Starting phenix.real_space_refine
on Thu Mar 14 20:33:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shn_25131/03_2024/7shn_25131_updated.pdb"
  }
  resolution = 3.1
  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=   0.008 sd=   0.071
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      46      5.16       5
     C    6192      2.51       5
     N    1704      2.21       5
     O    1729      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   74": "NH1" <-> "NH2"
    Residue "A PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  113": "NH1" <-> "NH2"
    Residue "A ARG  120": "NH1" <-> "NH2"
    Residue "A ASP  126": "OD1" <-> "OD2"
    Residue "A ARG  128": "NH1" <-> "NH2"
    Residue "A PHE  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  153": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  165": "NH1" <-> "NH2"
    Residue "A TYR  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  189": "NH1" <-> "NH2"
    Residue "A TYR  227": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  236": "NH1" <-> "NH2"
    Residue "A PHE  261": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  280": "NH1" <-> "NH2"
    Residue "A ARG  285": "NH1" <-> "NH2"
    Residue "A GLU  300": "OE1" <-> "OE2"
    Residue "A GLU  323": "OE1" <-> "OE2"
    Residue "A ARG  324": "NH1" <-> "NH2"
    Residue "A TYR  327": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  333": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  374": "OE1" <-> "OE2"
    Residue "A PHE  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  408": "OE1" <-> "OE2"
    Residue "A PHE  423": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  428": "OD1" <-> "OD2"
    Residue "A PHE  434": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  436": "NH1" <-> "NH2"
    Residue "A ARG  464": "NH1" <-> "NH2"
    Residue "A GLU  471": "OE1" <-> "OE2"
    Residue "A GLU  477": "OE1" <-> "OE2"
    Residue "A PHE  517": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  518": "NH1" <-> "NH2"
    Residue "A TYR  541": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  564": "OE1" <-> "OE2"
    Residue "A ARG  568": "NH1" <-> "NH2"
    Residue "A ASP  575": "OD1" <-> "OD2"
    Residue "A GLU  577": "OE1" <-> "OE2"
    Residue "A ASP  581": "OD1" <-> "OD2"
    Residue "A GLU  592": "OE1" <-> "OE2"
    Residue "A GLU  596": "OE1" <-> "OE2"
    Residue "A ASP  603": "OD1" <-> "OD2"
    Residue "A GLU  609": "OE1" <-> "OE2"
    Residue "A PHE  619": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  625": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  629": "OD1" <-> "OD2"
    Residue "A ASP  638": "OD1" <-> "OD2"
    Residue "A GLU  640": "OE1" <-> "OE2"
    Residue "A PHE  673": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  674": "OD1" <-> "OD2"
    Residue "A GLU  676": "OE1" <-> "OE2"
    Residue "B ARG   74": "NH1" <-> "NH2"
    Residue "B PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  113": "NH1" <-> "NH2"
    Residue "B ARG  120": "NH1" <-> "NH2"
    Residue "B ARG  128": "NH1" <-> "NH2"
    Residue "B PHE  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  153": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  165": "NH1" <-> "NH2"
    Residue "B TYR  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  189": "NH1" <-> "NH2"
    Residue "B TYR  227": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  236": "NH1" <-> "NH2"
    Residue "B PHE  261": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  267": "OE1" <-> "OE2"
    Residue "B GLU  278": "OE1" <-> "OE2"
    Residue "B ARG  280": "NH1" <-> "NH2"
    Residue "B ARG  285": "NH1" <-> "NH2"
    Residue "B ARG  324": "NH1" <-> "NH2"
    Residue "B TYR  327": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  333": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  371": "OE1" <-> "OE2"
    Residue "B GLU  380": "OE1" <-> "OE2"
    Residue "B PHE  385": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  400": "OE1" <-> "OE2"
    Residue "B GLU  411": "OE1" <-> "OE2"
    Residue "B PHE  423": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  427": "OE1" <-> "OE2"
    Residue "B PHE  434": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  436": "NH1" <-> "NH2"
    Residue "B ARG  464": "NH1" <-> "NH2"
    Residue "B ASP  469": "OD1" <-> "OD2"
    Residue "B GLU  499": "OE1" <-> "OE2"
    Residue "B PHE  517": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  518": "NH1" <-> "NH2"
    Residue "B TYR  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  541": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  568": "NH1" <-> "NH2"
    Residue "B ASP  575": "OD1" <-> "OD2"
    Residue "B GLU  577": "OE1" <-> "OE2"
    Residue "B GLU  592": "OE1" <-> "OE2"
    Residue "B GLU  596": "OE1" <-> "OE2"
    Residue "B GLU  609": "OE1" <-> "OE2"
    Residue "B PHE  619": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  629": "OD1" <-> "OD2"
    Residue "B ASP  638": "OD1" <-> "OD2"
    Residue "B PHE  644": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  649": "OD1" <-> "OD2"
    Residue "B PHE  673": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9677
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4771
          Classifications: {'peptide': 606}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 20, 'TRANS': 585}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'UNK:plan-1': 21}
          Unresolved non-hydrogen planarities: 21
    Chain: "B"
      Number of atoms: 4783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 607, 4783
          Classifications: {'peptide': 607}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 20, 'TRANS': 586}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'UNK:plan-1': 21}
          Unresolved non-hydrogen planarities: 21
    Chain: "A"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'3VV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 61
          Unusual residues: {'3VV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
  Time building chain proxies: 5.48, per 1000 atoms: 0.57
  Number of scatterers: 9677
  At special positions: 0
  Unit cell: (73.428, 141.792, 112.252, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     P       6     15.00
     O    1729      8.00
     N    1704      7.00
     C    6192      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: 3.76
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2274

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      55 helices and 6 sheets defined
      59.8% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 82
      removed outlier: 3.535A  pdb=" N   GLN A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TRP A  77 " --> pdb=" O   GLN A  73 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU A  81 " --> pdb=" O   TRP A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 98
      removed outlier: 4.162A  pdb=" N   LEU A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 123
      removed outlier: 3.634A  pdb=" N   ARG A 113 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   CYS A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 156
      removed outlier: 3.581A  pdb=" N   LEU A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      Proline residue:  A 143  - end of helix
      removed outlier: 3.774A  pdb=" N   ARG A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 3.644A  pdb=" N   ARG A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ARG A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 184
      No H-bonds generated for 'chain 'A' and resid 181 through 184'
    Processing helix  chain 'A' and resid 193 through 196
      No H-bonds generated for 'chain 'A' and resid 193 through 196'
    Processing helix  chain 'A' and resid 201 through 233
      removed outlier: 3.889A  pdb=" N   HIS A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      Proline residue:  A 218  - end of helix
      removed outlier: 3.849A  pdb=" N   SER A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 252
    Processing helix  chain 'A' and resid 269 through 284
      removed outlier: 3.585A  pdb=" N   GLY A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   MET A 282 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 295
    Processing helix  chain 'A' and resid 299 through 335
      removed outlier: 3.603A  pdb=" N   LEU A 306 " --> pdb=" O   GLU A 302 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   SER A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A 313 " --> pdb=" O   SER A 309 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A 321 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   TRP A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A 328 " --> pdb=" O   ARG A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 352
      removed outlier: 3.531A  pdb=" N   VAL A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      Proline residue:  A 350  - end of helix
    Processing helix  chain 'A' and resid 374 through 394
      removed outlier: 3.523A  pdb=" N   SER A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 403
    Processing helix  chain 'A' and resid 409 through 431
      removed outlier: 4.190A  pdb=" N   ARG A 418 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU A 427 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   GLN A 430 " --> pdb=" O   PHE A 426 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 520
      removed outlier: 3.573A  pdb=" N   ILE A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 538
      No H-bonds generated for 'chain 'A' and resid 536 through 538'
    Processing helix  chain 'A' and resid 554 through 556
      No H-bonds generated for 'chain 'A' and resid 554 through 556'
    Processing helix  chain 'A' and resid 563 through 569
      removed outlier: 3.588A  pdb=" N   GLN A 567 " --> pdb=" O   VAL A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 582
    Processing helix  chain 'A' and resid 601 through 604
      No H-bonds generated for 'chain 'A' and resid 601 through 604'
    Processing helix  chain 'A' and resid 607 through 620
      removed outlier: 3.557A  pdb=" N   PHE A 619 " --> pdb=" O   MET A 615 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR A 620 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 650
      removed outlier: 3.851A  pdb=" N   LYS A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ILE A 643 " --> pdb=" O   VAL A 639 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLN A 645 " --> pdb=" O   GLY A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 666
      No H-bonds generated for 'chain 'A' and resid 664 through 666'
    Processing helix  chain 'A' and resid 691 through 695
    Processing helix  chain 'A' and resid 698 through 706
      removed outlier: 3.616A  pdb=" N   UNK A 703 " --> pdb=" O   UNK A 699 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   UNK A 704 " --> pdb=" O   UNK A 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 82
      removed outlier: 3.587A  pdb=" N   GLN B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ARG B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B  81 " --> pdb=" O   TRP B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 98
      removed outlier: 4.488A  pdb=" N   LEU B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 123
      removed outlier: 3.600A  pdb=" N   LEU B 107 " --> pdb=" O   SER B 103 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG B 113 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 156
      removed outlier: 3.599A  pdb=" N   LEU B 142 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      Proline residue:  B 143  - end of helix
      removed outlier: 3.699A  pdb=" N   ARG B 152 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 161
      No H-bonds generated for 'chain 'B' and resid 158 through 161'
    Processing helix  chain 'B' and resid 163 through 174
      removed outlier: 3.814A  pdb=" N   ARG B 172 " --> pdb=" O   ALA B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 184
      No H-bonds generated for 'chain 'B' and resid 181 through 184'
    Processing helix  chain 'B' and resid 193 through 196
      No H-bonds generated for 'chain 'B' and resid 193 through 196'
    Processing helix  chain 'B' and resid 201 through 233
      removed outlier: 3.562A  pdb=" N   ALA B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   HIS B 210 " --> pdb=" O   ALA B 206 " (cutoff:3.500A)
      Proline residue:  B 218  - end of helix
      removed outlier: 3.900A  pdb=" N   SER B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 256
      removed outlier: 3.556A  pdb=" N   ILE B 246 " --> pdb=" O   TRP B 242 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA B 247 " --> pdb=" O   PRO B 243 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 288
      removed outlier: 3.514A  pdb=" N   ARG B 274 " --> pdb=" O   ALA B 270 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   VAL B 286 " --> pdb=" O   MET B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 295
    Processing helix  chain 'B' and resid 299 through 335
      removed outlier: 3.600A  pdb=" N   LEU B 306 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU B 313 " --> pdb=" O   SER B 309 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU B 321 " --> pdb=" O   ILE B 317 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   TRP B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL B 328 " --> pdb=" O   ARG B 324 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   MET B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 352
      removed outlier: 3.607A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 345 " (cutoff:3.500A)
      Proline residue:  B 350  - end of helix
    Processing helix  chain 'B' and resid 374 through 394
      removed outlier: 3.536A  pdb=" N   SER B 379 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR B 382 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLU B 383 " --> pdb=" O   SER B 379 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR B 393 " --> pdb=" O   ARG B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 403
      removed outlier: 3.562A  pdb=" N   GLU B 400 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG B 401 " --> pdb=" O   ASP B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 431
      removed outlier: 3.848A  pdb=" N   GLU B 411 " --> pdb=" O   LYS B 407 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ARG B 418 " --> pdb=" O   GLY B 414 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLU B 427 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN B 430 " --> pdb=" O   PHE B 426 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ARG B 431 " --> pdb=" O   GLU B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 520
      removed outlier: 3.670A  pdb=" N   ILE B 519 " --> pdb=" O   SER B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 538
      No H-bonds generated for 'chain 'B' and resid 536 through 538'
    Processing helix  chain 'B' and resid 563 through 569
    Processing helix  chain 'B' and resid 573 through 582
    Processing helix  chain 'B' and resid 588 through 590
      No H-bonds generated for 'chain 'B' and resid 588 through 590'
    Processing helix  chain 'B' and resid 601 through 604
      No H-bonds generated for 'chain 'B' and resid 601 through 604'
    Processing helix  chain 'B' and resid 607 through 620
      removed outlier: 3.689A  pdb=" N   MET B 618 " --> pdb=" O   GLY B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 650
      removed outlier: 3.807A  pdb=" N   LYS B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE B 643 " --> pdb=" O   VAL B 639 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLN B 645 " --> pdb=" O   GLY B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 664 through 666
      No H-bonds generated for 'chain 'B' and resid 664 through 666'
    Processing helix  chain 'B' and resid 691 through 695
    Processing helix  chain 'B' and resid 698 through 706
      removed outlier: 3.552A  pdb=" N   UNK B 703 " --> pdb=" O   UNK B 699 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 467 through 469
      removed outlier: 6.622A  pdb=" N   LEU A 531 " --> pdb=" O   VAL A 468 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 679 through 681
      removed outlier: 3.534A  pdb=" N   THR A 506 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE A 673 " --> pdb=" O   THR A 506 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 503 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   SER A 656 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   ALA A 626 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   ILE A 657 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   LEU A 628 " --> pdb=" O   ILE A 657 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 481 through 483
      removed outlier: 3.644A  pdb=" N   VAL A 490 " --> pdb=" O   ILE A 481 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   THR A 483 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   VAL A 488 " --> pdb=" O   THR A 483 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 475 through 477
    Processing sheet with id=  E, first strand: chain 'B' and resid 503 through 505
      removed outlier: 3.803A  pdb=" N   LEU B 503 " --> pdb=" O   LEU B 654 " (cutoff:3.500A)
      removed outlier: 5.643A  pdb=" N   ALA B 626 " --> pdb=" O   LEU B 655 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ILE B 657 " --> pdb=" O   ALA B 626 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU B 628 " --> pdb=" O   ILE B 657 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 481 through 483
      removed outlier: 3.606A  pdb=" N   VAL B 490 " --> pdb=" O   ILE B 481 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   THR B 483 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   VAL B 488 " --> pdb=" O   THR B 483 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1209 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: 2.91

  Time building geometry restraints manager: 4.03 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1535
        1.26 -     1.40: 2544
        1.40 -     1.54: 5657
        1.54 -     1.68: 69
        1.68 -     1.82: 78
  Bond restraints: 9883
  Sorted by residual:
  bond pdb=" C49 3VV A 800 "
       pdb=" O48 3VV A 800 "
    ideal  model  delta    sigma   weight residual
    1.621  1.271  0.350 2.00e-02 2.50e+03 3.05e+02
  bond pdb=" C49 3VV B 801 "
       pdb=" O48 3VV B 801 "
    ideal  model  delta    sigma   weight residual
    1.621  1.272  0.349 2.00e-02 2.50e+03 3.04e+02
  bond pdb=" C47 3VV A 800 "
       pdb=" O48 3VV A 800 "
    ideal  model  delta    sigma   weight residual
    1.286  1.606 -0.320 2.00e-02 2.50e+03 2.56e+02
  bond pdb=" C47 3VV B 801 "
       pdb=" O48 3VV B 801 "
    ideal  model  delta    sigma   weight residual
    1.286  1.605 -0.319 2.00e-02 2.50e+03 2.55e+02
  bond pdb=" C49 3VV B 801 "
       pdb=" C50 3VV B 801 "
    ideal  model  delta    sigma   weight residual
    1.291  1.559 -0.268 2.00e-02 2.50e+03 1.79e+02
  ... (remaining 9878 not shown)

  Histogram of bond angle deviations from ideal:
       97.89 -   105.30: 189
      105.30 -   112.71: 5040
      112.71 -   120.12: 4161
      120.12 -   127.53: 3895
      127.53 -   134.94: 109
  Bond angle restraints: 13394
  Sorted by residual:
  angle pdb=" C09 3VV B 801 "
        pdb=" C10 3VV B 801 "
        pdb=" C11 3VV B 801 "
      ideal   model   delta    sigma   weight residual
     152.65  120.93   31.72 3.00e+00 1.11e-01 1.12e+02
  angle pdb=" C09 3VV A 800 "
        pdb=" C10 3VV A 800 "
        pdb=" C11 3VV A 800 "
      ideal   model   delta    sigma   weight residual
     152.65  121.23   31.42 3.00e+00 1.11e-01 1.10e+02
  angle pdb=" C   ILE A 352 "
        pdb=" CA  ILE A 352 "
        pdb=" CB  ILE A 352 "
      ideal   model   delta    sigma   weight residual
     112.02  123.25  -11.23 1.31e+00 5.83e-01 7.35e+01
  angle pdb=" N   THR B 353 "
        pdb=" CA  THR B 353 "
        pdb=" C   THR B 353 "
      ideal   model   delta    sigma   weight residual
     112.93  121.49   -8.56 1.12e+00 7.97e-01 5.84e+01
  angle pdb=" N   ILE A 352 "
        pdb=" CA  ILE A 352 "
        pdb=" C   ILE A 352 "
      ideal   model   delta    sigma   weight residual
     110.53  103.49    7.04 9.40e-01 1.13e+00 5.61e+01
  ... (remaining 13389 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.88: 5746
       35.88 -    71.75: 133
       71.75 -   107.63: 13
      107.63 -   143.50: 0
      143.50 -   179.38: 2
  Dihedral angle restraints: 5894
    sinusoidal: 2365
      harmonic: 3529
  Sorted by residual:
  dihedral pdb=" CA  LEU A 190 "
           pdb=" C   LEU A 190 "
           pdb=" N   ARG A 191 "
           pdb=" CA  ARG A 191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.05  -29.95     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  MET B 186 "
           pdb=" C   MET B 186 "
           pdb=" N   ASP B 187 "
           pdb=" CA  ASP B 187 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.33   29.67     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" C   THR B 353 "
           pdb=" N   THR B 353 "
           pdb=" CA  THR B 353 "
           pdb=" CB  THR B 353 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.48   14.48     0      2.50e+00 1.60e-01 3.36e+01
  ... (remaining 5891 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.140: 1431
       0.140 -    0.279: 53
       0.279 -    0.419: 7
       0.419 -    0.559: 1
       0.559 -    0.698: 4
  Chirality restraints: 1496
  Sorted by residual:
  chirality pdb=" CA  ARG B 389 "
            pdb=" N   ARG B 389 "
            pdb=" C   ARG B 389 "
            pdb=" CB  ARG B 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.81    0.70 2.00e-01 2.50e+01 1.22e+01
  chirality pdb=" CA  THR B 353 "
            pdb=" N   THR B 353 "
            pdb=" C   THR B 353 "
            pdb=" CB  THR B 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.86    0.67 2.00e-01 2.50e+01 1.12e+01
  chirality pdb=" C52 3VV B 801 "
            pdb=" C47 3VV B 801 "
            pdb=" C50 3VV B 801 "
            pdb=" O53 3VV B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    1.95    0.61 2.00e-01 2.50e+01 9.38e+00
  ... (remaining 1493 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 389 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   ARG A 389 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ARG A 389 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ASN A 390 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 242 "   -0.052 5.00e-02 4.00e+02   7.78e-02 9.68e+00
        pdb=" N   PRO B 243 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO B 243 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 243 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 389 "   -0.015 2.00e-02 2.50e+03   3.07e-02 9.40e+00
        pdb=" C   ARG B 389 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ARG B 389 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ASN B 390 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 3340
        2.84 -     3.36: 8886
        3.36 -     3.87: 15856
        3.87 -     4.39: 19794
        4.39 -     4.90: 32541
  Nonbonded interactions: 80417
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 640 "
            pdb=" NH2 ARG B 660 "
     model   vdw
     2.330 2.520
  nonbonded pdb=" O   VAL A 250 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.338 2.440
  nonbonded pdb=" O   VAL A 123 "
            pdb=" NH1 ARG B 381 "
     model   vdw
     2.341 2.520
  nonbonded pdb=" O   TYR B 547 "
            pdb=" NH2 ARG B 617 "
     model   vdw
     2.369 2.520
  nonbonded pdb=" NH1 ARG A  89 "
            pdb=" OG  SER A 161 "
     model   vdw
     2.372 2.520
  ... (remaining 80412 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' and (resid 67 through 707 or (resid 800 and (name C07 or name C08 or  \ 
name C09 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ 
 or name C16 or name C17 or name C18 or name C21 or name C22 or name C24 or name \ 
 C26 or name C27 or name C29 or name C31 or name C33 or name C34 or name C35 or  \ 
name C36 or name C46 or name C47 or name C49 or name C50 or name C52 or name C59 \ 
 or name C61 or name C62 or name C65 or name C67 or name N23 or name N28 or name \ 
 N58 or name N60 or name N63 or name N64 or name N66 or name O19 or name O25 or  \ 
name O30 or name O32 or name O37 or name O39 or name O40 or name O41 or name O43 \ 
 or name O44 or name O45 or name O48 or name O51 or name O53 or name O55 or name \ 
 O56 or name O57 or name P38 or name P42 or name P54 or name S20))))
  selection = (chain 'B' and (resid 67 through 436 or resid 463 through 683 or (resid 684 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 685 through 707 or \ 
 resid 801))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:             0.010
  Extract box with map and model:          4.520
  Check model and map are aligned:         0.140
  Set scattering table:                    0.090
  Process input model:                     29.980
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
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      :  0.017   0.350   9883  Z= 1.041
  Angle     :  1.348  31.721  13394  Z= 0.686
  Chirality :  0.079   0.698   1496
  Planarity :  0.008   0.078   1689
  Dihedral  : 16.384 179.377   3620
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  9.04 %
    Favored  : 90.75 %
  Cbeta Deviations :  0.53 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.40 (0.15), residues: 1159
  helix: -4.51 (0.08), residues: 779
  sheet: -2.53 (0.68), residues: 49
  loop : -3.03 (0.26), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B 242 
 HIS   0.018   0.002   HIS A 283 
 PHE   0.024   0.004   PHE B 204 
 TYR   0.024   0.004   TYR A 174 
 ARG   0.016   0.001   ARG A 163 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ASP cc_start: 0.7873 (t70) cc_final: 0.7594 (t70)
REVERT: A  191 ARG cc_start: 0.7531 (mmp80) cc_final: 0.7209 (ttm110)
REVERT: A  195 GLN cc_start: 0.7575 (mt0) cc_final: 0.7356 (tt0)
REVERT: A  242 TRP cc_start: 0.7287 (t60) cc_final: 0.5664 (m100)
REVERT: A  317 ILE cc_start: 0.9024 (tt) cc_final: 0.8819 (tt)
REVERT: A  477 GLU cc_start: 0.7230 (mp0) cc_final: 0.6342 (mp0)
REVERT: A  600 ASP cc_start: 0.7866 (t0) cc_final: 0.7648 (t0)
REVERT: A  615 MET cc_start: 0.7802 (mmm) cc_final: 0.7584 (mmm)
REVERT: A  669 HIS cc_start: 0.6537 (m-70) cc_final: 0.5866 (m-70)
REVERT: B  115 ASP cc_start: 0.8095 (t70) cc_final: 0.7764 (t70)
REVERT: B  152 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7447 (mtp-110)
REVERT: B  282 MET cc_start: 0.8616 (tpp) cc_final: 0.8169 (mtp)
REVERT: B  502 HIS cc_start: 0.7225 (m90) cc_final: 0.6859 (m170)
REVERT: B  555 ASP cc_start: 0.8144 (t0) cc_final: 0.7767 (t0)
REVERT: B  600 ASP cc_start: 0.7581 (t0) cc_final: 0.7253 (t0)
REVERT: B  612 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7993 (mpt-90)
  outliers start: 2
  outliers final: 2
  residues processed: 166
  average time/residue: 0.3756
  time to fit residues: 76.4318
Evaluate side-chains
  127 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ARG
Chi-restraints excluded: chain B residue  588 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.0040
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0670
   chunk 94 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.4730

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN
A 133 GLN
A 136 GLN
A 169 HIS
A 185 ASN
A 289 ASN
A 307 GLN
A 316 GLN
A 420 HIS
A 430 GLN
A 478 ASN
A 544 GLN
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 GLN
B 136 GLN
B 169 HIS
B 185 ASN
B 256 ASN
B 307 GLN
B 316 GLN
B 420 HIS
B 430 GLN
** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN
B 502 HIS
B 556 GLN
B 567 GLN
** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 645 GLN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9883  Z= 0.156
  Angle     :  0.626   7.716  13394  Z= 0.320
  Chirality :  0.040   0.215   1496
  Planarity :  0.005   0.055   1689
  Dihedral  : 11.182 177.943   1416
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.41 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.19), residues: 1159
  helix: -2.58 (0.14), residues: 771
  sheet: -2.40 (0.68), residues: 55
  loop : -2.58 (0.28), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 242 
 HIS   0.004   0.001   HIS B 669 
 PHE   0.020   0.001   PHE B  71 
 TYR   0.018   0.001   TYR A 327 
 ARG   0.005   0.000   ARG B 234 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
REVERT: A  477 GLU cc_start: 0.7207 (mp0) cc_final: 0.6439 (mp0)
REVERT: B  282 MET cc_start: 0.8453 (tpp) cc_final: 0.8116 (mtp)
REVERT: B  433 HIS cc_start: 0.6724 (m-70) cc_final: 0.6324 (m-70)
REVERT: B  482 VAL cc_start: 0.8581 (p) cc_final: 0.8344 (p)
REVERT: B  600 ASP cc_start: 0.7658 (t0) cc_final: 0.7181 (t0)
REVERT: B  625 TYR cc_start: 0.7636 (m-80) cc_final: 0.7333 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 141
  average time/residue: 0.2944
  time to fit residues: 53.6680
Evaluate side-chains
  124 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  602 LYS
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  588 ILE
Chi-restraints excluded: chain B residue  659 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 74 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 109 optimal weight:   20.0000
   chunk 117 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 433 HIS
** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 611 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9883  Z= 0.232
  Angle     :  0.605   8.050  13394  Z= 0.300
  Chirality :  0.042   0.290   1496
  Planarity :  0.004   0.039   1689
  Dihedral  : 10.314 162.969   1412
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.04 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.23), residues: 1159
  helix: -1.30 (0.17), residues: 771
  sheet: -2.13 (0.70), residues: 54
  loop : -2.33 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 595 
 HIS   0.006   0.001   HIS B 502 
 PHE   0.016   0.001   PHE B 540 
 TYR   0.015   0.001   TYR A 327 
 ARG   0.009   0.001   ARG B 612 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
REVERT: A  477 GLU cc_start: 0.7442 (mp0) cc_final: 0.6500 (mp0)
REVERT: B  242 TRP cc_start: 0.6805 (OUTLIER) cc_final: 0.5711 (t60)
REVERT: B  282 MET cc_start: 0.8418 (tpp) cc_final: 0.8128 (mtp)
REVERT: B  431 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.7021 (mtm110)
REVERT: B  433 HIS cc_start: 0.6702 (m90) cc_final: 0.6156 (m-70)
REVERT: B  482 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8354 (p)
REVERT: B  501 MET cc_start: 0.6989 (pmm) cc_final: 0.6258 (tpt)
REVERT: B  554 ARG cc_start: 0.6973 (ttm110) cc_final: 0.6734 (ttm110)
REVERT: B  625 TYR cc_start: 0.7504 (m-80) cc_final: 0.7284 (m-80)
  outliers start: 31
  outliers final: 18
  residues processed: 138
  average time/residue: 0.2659
  time to fit residues: 48.8937
Evaluate side-chains
  127 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  602 LYS
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  482 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  588 ILE
Chi-restraints excluded: chain B residue  659 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:   20.0000
   chunk 82 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9990
   chunk 109 optimal weight:   20.0000
   chunk 115 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 556 GLN
A 611 GLN
A 669 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   9883  Z= 0.352
  Angle     :  0.645  12.545  13394  Z= 0.316
  Chirality :  0.045   0.288   1496
  Planarity :  0.004   0.048   1689
  Dihedral  :  9.922 152.990   1412
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 16.16 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.24), residues: 1159
  helix: -0.84 (0.18), residues: 767
  sheet: -2.09 (0.71), residues: 54
  loop : -1.92 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 242 
 HIS   0.009   0.001   HIS A 669 
 PHE   0.018   0.002   PHE B 540 
 TYR   0.017   0.002   TYR A 327 
 ARG   0.009   0.001   ARG A 163 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 ASP cc_start: 0.7887 (t70) cc_final: 0.7458 (t70)
REVERT: A  325 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8099 (tt)
REVERT: A  331 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7695 (tt0)
REVERT: A  431 ARG cc_start: 0.7035 (ptt90) cc_final: 0.6366 (ptt-90)
REVERT: A  433 HIS cc_start: 0.6714 (m-70) cc_final: 0.6147 (m90)
REVERT: A  477 GLU cc_start: 0.7441 (mp0) cc_final: 0.6593 (mp0)
REVERT: B  242 TRP cc_start: 0.6741 (OUTLIER) cc_final: 0.5710 (t60)
REVERT: B  282 MET cc_start: 0.8477 (tpp) cc_final: 0.8110 (mtp)
REVERT: B  477 GLU cc_start: 0.7593 (mp0) cc_final: 0.6903 (mp0)
REVERT: B  482 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8431 (p)
REVERT: B  501 MET cc_start: 0.7152 (pmm) cc_final: 0.6707 (tpt)
REVERT: B  554 ARG cc_start: 0.6969 (ttm110) cc_final: 0.6685 (ttm110)
REVERT: B  600 ASP cc_start: 0.7667 (t0) cc_final: 0.7148 (t0)
  outliers start: 40
  outliers final: 24
  residues processed: 146
  average time/residue: 0.2630
  time to fit residues: 51.1495
Evaluate side-chains
  143 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  331 GLU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  602 LYS
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  192 ASN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  482 VAL
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  659 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 98 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 59 optimal weight:   40.0000
   chunk 104 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 556 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9883  Z= 0.243
  Angle     :  0.589  10.007  13394  Z= 0.289
  Chirality :  0.041   0.262   1496
  Planarity :  0.004   0.038   1689
  Dihedral  :  9.490 146.187   1410
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 16.87 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.24), residues: 1159
  helix: -0.48 (0.19), residues: 773
  sheet: -1.93 (0.71), residues: 54
  loop : -1.79 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 242 
 HIS   0.004   0.001   HIS A 669 
 PHE   0.016   0.001   PHE B 252 
 TYR   0.014   0.001   TYR B 310 
 ARG   0.007   0.000   ARG A 163 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7574 (tt0)
REVERT: A  431 ARG cc_start: 0.6993 (ptt90) cc_final: 0.6692 (ptt-90)
REVERT: A  433 HIS cc_start: 0.6669 (m-70) cc_final: 0.6233 (m90)
REVERT: A  477 GLU cc_start: 0.7619 (mp0) cc_final: 0.6934 (mp0)
REVERT: B  242 TRP cc_start: 0.6754 (OUTLIER) cc_final: 0.5685 (t60)
REVERT: B  282 MET cc_start: 0.8434 (tpp) cc_final: 0.8076 (mtp)
REVERT: B  477 GLU cc_start: 0.7597 (mp0) cc_final: 0.6974 (mp0)
REVERT: B  482 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8355 (p)
REVERT: B  501 MET cc_start: 0.7105 (pmm) cc_final: 0.6606 (tpt)
REVERT: B  539 MET cc_start: 0.8384 (mtt) cc_final: 0.8161 (mtt)
REVERT: B  554 ARG cc_start: 0.6954 (ttm110) cc_final: 0.6636 (ttm110)
REVERT: B  600 ASP cc_start: 0.7623 (t0) cc_final: 0.7106 (t0)
  outliers start: 41
  outliers final: 26
  residues processed: 135
  average time/residue: 0.2731
  time to fit residues: 48.9767
Evaluate side-chains
  136 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  331 GLU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  602 LYS
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  192 ASN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  482 VAL
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  659 HIS
Chi-restraints excluded: chain B residue  684 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 104 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0060
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 116 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    0.8598

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

Flipped N/Q/H residues before XYZ refinement:
A 556 GLN
B 136 GLN
B 621 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9883  Z= 0.179
  Angle     :  0.546   9.387  13394  Z= 0.267
  Chirality :  0.040   0.231   1496
  Planarity :  0.003   0.033   1689
  Dihedral  :  8.944 132.260   1410
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.48 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.25), residues: 1159
  helix: -0.01 (0.19), residues: 776
  sheet: -1.87 (0.71), residues: 54
  loop : -1.76 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 137 
 HIS   0.005   0.001   HIS A 502 
 PHE   0.018   0.001   PHE B 252 
 TYR   0.013   0.001   TYR B 310 
 ARG   0.006   0.000   ARG B 152 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 1.108 
Fit side-chains
REVERT: A  431 ARG cc_start: 0.7026 (ptt90) cc_final: 0.6681 (ptt-90)
REVERT: A  433 HIS cc_start: 0.6686 (m-70) cc_final: 0.6098 (m90)
REVERT: A  477 GLU cc_start: 0.7687 (mp0) cc_final: 0.7079 (mp0)
REVERT: A  544 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7396 (tp40)
REVERT: B  242 TRP cc_start: 0.6697 (OUTLIER) cc_final: 0.6461 (t-100)
REVERT: B  282 MET cc_start: 0.8393 (tpp) cc_final: 0.8019 (mtp)
REVERT: B  477 GLU cc_start: 0.7651 (mp0) cc_final: 0.6980 (mp0)
REVERT: B  501 MET cc_start: 0.7068 (pmm) cc_final: 0.6481 (tpt)
REVERT: B  554 ARG cc_start: 0.6928 (ttm110) cc_final: 0.6597 (ttm110)
  outliers start: 38
  outliers final: 22
  residues processed: 136
  average time/residue: 0.2373
  time to fit residues: 44.1330
Evaluate side-chains
  130 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  242 TRP
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  659 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 115 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 53 optimal weight:   20.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 556 GLN
B 136 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9883  Z= 0.204
  Angle     :  0.553   8.818  13394  Z= 0.270
  Chirality :  0.040   0.217   1496
  Planarity :  0.003   0.034   1689
  Dihedral  :  8.670 117.579   1410
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.68 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.25), residues: 1159
  helix:  0.22 (0.19), residues: 776
  sheet: -1.75 (0.71), residues: 54
  loop : -1.63 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 595 
 HIS   0.004   0.001   HIS A 502 
 PHE   0.018   0.001   PHE B 252 
 TYR   0.014   0.001   TYR B 310 
 ARG   0.007   0.000   ARG B 152 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 1.080 
Fit side-chains
REVERT: A  115 ASP cc_start: 0.7922 (t70) cc_final: 0.7557 (t70)
REVERT: A  331 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7522 (tt0)
REVERT: A  431 ARG cc_start: 0.7003 (ptt90) cc_final: 0.6656 (ptt-90)
REVERT: A  433 HIS cc_start: 0.6683 (m-70) cc_final: 0.6089 (m90)
REVERT: A  477 GLU cc_start: 0.7700 (mp0) cc_final: 0.7127 (mp0)
REVERT: B  282 MET cc_start: 0.8397 (tpp) cc_final: 0.8008 (mtp)
REVERT: B  433 HIS cc_start: 0.6763 (m90) cc_final: 0.6392 (m-70)
REVERT: B  477 GLU cc_start: 0.7599 (mp0) cc_final: 0.7353 (mp0)
REVERT: B  501 MET cc_start: 0.7113 (pmm) cc_final: 0.6539 (tpt)
REVERT: B  554 ARG cc_start: 0.6884 (ttm110) cc_final: 0.6552 (ttm110)
  outliers start: 35
  outliers final: 27
  residues processed: 131
  average time/residue: 0.2408
  time to fit residues: 43.1925
Evaluate side-chains
  134 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  331 GLU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  192 ASN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  659 HIS
Chi-restraints excluded: chain B residue  684 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 105 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 556 GLN
B 136 GLN
B 544 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9883  Z= 0.168
  Angle     :  0.545  11.901  13394  Z= 0.266
  Chirality :  0.039   0.192   1496
  Planarity :  0.003   0.035   1689
  Dihedral  :  8.431 106.501   1410
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.60 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.26), residues: 1159
  helix:  0.49 (0.19), residues: 776
  sheet: -1.65 (0.73), residues: 54
  loop : -1.57 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 601 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.019   0.001   PHE B 252 
 TYR   0.012   0.001   TYR B 310 
 ARG   0.015   0.001   ARG B 538 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A  115 ASP cc_start: 0.7902 (t70) cc_final: 0.7530 (t70)
REVERT: A  431 ARG cc_start: 0.6981 (ptt90) cc_final: 0.6644 (ptt-90)
REVERT: A  433 HIS cc_start: 0.6717 (m-70) cc_final: 0.6099 (m90)
REVERT: A  477 GLU cc_start: 0.7715 (mp0) cc_final: 0.7138 (mp0)
REVERT: B  282 MET cc_start: 0.8370 (tpp) cc_final: 0.7959 (mtp)
REVERT: B  477 GLU cc_start: 0.7593 (mp0) cc_final: 0.6906 (mp0)
REVERT: B  501 MET cc_start: 0.7070 (pmm) cc_final: 0.6542 (tpt)
REVERT: B  554 ARG cc_start: 0.6828 (ttm110) cc_final: 0.6493 (ttm110)
  outliers start: 33
  outliers final: 27
  residues processed: 134
  average time/residue: 0.2210
  time to fit residues: 42.0061
Evaluate side-chains
  136 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  192 ASN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  659 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    0.0870
   chunk 101 optimal weight:    4.9990
   chunk 107 optimal weight:   20.0000
   chunk 64 optimal weight:    0.6980
   chunk 46 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
B 556 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9883  Z= 0.172
  Angle     :  0.537   8.876  13394  Z= 0.263
  Chirality :  0.039   0.177   1496
  Planarity :  0.003   0.042   1689
  Dihedral  :  8.290  96.235   1410
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 18.70 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 1159
  helix:  0.59 (0.19), residues: 782
  sheet: -1.59 (0.73), residues: 54
  loop : -1.53 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 601 
 HIS   0.004   0.001   HIS A 502 
 PHE   0.019   0.001   PHE B 252 
 TYR   0.013   0.001   TYR B 310 
 ARG   0.015   0.001   ARG B 538 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A  115 ASP cc_start: 0.7908 (t70) cc_final: 0.7533 (t70)
REVERT: A  331 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7514 (tt0)
REVERT: A  431 ARG cc_start: 0.6990 (ptt90) cc_final: 0.6743 (ptt-90)
REVERT: A  433 HIS cc_start: 0.6758 (m-70) cc_final: 0.6170 (m90)
REVERT: A  477 GLU cc_start: 0.7702 (mp0) cc_final: 0.7122 (mp0)
REVERT: B  282 MET cc_start: 0.8339 (tpp) cc_final: 0.7904 (mtp)
REVERT: B  433 HIS cc_start: 0.6747 (m90) cc_final: 0.6382 (m-70)
REVERT: B  477 GLU cc_start: 0.7609 (mp0) cc_final: 0.6919 (mp0)
REVERT: B  501 MET cc_start: 0.7132 (pmm) cc_final: 0.6596 (tpt)
REVERT: B  554 ARG cc_start: 0.6823 (ttm110) cc_final: 0.6499 (ttm110)
  outliers start: 34
  outliers final: 30
  residues processed: 135
  average time/residue: 0.2195
  time to fit residues: 40.9325
Evaluate side-chains
  140 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  331 GLU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  598 MET
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  192 ASN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  659 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 119 optimal weight:   40.0000
   chunk 110 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 75 optimal weight:    0.2980
   chunk 101 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   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 136 GLN
A 318 ASN
** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 157 GLN
B 556 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9883  Z= 0.242
  Angle     :  0.567   8.741  13394  Z= 0.277
  Chirality :  0.041   0.183   1496
  Planarity :  0.004   0.044   1689
  Dihedral  :  8.275  95.540   1410
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.21 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.26), residues: 1159
  helix:  0.55 (0.19), residues: 782
  sheet: -1.63 (0.71), residues: 54
  loop : -1.47 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 601 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.019   0.001   PHE B 252 
 TYR   0.014   0.001   TYR A 327 
 ARG   0.014   0.001   ARG B 538 

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

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

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2318 Ramachandran restraints generated.
    1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 1.096 
Fit side-chains
REVERT: A  115 ASP cc_start: 0.7928 (t70) cc_final: 0.7538 (t70)
REVERT: A  331 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7531 (tt0)
REVERT: A  408 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7281 (pt0)
REVERT: A  431 ARG cc_start: 0.7003 (ptt90) cc_final: 0.6758 (ptt-90)
REVERT: A  433 HIS cc_start: 0.6745 (m-70) cc_final: 0.6154 (m90)
REVERT: A  477 GLU cc_start: 0.7701 (mp0) cc_final: 0.7130 (mp0)
REVERT: B  282 MET cc_start: 0.8378 (tpp) cc_final: 0.7931 (mtp)
REVERT: B  433 HIS cc_start: 0.6738 (m90) cc_final: 0.6371 (m-70)
REVERT: B  477 GLU cc_start: 0.7625 (mp0) cc_final: 0.6865 (mp0)
REVERT: B  501 MET cc_start: 0.7189 (pmm) cc_final: 0.6720 (tpt)
REVERT: B  554 ARG cc_start: 0.6780 (ttm110) cc_final: 0.6456 (ttm110)
  outliers start: 31
  outliers final: 30
  residues processed: 132
  average time/residue: 0.2138
  time to fit residues: 39.8438
Evaluate side-chains
  142 residues out of total 987 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  331 GLU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  598 MET
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  192 ASN
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  659 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 95 optimal weight:    0.5980
   chunk 39 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   chunk 83 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN
B 556 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.198529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.135824 restraints weight = 10747.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 3.01
r_work: 0.3375 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9883  Z= 0.159
  Angle     :  0.534   8.191  13394  Z= 0.261
  Chirality :  0.039   0.173   1496
  Planarity :  0.003   0.043   1689
  Dihedral  :  7.958  92.822   1410
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.51 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.26), residues: 1159
  helix:  0.75 (0.19), residues: 782
  sheet: -1.60 (0.72), residues: 54
  loop : -1.47 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 601 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.028   0.001   PHE B  71 
 TYR   0.012   0.001   TYR B 310 
 ARG   0.014   0.001   ARG B 538 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2350.13 seconds
wall clock time: 42 minutes 56.79 seconds (2576.79 seconds total)