA C 213 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ALA C 213 " --> pdb=" O   VAL C 186 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP C 188 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA C 211 " --> pdb=" O   ASP C 188 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL C 190 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL C 209 " --> pdb=" O   VAL C 190 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ALA C 192 " --> pdb=" O   MET C 207 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   MET C 207 " --> pdb=" O   THR C 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR C 543 " --> pdb=" O   ALA C 213 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 359 through 363
      removed outlier: 6.304A  pdb=" N   GLN C 381 " --> pdb=" O   LEU C 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET C 409 " --> pdb=" O   GLN C 459 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   SER C 461 " --> pdb=" O   MET C 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS C 411 " --> pdb=" O   SER C 461 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ALA C 463 " --> pdb=" O   HIS C 411 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ASN C 413 " --> pdb=" O   ALA C 463 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLY C 465 " --> pdb=" O   ASN C 413 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 395 through 396

    720 hydrogen bonds defined for protein.
    1980 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: 4.71

  Time building geometry restraints manager: 5.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4601
        1.34 -     1.45: 1539
        1.45 -     1.57: 7531
        1.57 -     1.69: 18
        1.69 -     1.80: 99
  Bond restraints: 13788
  Sorted by residual:
  bond pdb=" CB  GLU A 298 "
       pdb=" CG  GLU A 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.19e+00
  bond pdb=" CB  GLU C 298 "
       pdb=" CG  GLU C 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.16e+00
  bond pdb=" CB  GLU B 298 "
       pdb=" CG  GLU B 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.10e+00
  bond pdb=" CA  ILE C 366 "
       pdb=" CB  ILE C 366 "
    ideal  model  delta    sigma   weight residual
    1.537  1.523  0.014 1.29e-02 6.01e+03 1.25e+00
  bond pdb=" CA  ILE B 366 "
       pdb=" CB  ILE B 366 "
    ideal  model  delta    sigma   weight residual
    1.537  1.523  0.014 1.29e-02 6.01e+03 1.20e+00
  ... (remaining 13783 not shown)

  Histogram of bond angle deviations from ideal:
       99.55 -   106.44: 506
      106.44 -   113.34: 7590
      113.34 -   120.24: 5179
      120.24 -   127.14: 5334
      127.14 -   134.03: 165
  Bond angle restraints: 18774
  Sorted by residual:
  angle pdb=" CA  GLU A 298 "
        pdb=" CB  GLU A 298 "
        pdb=" CG  GLU A 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.52   -9.42 2.00e+00 2.50e-01 2.22e+01
  angle pdb=" CA  GLU B 298 "
        pdb=" CB  GLU B 298 "
        pdb=" CG  GLU B 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.49   -9.39 2.00e+00 2.50e-01 2.21e+01
  angle pdb=" CA  GLU C 298 "
        pdb=" CB  GLU C 298 "
        pdb=" CG  GLU C 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.48   -9.38 2.00e+00 2.50e-01 2.20e+01
  angle pdb=" CG1 ILE B 293 "
        pdb=" CB  ILE B 293 "
        pdb=" CG2 ILE B 293 "
      ideal   model   delta    sigma   weight residual
     110.70  101.52    9.18 3.00e+00 1.11e-01 9.36e+00
  angle pdb=" CG1 ILE C 293 "
        pdb=" CB  ILE C 293 "
        pdb=" CG2 ILE C 293 "
      ideal   model   delta    sigma   weight residual
     110.70  101.54    9.16 3.00e+00 1.11e-01 9.31e+00
  ... (remaining 18769 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 7259
       16.59 -    33.19: 768
       33.19 -    49.78: 256
       49.78 -    66.38: 54
       66.38 -    82.97: 15
  Dihedral angle restraints: 8352
    sinusoidal: 3312
      harmonic: 5040
  Sorted by residual:
  dihedral pdb=" CA  VAL C 507 "
           pdb=" C   VAL C 507 "
           pdb=" N   ASP C 508 "
           pdb=" CA  ASP C 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.33  -17.67     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  VAL B 507 "
           pdb=" C   VAL B 507 "
           pdb=" N   ASP B 508 "
           pdb=" CA  ASP B 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  VAL A 507 "
           pdb=" C   VAL A 507 "
           pdb=" N   ASP A 508 "
           pdb=" CA  ASP A 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 8349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1553
       0.046 -    0.091: 483
       0.091 -    0.137: 136
       0.137 -    0.183: 9
       0.183 -    0.229: 3
  Chirality restraints: 2184
  Sorted by residual:
  chirality pdb=" CB  ILE B 293 "
            pdb=" CA  ILE B 293 "
            pdb=" CG1 ILE B 293 "
            pdb=" CG2 ILE B 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  ILE C 293 "
            pdb=" CA  ILE C 293 "
            pdb=" CG1 ILE C 293 "
            pdb=" CG2 ILE C 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  ILE A 293 "
            pdb=" CA  ILE A 293 "
            pdb=" CG1 ILE A 293 "
            pdb=" CG2 ILE A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 2181 not shown)

  Planarity restraints: 2439
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 444 "   -0.033 5.00e-02 4.00e+02   4.90e-02 3.84e+00
        pdb=" N   PRO C 445 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO C 445 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 445 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 444 "   -0.033 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO B 445 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 445 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 445 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 444 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.80e+00
        pdb=" N   PRO A 445 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 445 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 445 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2436 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 273
        2.66 -     3.22: 12389
        3.22 -     3.78: 19572
        3.78 -     4.34: 28398
        4.34 -     4.90: 48333
  Nonbonded interactions: 108965
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 418 "
            pdb=" O   ALA B 463 "
     model   vdw
     2.102 2.440
  nonbonded pdb=" OG  SER A 418 "
            pdb=" O   ALA A 463 "
     model   vdw
     2.102 2.440
  nonbonded pdb=" OG  SER C 418 "
            pdb=" O   ALA C 463 "
     model   vdw
     2.103 2.440
  nonbonded pdb=" OE2 GLU C  77 "
            pdb=" OH  TYR C 138 "
     model   vdw
     2.153 2.440
  nonbonded pdb=" OE2 GLU B  77 "
            pdb=" OH  TYR B 138 "
     model   vdw
     2.153 2.440
  ... (remaining 108960 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'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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=0.30 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          6.290
  Check model and map are aligned:         0.210
  Set scattering table:                    0.120
  Process input model:                     36.660
  Find NCS groups from input model:        0.860
  Set up NCS constraints:                  0.140
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
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      :  0.006   0.047  13788  Z= 0.416
  Angle     :  0.671   9.415  18774  Z= 0.375
  Chirality :  0.048   0.229   2184
  Planarity :  0.004   0.049   2439
  Dihedral  : 16.010  82.970   5112
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 15.84 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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: -2.06 (0.18), residues: 1755
  helix: -0.76 (0.20), residues: 549
  sheet: -0.72 (0.23), residues: 444
  loop : -2.17 (0.21), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 173 
 HIS   0.001   0.000   HIS B 370 
 PHE   0.016   0.001   PHE A 157 
 TYR   0.011   0.002   TYR A  45 
 ARG   0.005   0.000   ARG B 313 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 90
    poor density    : 193
  time to evaluate  : 1.379 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7378 (ptpt)
REVERT: A   79 MET cc_start: 0.8695 (tpp) cc_final: 0.8370 (tpp)
REVERT: A  130 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7981 (mtt)
REVERT: A  356 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7221 (mt)
REVERT: B   74 ASP cc_start: 0.7829 (m-30) cc_final: 0.7628 (m-30)
REVERT: B  329 PHE cc_start: 0.8412 (t80) cc_final: 0.8060 (t80)
REVERT: B  348 ILE cc_start: 0.8425 (pt) cc_final: 0.8210 (pt)
REVERT: B  356 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7440 (mt)
REVERT: B  397 ILE cc_start: 0.8574 (mm) cc_final: 0.8334 (mm)
REVERT: C   63 LYS cc_start: 0.7607 (ptpp) cc_final: 0.7272 (ptpp)
REVERT: C   95 ARG cc_start: 0.7801 (ptt180) cc_final: 0.7391 (ptm-80)
REVERT: C  122 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7202 (tm-30)
REVERT: C  130 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8290 (mtt)
REVERT: C  383 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8177 (tp)
  outliers start: 90
  outliers final: 49
  residues processed: 272
  average time/residue: 0.2474
  time to fit residues: 98.6712
Evaluate side-chains
  223 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 168
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  549 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   59 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  130 MET
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  449 SER
Chi-restraints excluded: chain C residue  471 SER
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:    5.9990
   chunk 131 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 88 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 136 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 158 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A  61 ASN
A 339 GLN
A 381 GLN
A 467 ASN
A 546 GLN
B  61 ASN
B 339 GLN
B 381 GLN
B 467 ASN
B 546 GLN
C  36 GLN
C  61 ASN
C 381 GLN
C 396 GLN
C 467 ASN
C 546 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13788  Z= 0.216
  Angle     :  0.526   5.657  18774  Z= 0.275
  Chirality :  0.044   0.137   2184
  Planarity :  0.004   0.035   2439
  Dihedral  :  6.766  48.722   2123
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.94 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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: -0.60 (0.20), residues: 1755
  helix:  1.07 (0.22), residues: 555
  sheet: -0.30 (0.23), residues: 450
  loop : -1.57 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 173 
 HIS   0.002   0.000   HIS A 370 
 PHE   0.015   0.001   PHE A 157 
 TYR   0.013   0.001   TYR B  80 
 ARG   0.004   0.000   ARG C 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 177
  time to evaluate  : 1.457 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.7908 (m-80) cc_final: 0.7542 (m-80)
REVERT: A  122 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7073 (tm-30)
REVERT: B  348 ILE cc_start: 0.8351 (pt) cc_final: 0.8151 (pt)
REVERT: B  397 ILE cc_start: 0.8595 (mm) cc_final: 0.8384 (mm)
REVERT: C  122 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7290 (tm-30)
  outliers start: 42
  outliers final: 31
  residues processed: 213
  average time/residue: 0.2613
  time to fit residues: 82.1536
Evaluate side-chains
  205 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 131 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 158 optimal weight:    3.9990
   chunk 171 optimal weight:    4.9990
   chunk 140 optimal weight:    2.9990
   chunk 156 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
C 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13788  Z= 0.311
  Angle     :  0.567   5.758  18774  Z= 0.295
  Chirality :  0.045   0.141   2184
  Planarity :  0.004   0.036   2439
  Dihedral  :  6.152  49.047   2079
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.02 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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: -0.23 (0.20), residues: 1755
  helix:  1.35 (0.22), residues: 558
  sheet: -0.07 (0.23), residues: 450
  loop : -1.36 (0.22), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 173 
 HIS   0.002   0.000   HIS C 410 
 PHE   0.019   0.001   PHE A 533 
 TYR   0.014   0.002   TYR C  80 
 ARG   0.005   0.000   ARG C 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 173
  time to evaluate  : 1.436 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.7967 (m-80) cc_final: 0.7648 (m-80)
REVERT: A  122 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7185 (tm-30)
REVERT: B  348 ILE cc_start: 0.8343 (pt) cc_final: 0.8117 (pt)
REVERT: B  397 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8461 (mm)
REVERT: C  111 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7993 (mp)
REVERT: C  122 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7261 (tm-30)
REVERT: C  397 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8326 (mm)
  outliers start: 65
  outliers final: 46
  residues processed: 224
  average time/residue: 0.2437
  time to fit residues: 81.0890
Evaluate side-chains
  220 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 169
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  397 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  498 MET
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 156 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 158 optimal weight:    0.8980
   chunk 168 optimal weight:    4.9990
   chunk 150 optimal weight:    0.0170
   chunk 45 optimal weight:    2.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
C 396 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13788  Z= 0.184
  Angle     :  0.499  11.313  18774  Z= 0.258
  Chirality :  0.043   0.134   2184
  Planarity :  0.004   0.034   2439
  Dihedral  :  5.806  48.950   2076
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.75 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 (0.20), residues: 1755
  helix:  1.76 (0.22), residues: 555
  sheet:  0.15 (0.23), residues: 450
  loop : -1.09 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 173 
 HIS   0.001   0.000   HIS C 410 
 PHE   0.013   0.001   PHE A 157 
 TYR   0.012   0.001   TYR C  80 
 ARG   0.005   0.000   ARG B 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 175
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.7949 (m-80) cc_final: 0.7672 (m-80)
REVERT: A  122 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7183 (tm-30)
REVERT: A  393 MET cc_start: 0.9032 (mmm) cc_final: 0.8687 (mmp)
REVERT: B  348 ILE cc_start: 0.8292 (pt) cc_final: 0.8056 (pt)
REVERT: B  397 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8395 (mm)
REVERT: C  111 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: C  122 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7297 (tm-30)
REVERT: C  532 ASP cc_start: 0.7098 (p0) cc_final: 0.6863 (p0)
  outliers start: 48
  outliers final: 32
  residues processed: 211
  average time/residue: 0.2423
  time to fit residues: 76.3227
Evaluate side-chains
  206 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 170
  time to evaluate  : 1.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 125 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   chunk 143 optimal weight:    9.9990
   chunk 116 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 150 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
C  36 GLN
C 413 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  13788  Z= 0.451
  Angle     :  0.640  11.509  18774  Z= 0.327
  Chirality :  0.048   0.147   2184
  Planarity :  0.005   0.035   2439
  Dihedral  :  5.972  51.072   2068
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 19.23 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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: -0.01 (0.20), residues: 1755
  helix:  1.37 (0.22), residues: 558
  sheet:  0.15 (0.24), residues: 450
  loop : -1.16 (0.22), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 173 
 HIS   0.003   0.001   HIS C 410 
 PHE   0.021   0.002   PHE A 533 
 TYR   0.014   0.002   TYR B  80 
 ARG   0.008   0.000   ARG C 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 80
    poor density    : 168
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7257 (tm-30)
REVERT: A  130 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8010 (mtt)
REVERT: A  462 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7641 (mm-30)
REVERT: B  348 ILE cc_start: 0.8281 (pt) cc_final: 0.8062 (pt)
REVERT: B  462 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7508 (mt-10)
REVERT: B  532 ASP cc_start: 0.6809 (p0) cc_final: 0.6552 (p0)
REVERT: C  111 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8115 (mp)
REVERT: C  122 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7278 (tm-30)
REVERT: C  376 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7584 (pt0)
REVERT: C  397 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8325 (mm)
REVERT: C  462 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7671 (mm-30)
REVERT: C  532 ASP cc_start: 0.7143 (p0) cc_final: 0.6898 (p0)
  outliers start: 80
  outliers final: 61
  residues processed: 231
  average time/residue: 0.2365
  time to fit residues: 82.0085
Evaluate side-chains
  237 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 70
    poor density    : 167
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  549 THR
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  572 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  189 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  376 GLU
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  397 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  498 MET
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  563 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 151 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 168 optimal weight:    0.5980
   chunk 139 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 88 optimal weight:   20.0000
   chunk 162 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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: 0.7820
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13788  Z= 0.204
  Angle     :  0.520  13.094  18774  Z= 0.265
  Chirality :  0.043   0.172   2184
  Planarity :  0.004   0.035   2439
  Dihedral  :  5.645  50.577   2068
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 21.19 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.42 (0.20), residues: 1755
  helix:  1.80 (0.22), residues: 555
  sheet:  0.32 (0.23), residues: 450
  loop : -0.90 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 173 
 HIS   0.001   0.000   HIS C 410 
 PHE   0.014   0.001   PHE A 157 
 TYR   0.012   0.001   TYR C  80 
 ARG   0.006   0.000   ARG A 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 177
  time to evaluate  : 1.604 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7246 (tm-30)
REVERT: B  348 ILE cc_start: 0.8240 (pt) cc_final: 0.7998 (pt)
REVERT: B  462 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7404 (mt-10)
REVERT: C  111 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7939 (mp)
REVERT: C  122 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7274 (tm-30)
REVERT: C  397 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8274 (mm)
REVERT: C  462 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7593 (mm-30)
REVERT: C  532 ASP cc_start: 0.7092 (p0) cc_final: 0.6870 (p0)
  outliers start: 60
  outliers final: 46
  residues processed: 223
  average time/residue: 0.2408
  time to fit residues: 80.0686
Evaluate side-chains
  223 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 171
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  189 MET
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  397 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  563 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 141 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 167 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 467 ASN
C 345 HIS
C 396 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13788  Z= 0.217
  Angle     :  0.520  12.174  18774  Z= 0.265
  Chirality :  0.043   0.135   2184
  Planarity :  0.004   0.045   2439
  Dihedral  :  5.545  51.562   2068
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 21.19 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.54 (0.20), residues: 1755
  helix:  1.79 (0.22), residues: 561
  sheet:  0.46 (0.24), residues: 450
  loop : -0.80 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 173 
 HIS   0.002   0.000   HIS C 410 
 PHE   0.014   0.001   PHE A 157 
 TYR   0.012   0.001   TYR C  80 
 ARG   0.006   0.000   ARG B 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 173
  time to evaluate  : 1.507 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7264 (tm-30)
REVERT: A  462 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7613 (mm-30)
REVERT: A  467 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.6978 (t160)
REVERT: B  348 ILE cc_start: 0.8210 (pt) cc_final: 0.7967 (pt)
REVERT: B  462 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7373 (mt-10)
REVERT: B  532 ASP cc_start: 0.6978 (p0) cc_final: 0.6607 (p0)
REVERT: C  111 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7934 (mp)
REVERT: C  122 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7183 (tm-30)
REVERT: C  462 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7594 (mm-30)
  outliers start: 64
  outliers final: 54
  residues processed: 221
  average time/residue: 0.2445
  time to fit residues: 80.9076
Evaluate side-chains
  233 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 172
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  467 ASN
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  572 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  189 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  498 MET
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  563 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 106 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 131 optimal weight:    0.9980
   chunk 152 optimal weight:    0.9990
   chunk 160 optimal weight:    0.7980
   chunk 146 optimal weight:    9.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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: 0.7816
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13788  Z= 0.215
  Angle     :  0.518  11.862  18774  Z= 0.264
  Chirality :  0.043   0.136   2184
  Planarity :  0.004   0.034   2439
  Dihedral  :  5.517  51.851   2068
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 20.54 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.67 (0.20), residues: 1755
  helix:  1.92 (0.22), residues: 558
  sheet:  0.54 (0.24), residues: 450
  loop : -0.74 (0.22), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 173 
 HIS   0.002   0.000   HIS C 410 
 PHE   0.014   0.001   PHE A 157 
 TYR   0.012   0.001   TYR C  80 
 ARG   0.006   0.000   ARG B 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 174
  time to evaluate  : 1.369 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7300 (tm-30)
REVERT: A  130 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7876 (mtt)
REVERT: A  462 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7609 (mm-30)
REVERT: B  348 ILE cc_start: 0.8183 (pt) cc_final: 0.7922 (pt)
REVERT: B  462 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7360 (mt-10)
REVERT: B  506 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.5877 (p0)
REVERT: B  532 ASP cc_start: 0.6956 (p0) cc_final: 0.6591 (p0)
REVERT: C  111 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7929 (mp)
REVERT: C  122 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7196 (tm-30)
REVERT: C  346 PHE cc_start: 0.6893 (m-80) cc_final: 0.6685 (m-80)
REVERT: C  462 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7583 (mm-30)
  outliers start: 75
  outliers final: 58
  residues processed: 227
  average time/residue: 0.2363
  time to fit residues: 80.2562
Evaluate side-chains
  238 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 172
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  572 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  189 MET
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  498 MET
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  563 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 156 optimal weight:    0.9990
   chunk 160 optimal weight:    0.6980
   chunk 94 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 141 optimal weight:    5.9990
   chunk 147 optimal weight:    1.9990
   chunk 155 optimal weight:    0.0370
   chunk 102 optimal weight:    0.5980
   chunk 165 optimal weight:    2.9990
   overall best weight:    0.6662

-------------------------------------------------------------------------------
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: 0.7794
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13788  Z= 0.174
  Angle     :  0.494  11.587  18774  Z= 0.252
  Chirality :  0.042   0.137   2184
  Planarity :  0.004   0.053   2439
  Dihedral  :  5.396  51.982   2068
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 21.40 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.20), residues: 1755
  helix:  2.02 (0.22), residues: 558
  sheet:  0.62 (0.24), residues: 444
  loop : -0.59 (0.23), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 173 
 HIS   0.001   0.000   HIS B  65 
 PHE   0.013   0.001   PHE A 157 
 TYR   0.012   0.001   TYR C  80 
 ARG   0.005   0.000   ARG B 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 173
  time to evaluate  : 2.020 
Fit side-chains
REVERT: A   63 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7170 (ptpt)
REVERT: A   66 PHE cc_start: 0.8103 (m-80) cc_final: 0.7532 (t80)
REVERT: A  130 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7851 (mtt)
REVERT: A  462 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7556 (mm-30)
REVERT: B  330 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.7158 (mtm-85)
REVERT: B  348 ILE cc_start: 0.8160 (pt) cc_final: 0.7897 (pt)
REVERT: B  462 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7318 (mt-10)
REVERT: B  506 ASP cc_start: 0.6434 (OUTLIER) cc_final: 0.6083 (p0)
REVERT: B  532 ASP cc_start: 0.6960 (p0) cc_final: 0.6603 (p0)
REVERT: C  122 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7207 (tm-30)
REVERT: C  346 PHE cc_start: 0.6865 (m-80) cc_final: 0.6664 (m-80)
  outliers start: 60
  outliers final: 49
  residues processed: 216
  average time/residue: 0.2501
  time to fit residues: 80.2275
Evaluate side-chains
  225 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 170
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  572 THR
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  506 ASP
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9980
   chunk 173 optimal weight:    0.1980
   chunk 159 optimal weight:    1.9990
   chunk 138 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 106 optimal weight:    0.5980
   chunk 84 optimal weight:    6.9990
   chunk 109 optimal weight:    4.9990
   chunk 147 optimal weight:    7.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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: 0.7787
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13788  Z= 0.168
  Angle     :  0.493  11.392  18774  Z= 0.251
  Chirality :  0.042   0.136   2184
  Planarity :  0.004   0.045   2439
  Dihedral  :  4.869  53.241   2058
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 21.69 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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:  0.95 (0.20), residues: 1755
  helix:  2.10 (0.22), residues: 558
  sheet:  0.69 (0.24), residues: 444
  loop : -0.51 (0.23), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 173 
 HIS   0.006   0.001   HIS B  65 
 PHE   0.013   0.001   PHE B 157 
 TYR   0.011   0.001   TYR C  80 
 ARG   0.007   0.000   ARG A 330 

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 172
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7181 (ptpt)
REVERT: A   66 PHE cc_start: 0.8078 (m-80) cc_final: 0.7478 (t80)
REVERT: A  130 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7806 (mtt)
REVERT: A  238 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6513 (tp30)
REVERT: A  330 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7344 (mtm-85)
REVERT: A  462 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7570 (mm-30)
REVERT: B  348 ILE cc_start: 0.8151 (pt) cc_final: 0.7895 (pt)
REVERT: B  462 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7305 (mt-10)
REVERT: B  532 ASP cc_start: 0.6971 (p0) cc_final: 0.6619 (p0)
REVERT: C  122 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7212 (tm-30)
  outliers start: 58
  outliers final: 47
  residues processed: 214
  average time/residue: 0.2467
  time to fit residues: 77.7690
Evaluate side-chains
  223 residues out of total 1383 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 170
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  572 THR
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 127 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 138 optimal weight:    0.4980
   chunk 57 optimal weight:    0.7980
   chunk 141 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.164996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.123973 restraints weight = 14330.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.95
r_work: 0.3334 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13788  Z= 0.305
  Angle     :  0.564  11.262  18774  Z= 0.288
  Chirality :  0.045   0.138   2184
  Planarity :  0.004   0.040   2439
  Dihedral  :  5.120  57.089   2058
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 21.19 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.20), residues: 1755
  helix:  1.81 (0.22), residues: 561
  sheet:  0.56 (0.24), residues: 444
  loop : -0.57 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 173 
 HIS   0.002   0.000   HIS C 410 
 PHE   0.018   0.002   PHE A 533 
 TYR   0.013   0.002   TYR C  80 
 ARG   0.007   0.000   ARG B 330 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2908.20 seconds
wall clock time: 53 minutes 21.14 seconds (3201.14 seconds total)