Starting phenix.real_space_refine
on Thu Feb 15 11:49:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/02_2024/6qc6_4498_updated.pdb"
  }
  resolution = 4.1
  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=   0.000 sd=   0.022
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: 7
    Type Number    sf(0)   Gaussians
     Fe     28      7.16       5
     Zn      1      6.06       5
     P      12      5.49       5
     S     462      5.16       5
     C   42100      2.51       5
     N   11025      2.21       5
     O   11716      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "V1 PHE   22": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V1 ARG   32": "NH1" <-> "NH2"
    Residue "V1 ARG  237": "NH1" <-> "NH2"
    Residue "V1 ARG  423": "NH1" <-> "NH2"
    Residue "V2 ARG  187": "NH1" <-> "NH2"
    Residue "V2 PHE  191": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V2 PHE  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S1 TYR  613": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S2 TYR  108": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S2 TYR  275": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S7 ARG  174": "NH1" <-> "NH2"
    Residue "S7 ARG  178": "NH1" <-> "NH2"
    Residue "S8 TYR  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V3 PHE   61": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S6 TYR   23": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S4 ARG   64": "NH1" <-> "NH2"
    Residue "A9 ARG   97": "NH1" <-> "NH2"
    Residue "A9 PHE  178": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A9 ARG  186": "NH1" <-> "NH2"
    Residue "A9 ARG  292": "NH1" <-> "NH2"
    Residue "A2 ARG   33": "NH1" <-> "NH2"
    Residue "A6 ARG   22": "NH1" <-> "NH2"
    Residue "AL PHE   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AL ARG  106": "NH1" <-> "NH2"
    Residue "AL PHE  108": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AA TYR   17": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D1 TYR  142": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D1 ARG  195": "NH1" <-> "NH2"
    Residue "D1 TYR  250": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D1 ARG  274": "NH1" <-> "NH2"
    Residue "D6 PHE   20": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D6 PHE  136": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D6 ARG  173": "NH1" <-> "NH2"
    Residue "D5 PHE   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D5 TYR  159": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D5 TYR  422": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D5 TYR  485": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D4 TYR  406": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D2 PHE  292": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AK ARG   19": "NH1" <-> "NH2"
    Residue "B5 ARG   26": "NH1" <-> "NH2"
    Residue "AJ ARG   95": "NH1" <-> "NH2"
    Residue "AJ PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AJ TYR  304": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "AJ ARG  305": "NH1" <-> "NH2"
    Residue "A3 ARG   46": "NH1" <-> "NH2"
    Residue "C2 ARG    5": "NH1" <-> "NH2"
    Residue "C2 ARG  120": "NH1" <-> "NH2"
    Residue "B4 ARG   41": "NH1" <-> "NH2"
    Residue "AM ARG   26": "NH1" <-> "NH2"
    Residue "AM ARG   81": "NH1" <-> "NH2"
    Residue "B9 ARG   92": "NH1" <-> "NH2"
    Residue "B9 ARG  128": "NH1" <-> "NH2"
    Residue "B9 ARG  176": "NH1" <-> "NH2"
    Residue "B8 ARG   70": "NH1" <-> "NH2"
    Residue "BK TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A1 ARG   25": "NH1" <-> "NH2"
    Residue "A1 TYR   61": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.20s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 65344
  Number of models: 1
  Model: ""
    Number of chains: 58
    Chain: "V1"
      Number of atoms: 3312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3312
          Classifications: {'peptide': 430}
          Link IDs: {'PTRANS': 21, 'TRANS': 408}
    Chain: "V2"
      Number of atoms: 1647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1647
          Classifications: {'peptide': 212}
          Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 189}
    Chain: "S1"
      Number of atoms: 5275
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 688, 5275
          Classifications: {'peptide': 688}
          Link IDs: {'CIS': 3, 'PTRANS': 32, 'TRANS': 652}
    Chain: "S2"
      Number of atoms: 3414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3414
          Classifications: {'peptide': 424}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 396}
          Chain breaks: 1
    Chain: "S3"
      Number of atoms: 1726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1726
          Classifications: {'peptide': 208}
          Link IDs: {'PTRANS': 15, 'TRANS': 192}
    Chain: "S7"
      Number of atoms: 1247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1247
          Classifications: {'peptide': 156}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145}
    Chain: "S8"
      Number of atoms: 1414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1414
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 10, 'TRANS': 165}
    Chain: "V3"
      Number of atoms: 345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 345
          Classifications: {'peptide': 41}
          Link IDs: {'PTRANS': 3, 'TRANS': 37}
    Chain: "S6"
      Number of atoms: 737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 737
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "S4"
      Number of atoms: 1024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 1024
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 6, 'TRANS': 119}
    Chain: "A9"
      Number of atoms: 2293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2293
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 14, 'TRANS': 272}
          Chain breaks: 2
    Chain: "A2"
      Number of atoms: 665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 665
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 4, 'TRANS': 77}
    Chain: "A5"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 901
          Classifications: {'peptide': 111}
          Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 101}
    Chain: "A6"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 969
          Classifications: {'peptide': 114}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106}
    Chain: "A7"
      Number of atoms: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 757
          Classifications: {'peptide': 95}
          Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 82}
          Chain breaks: 1
    Chain: "AL"
      Number of atoms: 1201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1201
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 11, 'TRANS': 132}
    Chain: "AA"
      Number of atoms: 645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 645
          Classifications: {'peptide': 80}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 76}
    Chain: "D3"
      Number of atoms: 728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 728
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 4, 'TRANS': 85}
          Chain breaks: 1
    Chain: "D1"
      Number of atoms: 2415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2415
          Classifications: {'peptide': 303}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 279}
          Chain breaks: 1
    Chain: "D6"
      Number of atoms: 1308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1308
          Classifications: {'peptide': 171}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 164}
          Chain breaks: 1
    Chain: "4L"
      Number of atoms: 748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 748
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 96}
    Chain: "D5"
      Number of atoms: 4805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4805
          Classifications: {'peptide': 606}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 578}
    Chain: "D4"
      Number of atoms: 3646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 459, 3646
          Classifications: {'peptide': 459}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437}
    Chain: "D2"
      Number of atoms: 2724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2724
          Classifications: {'peptide': 347}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 326}
    Chain: "AK"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1025
          Classifications: {'peptide': 140}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132}
    Chain: "B5"
      Number of atoms: 1156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1156
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 128}
    Chain: "AB"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 702
          Classifications: {'peptide': 87}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 81}
    Chain: "A8"
      Number of atoms: 1404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1404
          Classifications: {'peptide': 171}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156}
    Chain: "BJ"
      Number of atoms: 1441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1441
          Classifications: {'peptide': 171}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 159}
    Chain: "AJ"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2583
          Classifications: {'peptide': 319}
          Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 298}
    Chain: "S5"
      Number of atoms: 822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 822
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
    Chain: "A3"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 582
          Classifications: {'peptide': 74}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 62}
    Chain: "B3"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 578
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "C2"
      Number of atoms: 997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 997
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 106}
    Chain: "B4"
      Number of atoms: 1059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1059
          Classifications: {'peptide': 128}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117}
    Chain: "AM"
      Number of atoms: 1143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1143
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
    Chain: "B6"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 815
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 12, 'TRANS': 83}
          Chain breaks: 1
    Chain: "B7"
      Number of atoms: 1026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 1026
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 7, 'TRANS': 111}
    Chain: "B9"
      Number of atoms: 1515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1515
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 16, 'TRANS': 159}
    Chain: "B2"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 563
          Classifications: {'peptide': 65}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 56}
    Chain: "B8"
      Number of atoms: 1324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1324
          Classifications: {'peptide': 157}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 135}
    Chain: "BK"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 853
          Classifications: {'peptide': 102}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 93}
    Chain: "C1"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 391
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 3, 'TRANS': 42}
    Chain: "B1"
      Number of atoms: 449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 449
          Classifications: {'peptide': 52}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49}
    Chain: "A1"
      Number of atoms: 577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 577
          Classifications: {'peptide': 70}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 67}
    Chain: "V1"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 39
          Unusual residues: {'FMN': 1, 'SF4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "V2"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'FES': 1}
          Classifications: {'undetermined': 1}
    Chain: "S1"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 20
          Unusual residues: {'FES': 1, 'SF4': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "S7"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}
    Chain: "S8"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'SF4': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "S6"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "A9"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'NDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "AA"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'ZMP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
    Chain: "D1"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'3PE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 25
    Chain: "D5"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 60
          Unusual residues: {'CDL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 40
    Chain: "D4"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 68
          Unusual residues: {'3PE': 1, 'PC1': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 37
    Chain: "AB"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ZMP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
    Chain: "B8"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 38
          Unusual residues: {'3PE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 13

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2715  SG  CYSV1 365      48.225 165.422 146.700  1.00 22.71           S
  ATOM   3039  SG  CYSV1 405      49.721 167.960 152.622  1.00 35.26           S
  ATOM   2695  SG  CYSV1 362      53.954 166.134 147.839  1.00 49.95           S
  ATOM   2676  SG  CYSV1 359      50.455 171.732 147.580  1.00 33.25           S
  ATOM   4116  SG  CYSV2 103      30.010 174.921 152.659  1.00 71.72           S
  ATOM   4150  SG  CYSV2 108      27.213 173.005 154.928  1.00 46.44           S
  ATOM   4430  SG  CYSV2 144      33.958 174.100 156.175  1.00 62.59           S
  ATOM   4453  SG  CYSV2 148      31.784 173.020 158.750  1.00 82.67           S
  ATOM   5785  SG  CYSS1 114      60.691 159.297 128.639  1.00 33.03           S
  ATOM   5724  SG  CYSS1 105      55.835 156.808 125.154  1.00 19.49           S
  ATOM   5745  SG  CYSS1 108      58.138 162.746 123.736  1.00 17.62           S
  ATOM   6117  SG  CYSS1 156      60.245 168.535 136.122  1.00 22.66           S
  ATOM   6094  SG  CYSS1 153      54.632 170.309 133.028  1.00 24.73           S
  ATOM   6141  SG  CYSS1 159      59.524 174.471 133.536  1.00 19.06           S
  ATOM   6471  SG  CYSS1 203      60.311 169.197 129.856  1.00 22.00           S
  ATOM   5230  SG  CYSS1  41      62.077 166.678 143.018  1.00 18.85           S
  ATOM   5316  SG  CYSS1  52      61.367 163.079 141.979  1.00 22.33           S
  ATOM   5341  SG  CYSS1  55      63.947 161.723 147.190  1.00 34.48           S
  ATOM   5442  SG  CYSS1  69      64.309 165.580 147.546  1.00 37.88           S
  ATOM  16127  SG  CYSS7 119      71.224 134.140 102.159  1.00 32.66           S
  ATOM  16357  SG  CYSS7 149      65.463 134.346 103.830  1.00 32.00           S
  ATOM  15629  SG  CYSS7  55      66.921 130.562  98.527  1.00 52.61           S
  ATOM  15623  SG  CYSS7  54      68.382 128.334 104.075  1.00 47.74           S
  ATOM  17549  SG  CYSS8 116      61.813 142.180 103.705  1.00 24.05           S
  ATOM  17596  SG  CYSS8 122      58.352 145.026 108.388  1.00 17.04           S
  ATOM  17323  SG  CYSS8  87      64.845 145.759 108.376  1.00 17.94           S
  ATOM  17625  SG  CYSS8 126      53.380 151.017 112.003  1.00 19.83           S
  ATOM  17296  SG  CYSS8  83      59.644 151.245 110.024  1.00 13.82           S
  ATOM  17254  SG  CYSS8  77      55.690 156.160 108.587  1.00 17.08           S
  ATOM  17273  SG  CYSS8  80      57.282 154.793 114.931  1.00 15.00           S
  ATOM  18846  SG  CYSS6  59      41.491 160.874 116.776  1.00 36.24           S
  ATOM  19024  SG  CYSS6  84      45.230 162.488 116.521  1.00 29.73           S
  ATOM  19046  SG  CYSS6  87      42.675 160.703 114.462  1.00 25.07           S

  Time building chain proxies: 28.17, per 1000 atoms: 0.43
  Number of scatterers: 65344
  At special positions: 0
  Unit cell: (249.2, 222.6, 201.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     Fe     28     26.01
     S     462     16.00
     P      12     15.00
     O   11716      8.00
     N   11025      7.00
     C   42100      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYSAK  17 " - pdb=" SG  CYSAK  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYSAK  94 " - pdb=" SG  CYSAK 114 " distance=2.03
    Simple disulfide: pdb=" SG  CYSA8  35 " - pdb=" SG  CYSA8  65 " distance=2.04
    Simple disulfide: pdb=" SG  CYSA8  45 " - pdb=" SG  CYSA8  55 " distance=2.04
    Simple disulfide: pdb=" SG  CYSA8  77 " - pdb=" SG  CYSA8 109 " distance=2.02
    Simple disulfide: pdb=" SG  CYSA8  87 " - pdb=" SG  CYSA8  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYSBJ  76 " - pdb=" SG  CYSBJ  83 " distance=2.04
    Simple disulfide: pdb=" SG  CYSBJ 112 " - pdb=" SG  CYSBJ 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYSS5  32 " - pdb=" SG  CYSS5  65 " distance=2.04
    Simple disulfide: pdb=" SG  CYSS5  42 " - pdb=" SG  CYSS5  55 " distance=2.03
    Simple disulfide: pdb=" SG  CYSB7  58 " - pdb=" SG  CYSB7  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYSB7  68 " - pdb=" SG  CYSB7  79 " distance=2.04

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 20.32
  Conformation dependent library (CDL) restraints added in 8.6 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" FESS1 803 "
        pdb="FE1  FESS1 803 " - pdb=" SG  CYSS1  52 "
        pdb="FE2  FESS1 803 " - pdb=" SG  CYSS1  55 "
        pdb="FE1  FESS1 803 " - pdb=" SG  CYSS1  41 "
        pdb="FE2  FESS1 803 " - pdb=" SG  CYSS1  69 "
      pdb=" FESV2 300 "
        pdb="FE2  FESV2 300 " - pdb=" SG  CYSV2 148 "
        pdb="FE2  FESV2 300 " - pdb=" SG  CYSV2 144 "
        pdb="FE1  FESV2 300 " - pdb=" SG  CYSV2 103 "
        pdb="FE1  FESV2 300 " - pdb=" SG  CYSV2 108 "
      pdb=" SF4S1 801 "
        pdb="FE3  SF4S1 801 " - pdb=" NE2 HISS1 101 "
        pdb="FE4  SF4S1 801 " - pdb=" SG  CYSS1 108 "
        pdb="FE1  SF4S1 801 " - pdb=" SG  CYSS1 114 "
        pdb="FE2  SF4S1 801 " - pdb=" SG  CYSS1 105 "
      pdb=" SF4S1 802 "
        pdb="FE2  SF4S1 802 " - pdb=" SG  CYSS1 153 "
        pdb="FE3  SF4S1 802 " - pdb=" SG  CYSS1 159 "
        pdb="FE1  SF4S1 802 " - pdb=" SG  CYSS1 156 "
        pdb="FE4  SF4S1 802 " - pdb=" SG  CYSS1 203 "
      pdb=" SF4S7 300 "
        pdb="FE1  SF4S7 300 " - pdb=" SG  CYSS7 119 "
        pdb="FE2  SF4S7 300 " - pdb=" SG  CYSS7 149 "
        pdb="FE3  SF4S7 300 " - pdb=" SG  CYSS7  55 "
        pdb="FE4  SF4S7 300 " - pdb=" SG  CYSS7  54 "
      pdb=" SF4S8 201 "
        pdb="FE3  SF4S8 201 " - pdb=" SG  CYSS8 122 "
        pdb="FE2  SF4S8 201 " - pdb=" SG  CYSS8 116 "
        pdb="FE4  SF4S8 201 " - pdb=" SG  CYSS8  87 "
        pdb="FE1  SF4S8 201 " - pdb=" SG  CYSS8 119 "
      pdb=" SF4S8 202 "
        pdb="FE1  SF4S8 202 " - pdb=" SG  CYSS8 126 "
        pdb="FE4  SF4S8 202 " - pdb=" SG  CYSS8  80 "
        pdb="FE2  SF4S8 202 " - pdb=" SG  CYSS8  83 "
        pdb="FE3  SF4S8 202 " - pdb=" SG  CYSS8  77 "
      pdb=" SF4V1 500 "
        pdb="FE1  SF4V1 500 " - pdb=" SG  CYSV1 365 "
        pdb="FE3  SF4V1 500 " - pdb=" SG  CYSV1 362 "
        pdb="FE2  SF4V1 500 " - pdb=" SG  CYSV1 405 "
        pdb="FE4  SF4V1 500 " - pdb=" SG  CYSV1 359 "
      Number of angles added : 81
    Zn2+ tetrahedral coordination
      pdb="  ZNS6 300 "
        pdb="ZN    ZNS6 300 " - pdb=" NE2 HISS6  68 "
        pdb="ZN    ZNS6 300 " - pdb=" SG  CYSS6  87 "
        pdb="ZN    ZNS6 300 " - pdb=" SG  CYSS6  59 "
        pdb="ZN    ZNS6 300 " - pdb=" SG  CYSS6  84 "
      Number of angles added : 3


  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  15196

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      299 helices and 28 sheets defined
      48.2% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 8.89
  Creating SS restraints...
    Processing helix  chain 'V1' and resid 33 through 38
    Processing helix  chain 'V1' and resid 45 through 49
    Processing helix  chain 'V1' and resid 53 through 63
    Processing helix  chain 'V1' and resid 75 through 81
    Processing helix  chain 'V1' and resid 106 through 113
      removed outlier: 4.280A  pdb=" N   ILEV1 110 " --> pdb=" O   LYSV1 106 " (cutoff:3.500A)
    Processing helix  chain 'V1' and resid 115 through 127
    Processing helix  chain 'V1' and resid 143 through 158
    Processing helix  chain 'V1' and resid 185 through 187
      No H-bonds generated for 'chain 'V1' and resid 185 through 187'
    Processing helix  chain 'V1' and resid 191 through 196
    Processing helix  chain 'V1' and resid 225 through 236
      Proline residue: V1 232  - end of helix
      removed outlier: 3.811A  pdb=" N   CYSV1 235 " --> pdb=" O   SERV1 231 " (cutoff:3.500A)
    Processing helix  chain 'V1' and resid 276 through 281
    Processing helix  chain 'V1' and resid 291 through 293
      No H-bonds generated for 'chain 'V1' and resid 291 through 293'
    Processing helix  chain 'V1' and resid 309 through 314
      removed outlier: 4.959A  pdb=" N   THRV1 314 " --> pdb=" O   SERV1 310 " (cutoff:3.500A)
    Processing helix  chain 'V1' and resid 319 through 324
    Processing helix  chain 'V1' and resid 343 through 356
    Processing helix  chain 'V1' and resid 363 through 380
    Processing helix  chain 'V1' and resid 386 through 399
    Processing helix  chain 'V1' and resid 407 through 421
      Proline residue: V1 414  - end of helix
    Processing helix  chain 'V1' and resid 423 through 437
    Processing helix  chain 'V2' and resid 25 through 37
    Processing helix  chain 'V2' and resid 43 through 57
      removed outlier: 3.920A  pdb=" N   VALV2  47 " --> pdb=" O   ALAV2  44 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   LEUV2  48 " --> pdb=" O   ALAV2  45 " (cutoff:3.500A)
      Proline residue: V2  49  - end of helix
    Processing helix  chain 'V2' and resid 63 through 72
    Processing helix  chain 'V2' and resid 77 through 86
    Processing helix  chain 'V2' and resid 107 through 110
      No H-bonds generated for 'chain 'V2' and resid 107 through 110'
    Processing helix  chain 'V2' and resid 113 through 124
    Processing helix  chain 'V2' and resid 166 through 177
    Processing helix  chain 'S1' and resid 13 through 15
      No H-bonds generated for 'chain 'S1' and resid 13 through 15'
    Processing helix  chain 'S1' and resid 26 through 33
    Processing helix  chain 'S1' and resid 84 through 97
    Processing helix  chain 'S1' and resid 116 through 123
    Processing helix  chain 'S1' and resid 159 through 165
    Processing helix  chain 'S1' and resid 197 through 202
      removed outlier: 3.545A  pdb=" N   ILES1 200 " --> pdb=" O   GLYS1 197 " (cutoff:3.500A)
    Processing helix  chain 'S1' and resid 265 through 268
      No H-bonds generated for 'chain 'S1' and resid 265 through 268'
    Processing helix  chain 'S1' and resid 271 through 275
    Processing helix  chain 'S1' and resid 296 through 309
    Processing helix  chain 'S1' and resid 325 through 338
    Processing helix  chain 'S1' and resid 359 through 362
      removed outlier: 4.040A  pdb=" N   TYRS1 362 " --> pdb=" O   ARGS1 359 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S1' and resid 359 through 362'
    Processing helix  chain 'S1' and resid 369 through 371
      No H-bonds generated for 'chain 'S1' and resid 369 through 371'
    Processing helix  chain 'S1' and resid 389 through 401
    Processing helix  chain 'S1' and resid 426 through 434
    Processing helix  chain 'S1' and resid 440 through 444
    Processing helix  chain 'S1' and resid 456 through 458
      No H-bonds generated for 'chain 'S1' and resid 456 through 458'
    Processing helix  chain 'S1' and resid 463 through 479
    Processing helix  chain 'S1' and resid 497 through 504
    Processing helix  chain 'S1' and resid 512 through 516
    Processing helix  chain 'S1' and resid 566 through 568
      No H-bonds generated for 'chain 'S1' and resid 566 through 568'
    Processing helix  chain 'S1' and resid 596 through 606
    Processing helix  chain 'S1' and resid 616 through 626
    Processing helix  chain 'S1' and resid 628 through 630
      No H-bonds generated for 'chain 'S1' and resid 628 through 630'
    Processing helix  chain 'S1' and resid 642 through 650
      removed outlier: 4.174A  pdb=" N   LYSS1 650 " --> pdb=" O   SERS1 646 " (cutoff:3.500A)
    Processing helix  chain 'S1' and resid 668 through 673
    Processing helix  chain 'S1' and resid 676 through 679
      No H-bonds generated for 'chain 'S1' and resid 676 through 679'
    Processing helix  chain 'S1' and resid 683 through 692
    Processing helix  chain 'S2' and resid 8 through 13
    Processing helix  chain 'S2' and resid 87 through 92
    Processing helix  chain 'S2' and resid 96 through 105
      Proline residue: S2 101  - end of helix
    Processing helix  chain 'S2' and resid 113 through 126
    Processing helix  chain 'S2' and resid 132 through 161
    Processing helix  chain 'S2' and resid 164 through 184
      removed outlier: 4.136A  pdb=" N   PHES2 168 " --> pdb=" O   METS2 164 " (cutoff:3.500A)
    Processing helix  chain 'S2' and resid 208 through 228
    Processing helix  chain 'S2' and resid 233 through 238
    Processing helix  chain 'S2' and resid 247 through 252
    Processing helix  chain 'S2' and resid 257 through 262
    Processing helix  chain 'S2' and resid 269 through 272
      No H-bonds generated for 'chain 'S2' and resid 269 through 272'
    Processing helix  chain 'S2' and resid 277 through 280
    Processing helix  chain 'S2' and resid 293 through 316
    Processing helix  chain 'S2' and resid 335 through 339
    Processing helix  chain 'S2' and resid 343 through 353
    Processing helix  chain 'S2' and resid 394 through 405
      removed outlier: 4.269A  pdb=" N   GLYS2 401 " --> pdb=" O   ALAS2 397 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   LEUS2 402 " --> pdb=" O   HISS2 398 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   ASPS2 403 " --> pdb=" O   LEUS2 399 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LYSS2 404 " --> pdb=" O   ALAS2 400 " (cutoff:3.500A)
    Processing helix  chain 'S2' and resid 411 through 420
    Processing helix  chain 'S3' and resid 16 through 32
    Processing helix  chain 'S3' and resid 57 through 64
    Processing helix  chain 'S3' and resid 120 through 122
      No H-bonds generated for 'chain 'S3' and resid 120 through 122'
    Processing helix  chain 'S3' and resid 125 through 137
      removed outlier: 3.905A  pdb=" N   ASNS3 128 " --> pdb=" O   LYSS3 125 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   TRPS3 129 " --> pdb=" O   ALAS3 126 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILES3 134 " --> pdb=" O   GLUS3 131 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   METS3 137 " --> pdb=" O   ILES3 134 " (cutoff:3.500A)
    Processing helix  chain 'S3' and resid 207 through 209
      No H-bonds generated for 'chain 'S3' and resid 207 through 209'
    Processing helix  chain 'S7' and resid 25 through 43
    Processing helix  chain 'S7' and resid 55 through 62
    Processing helix  chain 'S7' and resid 70 through 72
      No H-bonds generated for 'chain 'S7' and resid 70 through 72'
    Processing helix  chain 'S7' and resid 94 through 105
      Proline residue: S7  98  - end of helix
    Processing helix  chain 'S7' and resid 124 through 126
      No H-bonds generated for 'chain 'S7' and resid 124 through 126'
    Processing helix  chain 'S7' and resid 153 through 168
    Processing helix  chain 'S7' and resid 172 through 178
    Processing helix  chain 'S8' and resid 14 through 26
    Processing helix  chain 'S8' and resid 28 through 41
    Processing helix  chain 'S8' and resid 82 through 86
    Processing helix  chain 'S8' and resid 121 through 125
    Processing helix  chain 'S8' and resid 151 through 159
    Processing helix  chain 'S8' and resid 163 through 171
    Processing helix  chain 'V3' and resid 50 through 57
    Processing helix  chain 'S6' and resid 24 through 27
      No H-bonds generated for 'chain 'S6' and resid 24 through 27'
    Processing helix  chain 'S6' and resid 42 through 45
      No H-bonds generated for 'chain 'S6' and resid 42 through 45'
    Processing helix  chain 'S4' and resid 19 through 21
      No H-bonds generated for 'chain 'S4' and resid 19 through 21'
    Processing helix  chain 'S4' and resid 27 through 31
    Processing helix  chain 'S4' and resid 78 through 81
      removed outlier: 4.092A  pdb=" N   ASNS4  81 " --> pdb=" O   PROS4  78 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S4' and resid 78 through 81'
    Processing helix  chain 'S4' and resid 89 through 99
    Processing helix  chain 'S4' and resid 118 through 121
      No H-bonds generated for 'chain 'S4' and resid 118 through 121'
    Processing helix  chain 'A9' and resid 30 through 41
    Processing helix  chain 'A9' and resid 53 through 58
    Processing helix  chain 'A9' and resid 78 through 84
    Processing helix  chain 'A9' and resid 112 through 124
    Processing helix  chain 'A9' and resid 144 through 158
    Processing helix  chain 'A9' and resid 178 through 183
    Processing helix  chain 'A9' and resid 207 through 219
    Processing helix  chain 'A9' and resid 238 through 248
    Processing helix  chain 'A9' and resid 282 through 287
    Processing helix  chain 'A9' and resid 310 through 317
    Processing helix  chain 'A2' and resid 27 through 38
    Processing helix  chain 'A2' and resid 41 through 46
    Processing helix  chain 'A2' and resid 83 through 93
    Processing helix  chain 'A5' and resid 19 through 35
    Processing helix  chain 'A5' and resid 43 through 59
    Processing helix  chain 'A5' and resid 65 through 70
    Processing helix  chain 'A5' and resid 77 through 94
    Processing helix  chain 'A6' and resid 24 through 39
    Processing helix  chain 'A6' and resid 42 through 48
    Processing helix  chain 'A6' and resid 55 through 68
    Processing helix  chain 'A6' and resid 75 through 93
    Processing helix  chain 'A6' and resid 99 through 105
    Processing helix  chain 'A6' and resid 118 through 122
    Processing helix  chain 'A7' and resid 5 through 14
    Processing helix  chain 'AL' and resid 4 through 15
      removed outlier: 3.660A  pdb=" N   LEUAL  11 " --> pdb=" O   LEUAL   7 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLNAL  12 " --> pdb=" O   LYSAL   8 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLNAL  13 " --> pdb=" O   ARGAL   9 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   VALAL  14 " --> pdb=" O   GLYAL  10 " (cutoff:3.500A)
    Processing helix  chain 'AL' and resid 21 through 29
      removed outlier: 3.606A  pdb=" N   VALAL  26 " --> pdb=" O   GLYAL  22 " (cutoff:3.500A)
    Processing helix  chain 'AL' and resid 84 through 90
    Processing helix  chain 'AA' and resid 8 through 21
    Processing helix  chain 'AA' and resid 44 through 58
    Processing helix  chain 'AA' and resid 64 through 68
    Processing helix  chain 'AA' and resid 73 through 83
    Processing helix  chain 'D3' and resid 2 through 23
    Processing helix  chain 'D3' and resid 54 through 77
      removed outlier: 4.049A  pdb=" N   VALD3  58 " --> pdb=" O   LYSD3  54 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALAD3  59 " --> pdb=" O   PHED3  55 " (cutoff:3.500A)
      Proline residue: D3  74  - end of helix
      removed outlier: 5.355A  pdb=" N   TRPD3  77 " --> pdb=" O   LEUD3  73 " (cutoff:3.500A)
    Processing helix  chain 'D3' and resid 84 through 107
    Processing helix  chain 'D1' and resid 2 through 10
    Processing helix  chain 'D1' and resid 12 through 31
    Processing helix  chain 'D1' and resid 46 through 57
    Processing helix  chain 'D1' and resid 68 through 86
      Proline residue: D1  75  - end of helix
      removed outlier: 4.963A  pdb=" N   TRPD1  86 " --> pdb=" O   ALAD1  82 " (cutoff:3.500A)
    Processing helix  chain 'D1' and resid 102 through 123
    Processing helix  chain 'D1' and resid 126 through 140
    Processing helix  chain 'D1' and resid 145 through 157
      removed outlier: 4.160A  pdb=" N   METD1 156 " --> pdb=" O   SERD1 152 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ASND1 157 " --> pdb=" O   VALD1 153 " (cutoff:3.500A)
    Processing helix  chain 'D1' and resid 163 through 168
    Processing helix  chain 'D1' and resid 174 through 177
      No H-bonds generated for 'chain 'D1' and resid 174 through 177'
    Processing helix  chain 'D1' and resid 179 through 193
    Processing helix  chain 'D1' and resid 220 through 242
    Processing helix  chain 'D1' and resid 253 through 276
      removed outlier: 4.191A  pdb=" N   SERD1 276 " --> pdb=" O   TRPD1 272 " (cutoff:3.500A)
    Processing helix  chain 'D1' and resid 282 through 308
      Proline residue: D1 295  - end of helix
      Proline residue: D1 308  - end of helix
    Processing helix  chain 'D6' and resid 5 through 21
    Processing helix  chain 'D6' and resid 26 through 46
    Processing helix  chain 'D6' and resid 52 through 63
      removed outlier: 3.755A  pdb=" N   LEUD6  58 " --> pdb=" O   LEUD6  54 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEUD6  61 " --> pdb=" O   PHED6  57 " (cutoff:3.500A)
    Processing helix  chain 'D6' and resid 65 through 74
    Processing helix  chain 'D6' and resid 87 through 108
    Processing helix  chain 'D6' and resid 139 through 146
      removed outlier: 3.609A  pdb=" N   LEUD6 146 " --> pdb=" O   GLYD6 142 " (cutoff:3.500A)
    Processing helix  chain 'D6' and resid 151 through 171
      removed outlier: 3.681A  pdb=" N   ILED6 155 " --> pdb=" O   THRD6 151 " (cutoff:3.500A)
    Processing helix  chain '4L' and resid 3 through 20
    Processing helix  chain '4L' and resid 26 through 51
    Processing helix  chain '4L' and resid 59 through 84
    Processing helix  chain 'D5' and resid 2 through 23
      removed outlier: 3.914A  pdb=" N   LEUD5  15 " --> pdb=" O   THRD5  11 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THRD5  16 " --> pdb=" O   LEUD5  12 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   METD5  17 " --> pdb=" O   ILED5  13 " (cutoff:3.500A)
      Proline residue: D5  18  - end of helix
    Processing helix  chain 'D5' and resid 32 through 56
      removed outlier: 4.655A  pdb=" N   ILED5  49 " --> pdb=" O   ILED5  45 " (cutoff:3.500A)
      Proline residue: D5  50  - end of helix
    Processing helix  chain 'D5' and resid 84 through 107
      removed outlier: 4.503A  pdb=" N   VALD5  90 " --> pdb=" O   SERD5  86 " (cutoff:3.500A)
      Proline residue: D5  91  - end of helix
    Processing helix  chain 'D5' and resid 114 through 133
    Processing helix  chain 'D5' and resid 137 through 157
    Processing helix  chain 'D5' and resid 162 through 193
    Processing helix  chain 'D5' and resid 198 through 203
    Processing helix  chain 'D5' and resid 210 through 223
    Processing helix  chain 'D5' and resid 232 through 238
    Processing helix  chain 'D5' and resid 241 through 249
    Processing helix  chain 'D5' and resid 255 through 262
      removed outlier: 3.814A  pdb=" N   LEUD5 259 " --> pdb=" O   ALAD5 255 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEUD5 260 " --> pdb=" O   GLYD5 256 " (cutoff:3.500A)
    Processing helix  chain 'D5' and resid 271 through 292
    Processing helix  chain 'D5' and resid 298 through 318
    Processing helix  chain 'D5' and resid 322 through 349
    Processing helix  chain 'D5' and resid 367 through 379
    Processing helix  chain 'D5' and resid 387 through 400
      removed outlier: 4.059A  pdb=" N   SERD5 391 " --> pdb=" O   THRD5 387 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LYSD5 392 " --> pdb=" O   GLYD5 388 " (cutoff:3.500A)
    Processing helix  chain 'D5' and resid 408 through 431
    Processing helix  chain 'D5' and resid 448 through 470
      removed outlier: 5.924A  pdb=" N   GLYD5 465 " --> pdb=" O   SERD5 461 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   PHED5 466 " --> pdb=" O   LEUD5 462 " (cutoff:3.500A)
    Processing helix  chain 'D5' and resid 489 through 508
    Processing helix  chain 'D5' and resid 519 through 524
    Processing helix  chain 'D5' and resid 526 through 547
      removed outlier: 3.813A  pdb=" N   TYRD5 529 " --> pdb=" O   LEUD5 526 " (cutoff:3.500A)
      Proline residue: D5 530  - end of helix
      removed outlier: 3.618A  pdb=" N   METD5 533 " --> pdb=" O   PROD5 530 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   HISD5 534 " --> pdb=" O   THRD5 531 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   THRD5 537 " --> pdb=" O   HISD5 534 " (cutoff:3.500A)
      Proline residue: D5 538  - end of helix
      removed outlier: 4.124A  pdb=" N   ASND5 541 " --> pdb=" O   PROD5 538 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEUD5 542 " --> pdb=" O   TYRD5 539 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   METD5 544 " --> pdb=" O   ASND5 541 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SERD5 545 " --> pdb=" O   LEUD5 542 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLND5 546 " --> pdb=" O   THRD5 543 " (cutoff:3.500A)
    Processing helix  chain 'D5' and resid 555 through 561
    Processing helix  chain 'D5' and resid 564 through 577
    Processing helix  chain 'D5' and resid 585 through 599
    Processing helix  chain 'D4' and resid 2 through 4
      No H-bonds generated for 'chain 'D4' and resid 2 through 4'
    Processing helix  chain 'D4' and resid 6 through 16
      Proline residue: D4  13  - end of helix
      removed outlier: 3.844A  pdb=" N   TRPD4  16 " --> pdb=" O   METD4  12 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 23 through 41
      removed outlier: 3.945A  pdb=" N   LEUD4  41 " --> pdb=" O   THRD4  37 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 62 through 79
      Proline residue: D4  74  - end of helix
    Processing helix  chain 'D4' and resid 89 through 110
    Processing helix  chain 'D4' and resid 115 through 135
      Proline residue: D4 128  - end of helix
      removed outlier: 3.791A  pdb=" N   ILED4 131 " --> pdb=" O   VALD4 127 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 142 through 157
    Processing helix  chain 'D4' and resid 159 through 170
    Processing helix  chain 'D4' and resid 176 through 179
      No H-bonds generated for 'chain 'D4' and resid 176 through 179'
    Processing helix  chain 'D4' and resid 191 through 206
    Processing helix  chain 'D4' and resid 210 through 221
      removed outlier: 3.578A  pdb=" N   HISD4 213 " --> pdb=" O   TYRD4 210 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   LEUD4 214 " --> pdb=" O   GLYD4 211 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TRPD4 215 " --> pdb=" O   LEUD4 212 " (cutoff:3.500A)
      Proline residue: D4 217  - end of helix
      removed outlier: 3.523A  pdb=" N   VALD4 221 " --> pdb=" O   LYSD4 218 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 225 through 248
      removed outlier: 5.025A  pdb=" N   LEUD4 248 " --> pdb=" O   METD4 244 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 251 through 257
      removed outlier: 4.217A  pdb=" N   ASPD4 255 " --> pdb=" O   ASND4 251 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   PHED4 256 " --> pdb=" O   PROD4 252 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 259 through 277
      removed outlier: 3.923A  pdb=" N   LEUD4 277 " --> pdb=" O   SERD4 273 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 282 through 302
      removed outlier: 3.552A  pdb=" N   ILED4 286 " --> pdb=" O   LYSD4 283 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 306 through 336
    Processing helix  chain 'D4' and resid 355 through 366
    Processing helix  chain 'D4' and resid 373 through 388
    Processing helix  chain 'D4' and resid 393 through 414
      removed outlier: 3.627A  pdb=" N   THRD4 414 " --> pdb=" O   METD4 410 " (cutoff:3.500A)
    Processing helix  chain 'D4' and resid 431 through 449
      removed outlier: 3.694A  pdb=" N   LEUD4 442 " --> pdb=" O   SERD4 438 " (cutoff:3.500A)
      Proline residue: D4 443  - end of helix
    Processing helix  chain 'D2' and resid 3 through 22
    Processing helix  chain 'D2' and resid 26 through 41
    Processing helix  chain 'D2' and resid 50 through 79
    Processing helix  chain 'D2' and resid 92 through 106
    Processing helix  chain 'D2' and resid 109 through 111
      No H-bonds generated for 'chain 'D2' and resid 109 through 111'
    Processing helix  chain 'D2' and resid 113 through 120
      removed outlier: 4.536A  pdb=" N   GLUD2 117 " --> pdb=" O   PHED2 113 " (cutoff:3.500A)
    Processing helix  chain 'D2' and resid 124 through 148
      Proline residue: D2 138  - end of helix
      removed outlier: 3.963A  pdb=" N   VALD2 141 " --> pdb=" O   ALAD2 137 " (cutoff:3.500A)
      Proline residue: D2 147  - end of helix
    Processing helix  chain 'D2' and resid 151 through 167
    Processing helix  chain 'D2' and resid 175 through 192
    Processing helix  chain 'D2' and resid 198 through 220
    Processing helix  chain 'D2' and resid 227 through 236
    Processing helix  chain 'D2' and resid 239 through 252
    Processing helix  chain 'D2' and resid 258 through 271
      Proline residue: D2 262  - end of helix
      removed outlier: 4.204A  pdb=" N   METD2 265 " --> pdb=" O   PROD2 262 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLUD2 269 " --> pdb=" O   ILED2 266 " (cutoff:3.500A)
    Processing helix  chain 'D2' and resid 277 through 300
      removed outlier: 4.254A  pdb=" N   LEUD2 290 " --> pdb=" O   ALAD2 286 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   TYRD2 291 " --> pdb=" O   LEUD2 287 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   PHED2 292 " --> pdb=" O   LEUD2 288 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   TYRD2 293 " --> pdb=" O   ASND2 289 " (cutoff:3.500A)
    Processing helix  chain 'D2' and resid 311 through 314
      No H-bonds generated for 'chain 'D2' and resid 311 through 314'
    Processing helix  chain 'D2' and resid 327 through 334
    Processing helix  chain 'D2' and resid 340 through 345
      removed outlier: 3.852A  pdb=" N   SERD2 344 " --> pdb=" O   PROD2 341 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILED2 345 " --> pdb=" O   ILED2 342 " (cutoff:3.500A)
    Processing helix  chain 'AK' and resid 2 through 10
    Processing helix  chain 'AK' and resid 19 through 42
    Processing helix  chain 'AK' and resid 48 through 79
    Processing helix  chain 'AK' and resid 87 through 104
    Processing helix  chain 'AK' and resid 108 through 130
    Processing helix  chain 'B5' and resid 16 through 46
      removed outlier: 4.912A  pdb=" N   THRB5  32 " --> pdb=" O   TYRB5  28 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILEB5  34 " --> pdb=" O   LEUB5  30 " (cutoff:3.500A)
      Proline residue: B5  35  - end of helix
    Processing helix  chain 'B5' and resid 70 through 78
    Processing helix  chain 'B5' and resid 83 through 117
    Processing helix  chain 'AB' and resid 8 through 20
    Processing helix  chain 'AB' and resid 44 through 58
    Processing helix  chain 'AB' and resid 73 through 84
    Processing helix  chain 'A8' and resid 21 through 26
    Processing helix  chain 'A8' and resid 28 through 33
    Processing helix  chain 'A8' and resid 39 through 48
    Processing helix  chain 'A8' and resid 56 through 75
    Processing helix  chain 'A8' and resid 80 through 89
    Processing helix  chain 'A8' and resid 101 through 113
    Processing helix  chain 'BJ' and resid 28 through 56
      removed outlier: 5.012A  pdb=" N   ARGBJ  42 " --> pdb=" O   LEUBJ  38 " (cutoff:3.500A)
      Proline residue: BJ  43  - end of helix
    Processing helix  chain 'BJ' and resid 81 through 115
      removed outlier: 4.649A  pdb=" N   GLUBJ  86 " --> pdb=" O   LEUBJ  82 " (cutoff:3.500A)
    Processing helix  chain 'BJ' and resid 125 through 141
    Processing helix  chain 'BJ' and resid 152 through 172
    Processing helix  chain 'AJ' and resid 5 through 10
    Processing helix  chain 'AJ' and resid 36 through 44
    Processing helix  chain 'AJ' and resid 58 through 61
      No H-bonds generated for 'chain 'AJ' and resid 58 through 61'
    Processing helix  chain 'AJ' and resid 79 through 84
    Processing helix  chain 'AJ' and resid 93 through 116
    Processing helix  chain 'AJ' and resid 128 through 141
    Processing helix  chain 'AJ' and resid 146 through 162
      removed outlier: 3.510A  pdb=" N   VALAJ 160 " --> pdb=" O   LYSAJ 156 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   CYSAJ 161 " --> pdb=" O   LYSAJ 157 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   GLUAJ 162 " --> pdb=" O   VALAJ 158 " (cutoff:3.500A)
    Processing helix  chain 'AJ' and resid 176 through 186
    Processing helix  chain 'AJ' and resid 189 through 192
      No H-bonds generated for 'chain 'AJ' and resid 189 through 192'
    Processing helix  chain 'AJ' and resid 197 through 208
    Processing helix  chain 'AJ' and resid 210 through 214
    Processing helix  chain 'AJ' and resid 231 through 239
    Processing helix  chain 'AJ' and resid 247 through 249
      No H-bonds generated for 'chain 'AJ' and resid 247 through 249'
    Processing helix  chain 'AJ' and resid 254 through 263
    Processing helix  chain 'AJ' and resid 269 through 272
      removed outlier: 3.946A  pdb=" N   TYRAJ 272 " --> pdb=" O   VALAJ 269 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'AJ' and resid 269 through 272'
    Processing helix  chain 'AJ' and resid 286 through 297
    Processing helix  chain 'S5' and resid 5 through 8
      No H-bonds generated for 'chain 'S5' and resid 5 through 8'
    Processing helix  chain 'S5' and resid 33 through 42
    Processing helix  chain 'S5' and resid 56 through 66
    Processing helix  chain 'S5' and resid 69 through 88
    Processing helix  chain 'A3' and resid 16 through 30
    Processing helix  chain 'A3' and resid 38 through 46
    Processing helix  chain 'B3' and resid 26 through 38
    Processing helix  chain 'B3' and resid 49 through 52
      No H-bonds generated for 'chain 'B3' and resid 49 through 52'
    Processing helix  chain 'B3' and resid 62 through 66
      removed outlier: 3.634A  pdb=" N   LEUB3  66 " --> pdb=" O   PHEB3  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B3' and resid 62 through 66'
    Processing helix  chain 'B3' and resid 73 through 82
    Processing helix  chain 'C2' and resid 16 through 19
    Processing helix  chain 'C2' and resid 29 through 48
    Processing helix  chain 'C2' and resid 58 through 96
    Processing helix  chain 'B4' and resid 20 through 22
      No H-bonds generated for 'chain 'B4' and resid 20 through 22'
    Processing helix  chain 'B4' and resid 26 through 48
    Processing helix  chain 'B4' and resid 62 through 71
    Processing helix  chain 'B4' and resid 83 through 93
    Processing helix  chain 'B4' and resid 95 through 117
    Processing helix  chain 'AM' and resid 31 through 69
    Processing helix  chain 'AM' and resid 71 through 96
    Processing helix  chain 'AM' and resid 130 through 135
    Processing helix  chain 'B6' and resid 5 through 24
    Processing helix  chain 'B6' and resid 68 through 84
      Proline residue: B6  77  - end of helix
    Processing helix  chain 'B6' and resid 87 through 91
    Processing helix  chain 'B7' and resid 2 through 9
    Processing helix  chain 'B7' and resid 42 through 47
    Processing helix  chain 'B7' and resid 59 through 71
    Processing helix  chain 'B7' and resid 81 through 118
    Processing helix  chain 'B9' and resid 11 through 29
    Processing helix  chain 'B9' and resid 34 through 47
    Processing helix  chain 'B9' and resid 57 through 72
    Processing helix  chain 'B9' and resid 94 through 96
      No H-bonds generated for 'chain 'B9' and resid 94 through 96'
    Processing helix  chain 'B9' and resid 108 through 113
    Processing helix  chain 'B9' and resid 115 through 130
    Processing helix  chain 'B9' and resid 134 through 142
    Processing helix  chain 'B9' and resid 167 through 170
      No H-bonds generated for 'chain 'B9' and resid 167 through 170'
    Processing helix  chain 'B2' and resid 19 through 42
    Processing helix  chain 'B8' and resid 5 through 7
      No H-bonds generated for 'chain 'B8' and resid 5 through 7'
    Processing helix  chain 'B8' and resid 18 through 26
    Processing helix  chain 'B8' and resid 81 through 83
      No H-bonds generated for 'chain 'B8' and resid 81 through 83'
    Processing helix  chain 'B8' and resid 99 through 121
    Processing helix  chain 'BK' and resid 51 through 63
      removed outlier: 3.987A  pdb=" N   VALBK  55 " --> pdb=" O   PROBK  51 " (cutoff:3.500A)
    Processing helix  chain 'BK' and resid 70 through 78
    Processing helix  chain 'BK' and resid 83 through 102
      removed outlier: 6.316A  pdb=" N   GLUBK  87 " --> pdb=" O   ARGBK  84 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   TRPBK  88 " --> pdb=" O   METBK  85 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLUBK  92 " --> pdb=" O   ALABK  89 " (cutoff:3.500A)
    Processing helix  chain 'C1' and resid 14 through 45
    Processing helix  chain 'B1' and resid 12 through 33
      removed outlier: 3.711A  pdb=" N   LEUB1  15 " --> pdb=" O   ILEB1  12 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   VALB1  16 " --> pdb=" O   HISB1  13 " (cutoff:3.500A)
      Proline residue: B1  17  - end of helix
    Processing helix  chain 'A1' and resid 6 through 29
      Proline residue: A1  19  - end of helix
    Processing helix  chain 'A1' and resid 42 through 54
    Processing sheet with id=  A, first strand: chain 'V1' and resid 221 through 223
      removed outlier: 6.278A  pdb=" N   ALAV1 133 " --> pdb=" O   LEUV1  93 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   VALV1  95 " --> pdb=" O   ALAV1 133 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   TYRV1 135 " --> pdb=" O   VALV1  95 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ASPV1 174 " --> pdb=" O   ALAV1 134 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ILEV1 136 " --> pdb=" O   ASPV1 174 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   PHEV1 176 " --> pdb=" O   ILEV1 136 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   ILEV1 138 " --> pdb=" O   PHEV1 176 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VALV1 178 " --> pdb=" O   ILEV1 138 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'V1' and resid 253 through 257
    Processing sheet with id=  C, first strand: chain 'V1' and resid 294 through 298
      removed outlier: 6.457A  pdb=" N   METV1 337 " --> pdb=" O   LEUV1 295 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   VALV1 297 " --> pdb=" O   ILEV1 335 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ILEV1 335 " --> pdb=" O   VALV1 297 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'V2' and resid 138 through 142
    Processing sheet with id=  E, first strand: chain 'S1' and resid 16 through 20
      removed outlier: 6.609A  pdb=" N   TRPS1  77 " --> pdb=" O   PHES1  12 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'S1' and resid 146 through 148
    Processing sheet with id=  G, first strand: chain 'S1' and resid 173 through 177
    Processing sheet with id=  H, first strand: chain 'S1' and resid 223 through 228
    Processing sheet with id=  I, first strand: chain 'S1' and resid 282 through 286
    Processing sheet with id=  J, first strand: chain 'S1' and resid 342 through 345
      removed outlier: 6.565A  pdb=" N   METS1 521 " --> pdb=" O   ALAS1 316 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ILES1 318 " --> pdb=" O   METS1 521 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   PHES1 523 " --> pdb=" O   ILES1 318 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VALS1 559 " --> pdb=" O   TYRS1 545 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   GLYS1 547 " --> pdb=" O   VALS1 559 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEUS1 561 " --> pdb=" O   GLYS1 547 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'S1' and resid 405 through 409
    Processing sheet with id=  L, first strand: chain 'S2' and resid 47 through 51
    Processing sheet with id=  M, first strand: chain 'S2' and resid 361 through 368
    Processing sheet with id=  N, first strand: chain 'S3' and resid 74 through 76
      removed outlier: 6.665A  pdb=" N   LEUS3  48 " --> pdb=" O   ARGS3 106 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   LYSS3 108 " --> pdb=" O   LEUS3  48 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   ILES3  50 " --> pdb=" O   LYSS3 108 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   TYRS3 110 " --> pdb=" O   ILES3  50 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ILES3  52 " --> pdb=" O   TYRS3 110 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'S3' and resid 172 through 177
    Processing sheet with id=  P, first strand: chain 'S7' and resid 47 through 49
      removed outlier: 7.002A  pdb=" N   VALS7  85 " --> pdb=" O   METS7  48 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   TYRS7 112 " --> pdb=" O   METS7  86 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   VALS7  88 " --> pdb=" O   TYRS7 112 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VALS7 114 " --> pdb=" O   VALS7  88 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ILES7 144 " --> pdb=" O   SERS7 115 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  P
    Processing sheet with id=  Q, first strand: chain 'S8' and resid 92 through 95
    Processing sheet with id=  R, first strand: chain 'S6' and resid 50 through 52
    Processing sheet with id=  S, first strand: chain 'S6' and resid 56 through 59
    Processing sheet with id=  T, first strand: chain 'S4' and resid 103 through 105
      removed outlier: 6.415A  pdb=" N   ALAS4  35 " --> pdb=" O   ASPS4 104 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'A9' and resid 90 through 92
      removed outlier: 6.342A  pdb=" N   GLNA9  44 " --> pdb=" O   ALAA9  21 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   VALA9  23 " --> pdb=" O   GLNA9  44 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ILEA9  46 " --> pdb=" O   VALA9  23 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   ILEA9  69 " --> pdb=" O   VALA9  47 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   TYRA9  49 " --> pdb=" O   ILEA9  69 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   META9  71 " --> pdb=" O   TYRA9  49 " (cutoff:3.500A)
    Processing sheet with id=  V, first strand: chain 'A9' and resid 130 through 134
      removed outlier: 6.399A  pdb=" N   THRA9 164 " --> pdb=" O   HISA9 131 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   SERA9 133 " --> pdb=" O   THRA9 164 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ILEA9 166 " --> pdb=" O   SERA9 133 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   PHEA9 228 " --> pdb=" O   LYSA9 167 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  V
    Processing sheet with id=  W, first strand: chain 'A9' and resid 170 through 172
      removed outlier: 3.546A  pdb=" N   VALA9 205 " --> pdb=" O   ASPA9 170 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'A2' and resid 53 through 56
    Processing sheet with id=  Y, first strand: chain 'AL' and resid 47 through 50
    Processing sheet with id=  Z, first strand: chain 'D5' and resid 61 through 67
    Processing sheet with id= AA, first strand: chain 'D4' and resid 50 through 52
    Processing sheet with id= AB, first strand: chain 'AJ' and resid 122 through 125
      removed outlier: 6.545A  pdb=" N   VALAJ 168 " --> pdb=" O   THRAJ  26 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   ASPAJ  28 " --> pdb=" O   VALAJ 168 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ILEAJ 170 " --> pdb=" O   ASPAJ  28 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   GLUAJ 219 " --> pdb=" O   VALAJ 169 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   TYRAJ 171 " --> pdb=" O   GLUAJ 219 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   LEUAJ 221 " --> pdb=" O   TYRAJ 171 " (cutoff:3.500A)

    2737 hydrogen bonds defined for protein.
    7839 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: 20.11

  Time building geometry restraints manager: 22.20 seconds

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

  Histogram of bond lengths:
        1.20 -     1.42: 27742
        1.42 -     1.64: 38428
        1.64 -     1.86: 750
        1.86 -     2.08: 0
        2.08 -     2.31: 80
  Bond restraints: 67000
  Sorted by residual:
  bond pdb=" C16 ZMPAA 101 "
       pdb=" N2  ZMPAA 101 "
    ideal  model  delta    sigma   weight residual
    1.452  1.341  0.111 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" O2B NDPA9 401 "
       pdb=" P2B NDPA9 401 "
    ideal  model  delta    sigma   weight residual
    1.833  1.624  0.209 3.80e-02 6.93e+02 3.04e+01
  bond pdb=" C16 ZMPAB 101 "
       pdb=" N2  ZMPAB 101 "
    ideal  model  delta    sigma   weight residual
    1.452  1.342  0.110 2.00e-02 2.50e+03 3.02e+01
  bond pdb=" C13 ZMPAA 101 "
       pdb=" N1  ZMPAA 101 "
    ideal  model  delta    sigma   weight residual
    1.451  1.342  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C13 ZMPAB 101 "
       pdb=" N1  ZMPAB 101 "
    ideal  model  delta    sigma   weight residual
    1.451  1.348  0.103 2.00e-02 2.50e+03 2.64e+01
  ... (remaining 66995 not shown)

  Histogram of bond angle deviations from ideal:
       69.02 -    84.73: 72
       84.73 -   100.44: 116
      100.44 -   116.15: 44159
      116.15 -   131.86: 46265
      131.86 -   147.57: 244
  Bond angle restraints: 90856
  Sorted by residual:
  angle pdb=" C   VALS3  37 "
        pdb=" N   GLNS3  38 "
        pdb=" CA  GLNS3  38 "
      ideal   model   delta    sigma   weight residual
     122.46  147.57  -25.11 1.80e+00 3.09e-01 1.95e+02
  angle pdb=" PA  NDPA9 401 "
        pdb=" O3  NDPA9 401 "
        pdb=" PN  NDPA9 401 "
      ideal   model   delta    sigma   weight residual
     107.74  130.91  -23.17 1.95e+00 2.62e-01 1.41e+02
  angle pdb=" S1  FESS1 803 "
        pdb="FE2  FESS1 803 "
        pdb=" S2  FESS1 803 "
      ideal   model   delta    sigma   weight residual
     104.33   91.96   12.37 1.14e+00 7.69e-01 1.18e+02
  angle pdb=" S1  FESV2 300 "
        pdb="FE2  FESV2 300 "
        pdb=" S2  FESV2 300 "
      ideal   model   delta    sigma   weight residual
     104.33   92.18   12.15 1.14e+00 7.69e-01 1.14e+02
  angle pdb="FE1  FESV2 300 "
        pdb=" S2  FESV2 300 "
        pdb="FE2  FESV2 300 "
      ideal   model   delta    sigma   weight residual
      75.66   87.74  -12.08 1.14e+00 7.69e-01 1.12e+02
  ... (remaining 90851 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.29: 39544
       30.29 -    60.58: 721
       60.58 -    90.86: 61
       90.86 -   121.15: 1
      121.15 -   151.44: 2
  Dihedral angle restraints: 40329
    sinusoidal: 16776
      harmonic: 23553
  Sorted by residual:
  dihedral pdb=" CA  PROB2  56 "
           pdb=" C   PROB2  56 "
           pdb=" N   SERB2  57 "
           pdb=" CA  SERB2  57 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -121.88  -58.12     0      5.00e+00 4.00e-02 1.35e+02
  dihedral pdb=" CA  LYSB3  22 "
           pdb=" C   LYSB3  22 "
           pdb=" N   ILEB3  23 "
           pdb=" CA  ILEB3  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -122.82  -57.18     0      5.00e+00 4.00e-02 1.31e+02
  dihedral pdb=" CA  PHEAJ 278 "
           pdb=" C   PHEAJ 278 "
           pdb=" N   LEUAJ 279 "
           pdb=" CA  LEUAJ 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  123.81   56.19     0      5.00e+00 4.00e-02 1.26e+02
  ... (remaining 40326 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    4.231: 9962
       4.231 -    8.462: 0
       8.462 -   12.693: 0
      12.693 -   16.925: 0
      16.925 -   21.156: 24
  Chirality restraints: 9986
  Sorted by residual:
  chirality pdb="FE4  SF4S7 300 "
            pdb=" S1  SF4S7 300 "
            pdb=" S2  SF4S7 300 "
            pdb=" S3  SF4S7 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.55  -10.60   21.16 2.00e-01 2.50e+01 1.12e+04
  chirality pdb="FE4  SF4V1 500 "
            pdb=" S1  SF4V1 500 "
            pdb=" S2  SF4V1 500 "
            pdb=" S3  SF4V1 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.55  -10.59   21.14 2.00e-01 2.50e+01 1.12e+04
  chirality pdb="FE4  SF4S1 802 "
            pdb=" S1  SF4S1 802 "
            pdb=" S2  SF4S1 802 "
            pdb=" S3  SF4S1 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.55  -10.56   21.12 2.00e-01 2.50e+01 1.12e+04
  ... (remaining 9983 not shown)

  Planarity restraints: 11476
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FMNV1 501 "    0.004 2.00e-02 2.50e+03   3.16e-02 4.75e+01
        pdb=" C10 FMNV1 501 "    0.045 2.00e-02 2.50e+03
        pdb=" C2  FMNV1 501 "   -0.025 2.00e-02 2.50e+03
        pdb=" C4  FMNV1 501 "    0.010 2.00e-02 2.50e+03
        pdb=" C4A FMNV1 501 "    0.039 2.00e-02 2.50e+03
        pdb=" C5A FMNV1 501 "    0.016 2.00e-02 2.50e+03
        pdb=" C6  FMNV1 501 "   -0.011 2.00e-02 2.50e+03
        pdb=" C7  FMNV1 501 "   -0.023 2.00e-02 2.50e+03
        pdb=" C7M FMNV1 501 "   -0.050 2.00e-02 2.50e+03
        pdb=" C8  FMNV1 501 "   -0.011 2.00e-02 2.50e+03
        pdb=" C8M FMNV1 501 "   -0.010 2.00e-02 2.50e+03
        pdb=" C9  FMNV1 501 "    0.008 2.00e-02 2.50e+03
        pdb=" C9A FMNV1 501 "    0.023 2.00e-02 2.50e+03
        pdb=" N1  FMNV1 501 "    0.016 2.00e-02 2.50e+03
        pdb=" N10 FMNV1 501 "    0.040 2.00e-02 2.50e+03
        pdb=" N3  FMNV1 501 "   -0.021 2.00e-02 2.50e+03
        pdb=" N5  FMNV1 501 "    0.027 2.00e-02 2.50e+03
        pdb=" O2  FMNV1 501 "   -0.087 2.00e-02 2.50e+03
        pdb=" O4  FMNV1 501 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VALS1 247 "   -0.020 2.00e-02 2.50e+03   4.06e-02 1.65e+01
        pdb=" C   VALS1 247 "    0.070 2.00e-02 2.50e+03
        pdb=" O   VALS1 247 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   METS1 248 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PROS5  94 "   -0.067 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PROS5  95 "    0.174 5.00e-02 4.00e+02
        pdb=" CA  PROS5  95 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PROS5  95 "   -0.057 5.00e-02 4.00e+02
  ... (remaining 11473 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 818
        2.65 -     3.21: 58455
        3.21 -     3.77: 103679
        3.77 -     4.34: 134606
        4.34 -     4.90: 216097
  Nonbonded interactions: 513655
  Sorted by model distance:
  nonbonded pdb=" CA  ALAS3  80 "
            pdb=" O   GLUS3  91 "
     model   vdw
     2.082 3.470
  nonbonded pdb=" OE1 GLUS2 224 "
            pdb=" OH  TYRS8  40 "
     model   vdw
     2.250 2.440
  nonbonded pdb=" O   ILEA9  19 "
            pdb=" OG  SERA9  43 "
     model   vdw
     2.251 2.440
  nonbonded pdb=" OG1 THRS6  12 "
            pdb=" O   THRS6  14 "
     model   vdw
     2.257 2.440
  nonbonded pdb=" OE1 GLUS8 138 "
            pdb=" OG  SERAL  80 "
     model   vdw
     2.258 2.440
  ... (remaining 513650 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 'AA' and (resid 5 through 84 or (resid 101 and (name C10 or name C11 or n \ 
ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18  \ 
or name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5  \ 
or name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or  \ 
name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or nam \ 
e S1 ))))
  selection = (chain 'AB' and (resid 5 through 84 or resid 101))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             8.290
  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:             0.080
  Extract box with map and model:          28.830
  Check model and map are aligned:         0.750
  Set scattering table:                    0.460
  Process input model:                     151.610
  Find NCS groups from input model:        2.470
  Set up NCS constraints:                  0.330
  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:             0.020
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  195.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.209  67000  Z= 0.393
  Angle     :  1.186  25.111  90856  Z= 0.621
  Chirality :  1.035  21.156   9986
  Planarity :  0.008   0.100  11476
  Dihedral  : 11.595 151.439  25097
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.29 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  5.42 %
    Favored  : 94.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.34 %
    Twisted Proline : 1.25 %
    Twisted General : 0.50 %

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: -4.07 (0.08), residues: 7979
  helix: -1.94 (0.06), residues: 4189
  sheet: -2.14 (0.25), residues: 372
  loop : -3.76 (0.09), residues: 3418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRPAM 141 
 HIS   0.019   0.002   HISBJ  55 
 PHE   0.044   0.003   PHED5 385 
 TYR   0.054   0.003   TYRAJ 206 
 ARG   0.016   0.001   ARGD5 262 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3303 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 3264
  time to evaluate  : 6.834 
Fit side-chains
   revert: symmetry clash
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REVERT: V1  102 PRO cc_start: 0.8811 (Cg_exo) cc_final: 0.8246 (Cg_endo)
REVERT: V1  341 THR cc_start: 0.7020 (p) cc_final: 0.6814 (t)
REVERT: V1  404 ILE cc_start: 0.9030 (mm) cc_final: 0.8755 (mt)
REVERT: V2   91 ASN cc_start: 0.8692 (p0) cc_final: 0.8458 (p0)
REVERT: S1  115 ASP cc_start: 0.7724 (m-30) cc_final: 0.6993 (m-30)
REVERT: S1  187 ILE cc_start: 0.8741 (pt) cc_final: 0.8184 (tt)
REVERT: S1  200 ILE cc_start: 0.9049 (pt) cc_final: 0.8834 (mt)
REVERT: S1  307 LEU cc_start: 0.8785 (tt) cc_final: 0.8576 (mt)
REVERT: S1  322 LEU cc_start: 0.8180 (mt) cc_final: 0.7977 (pp)
REVERT: S1  333 ASP cc_start: 0.6763 (t0) cc_final: 0.6169 (t0)
REVERT: S1  419 TYR cc_start: 0.7629 (p90) cc_final: 0.7363 (p90)
REVERT: S1  521 MET cc_start: 0.7481 (ttm) cc_final: 0.7001 (ttp)
REVERT: S1  549 HIS cc_start: 0.8001 (p90) cc_final: 0.7619 (p90)
REVERT: S2   28 TRP cc_start: 0.6685 (m-90) cc_final: 0.6295 (m-10)
REVERT: S2  137 ILE cc_start: 0.9341 (mt) cc_final: 0.9029 (tt)
REVERT: S2  149 ASN cc_start: 0.8771 (t0) cc_final: 0.8117 (t0)
REVERT: S2  155 THR cc_start: 0.9203 (p) cc_final: 0.8905 (p)
REVERT: S2  172 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7158 (tp30)
REVERT: S2  173 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7523 (mm-30)
REVERT: S2  222 ILE cc_start: 0.9140 (tp) cc_final: 0.8936 (tp)
REVERT: S2  228 MET cc_start: 0.8240 (tpt) cc_final: 0.7957 (tpt)
REVERT: S2  242 ILE cc_start: 0.7752 (pp) cc_final: 0.7165 (pp)
REVERT: S2  268 ASP cc_start: 0.7052 (t0) cc_final: 0.6520 (t0)
REVERT: S2  304 MET cc_start: 0.8679 (mtp) cc_final: 0.8234 (mtt)
REVERT: S2  337 GLU cc_start: 0.7577 (tt0) cc_final: 0.7364 (tt0)
REVERT: S2  391 ILE cc_start: 0.8811 (mp) cc_final: 0.8132 (mm)
REVERT: S2  402 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8139 (tm)
REVERT: S2  418 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8822 (mm)
REVERT: S3   75 LEU cc_start: 0.9042 (tp) cc_final: 0.8746 (tp)
REVERT: S3  128 ASN cc_start: 0.8582 (t0) cc_final: 0.8359 (t0)
REVERT: S3  131 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7301 (mt-10)
REVERT: S3  200 ASN cc_start: 0.7767 (m-40) cc_final: 0.7374 (p0)
REVERT: S7   32 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8093 (tptp)
REVERT: S7   54 CYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8878 (p)
REVERT: S7   79 SER cc_start: 0.8398 (t) cc_final: 0.7773 (p)
REVERT: S7   82 GLN cc_start: 0.7867 (pt0) cc_final: 0.7235 (tm-30)
REVERT: S7   92 LEU cc_start: 0.9502 (tp) cc_final: 0.9059 (mm)
REVERT: S7  142 VAL cc_start: 0.9297 (t) cc_final: 0.8729 (t)
REVERT: S8    4 TYR cc_start: 0.8596 (p90) cc_final: 0.8323 (p90)
REVERT: S8   34 LEU cc_start: 0.8568 (mm) cc_final: 0.8232 (mt)
REVERT: S8   36 MET cc_start: 0.7385 (tpt) cc_final: 0.6944 (tpt)
REVERT: S8   54 LYS cc_start: 0.7609 (mttt) cc_final: 0.7389 (mttt)
REVERT: S8   57 LEU cc_start: 0.8776 (mt) cc_final: 0.8139 (mt)
REVERT: S8   61 PHE cc_start: 0.8157 (t80) cc_final: 0.7558 (t80)
REVERT: S8   92 ILE cc_start: 0.9274 (mm) cc_final: 0.8985 (mm)
REVERT: S8  118 TYR cc_start: 0.8680 (m-80) cc_final: 0.8438 (m-80)
REVERT: S8  129 ASP cc_start: 0.8029 (m-30) cc_final: 0.7687 (m-30)
REVERT: S8  141 THR cc_start: 0.8739 (m) cc_final: 0.8150 (m)
REVERT: S8  164 GLU cc_start: 0.6482 (tp30) cc_final: 0.6225 (tp30)
REVERT: V3   41 LEU cc_start: 0.8345 (tt) cc_final: 0.8145 (pp)
REVERT: S6   72 TYR cc_start: 0.7755 (m-10) cc_final: 0.7444 (m-80)
REVERT: S4   44 ASN cc_start: 0.8216 (t0) cc_final: 0.7178 (t0)
REVERT: S4   98 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8127 (ttmm)
REVERT: A9   54 TYR cc_start: 0.7513 (t80) cc_final: 0.6848 (t80)
REVERT: A9   74 ASN cc_start: 0.7952 (p0) cc_final: 0.7662 (p0)
REVERT: A9  121 SER cc_start: 0.9313 (m) cc_final: 0.8963 (p)
REVERT: A9  154 LYS cc_start: 0.9188 (tttt) cc_final: 0.8716 (ttmt)
REVERT: A9  184 ASN cc_start: 0.8780 (t0) cc_final: 0.8551 (m-40)
REVERT: A9  310 LEU cc_start: 0.8672 (tp) cc_final: 0.8450 (pt)
REVERT: A6   28 LYS cc_start: 0.8813 (mttm) cc_final: 0.8576 (mttt)
REVERT: A6   57 GLN cc_start: 0.8060 (tt0) cc_final: 0.7750 (tp40)
REVERT: AL   56 PHE cc_start: 0.8399 (t80) cc_final: 0.8100 (t80)
REVERT: AL   59 HIS cc_start: 0.7359 (m-70) cc_final: 0.7150 (m-70)
REVERT: AL   85 GLU cc_start: 0.8888 (pm20) cc_final: 0.8618 (mp0)
REVERT: AA   11 ILE cc_start: 0.8806 (mm) cc_final: 0.8588 (mt)
REVERT: AA   21 LEU cc_start: 0.8961 (tp) cc_final: 0.8580 (mt)
REVERT: AA   48 VAL cc_start: 0.9228 (p) cc_final: 0.8947 (p)
REVERT: AA   74 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8235 (tp40)
REVERT: D3    4 MET cc_start: 0.7009 (ttt) cc_final: 0.6225 (tmm)
REVERT: D3   17 LEU cc_start: 0.9178 (mt) cc_final: 0.8923 (mt)
REVERT: D3   86 THR cc_start: 0.8759 (p) cc_final: 0.7944 (t)
REVERT: D1   26 LYS cc_start: 0.9366 (mmmm) cc_final: 0.8468 (mmmt)
REVERT: D1  133 LEU cc_start: 0.9469 (tp) cc_final: 0.9157 (tp)
REVERT: D1  271 LEU cc_start: 0.9292 (tm) cc_final: 0.8249 (tm)
REVERT: D1  282 TYR cc_start: 0.8500 (t80) cc_final: 0.7937 (t80)
REVERT: D1  283 ASP cc_start: 0.8343 (m-30) cc_final: 0.7908 (m-30)
REVERT: D1  286 MET cc_start: 0.8752 (mmt) cc_final: 0.8308 (mmm)
REVERT: D6    2 MET cc_start: 0.6484 (ptm) cc_final: 0.6182 (ptm)
REVERT: D6   65 MET cc_start: 0.8972 (mpm) cc_final: 0.8478 (mpm)
REVERT: D6  146 LEU cc_start: 0.8581 (tt) cc_final: 0.7988 (tt)
REVERT: 4L   24 SER cc_start: 0.8706 (p) cc_final: 0.8235 (p)
REVERT: 4L   25 HIS cc_start: 0.8688 (m-70) cc_final: 0.8048 (m-70)
REVERT: 4L   66 PHE cc_start: 0.8676 (m-80) cc_final: 0.8459 (m-80)
REVERT: 4L   81 VAL cc_start: 0.9383 (t) cc_final: 0.9176 (t)
REVERT: D5  102 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7598 (tp30)
REVERT: D5  116 GLN cc_start: 0.8012 (tt0) cc_final: 0.7724 (pt0)
REVERT: D5  136 ASN cc_start: 0.8090 (t0) cc_final: 0.7800 (t0)
REVERT: D5  154 LEU cc_start: 0.9246 (mt) cc_final: 0.8961 (tp)
REVERT: D5  197 ASP cc_start: 0.5443 (m-30) cc_final: 0.4916 (m-30)
REVERT: D5  233 LEU cc_start: 0.7459 (tp) cc_final: 0.7223 (tp)
REVERT: D5  243 VAL cc_start: 0.9250 (t) cc_final: 0.8156 (t)
REVERT: D5  270 ASN cc_start: 0.8097 (t0) cc_final: 0.7886 (t0)
REVERT: D5  309 GLN cc_start: 0.8876 (mm110) cc_final: 0.8547 (mm-40)
REVERT: D5  314 MET cc_start: 0.8577 (mmm) cc_final: 0.8299 (mmm)
REVERT: D5  326 PHE cc_start: 0.8105 (t80) cc_final: 0.7863 (t80)
REVERT: D5  355 ASP cc_start: 0.8088 (m-30) cc_final: 0.7452 (t0)
REVERT: D5  366 MET cc_start: 0.7241 (pmm) cc_final: 0.5996 (pmm)
REVERT: D5  370 THR cc_start: 0.8824 (p) cc_final: 0.8511 (t)
REVERT: D5  407 TRP cc_start: 0.7574 (t-100) cc_final: 0.6954 (t-100)
REVERT: D5  424 THR cc_start: 0.8816 (m) cc_final: 0.8531 (p)
REVERT: D5  458 LEU cc_start: 0.8260 (pp) cc_final: 0.8030 (pp)
REVERT: D5  573 MET cc_start: 0.7687 (mmm) cc_final: 0.7237 (mtt)
REVERT: D5  604 PHE cc_start: 0.8219 (m-10) cc_final: 0.7653 (m-80)
REVERT: D4    5 ILE cc_start: 0.9185 (mm) cc_final: 0.8651 (mm)
REVERT: D4    6 ILE cc_start: 0.8440 (tp) cc_final: 0.8226 (tp)
REVERT: D4   80 SER cc_start: 0.9099 (p) cc_final: 0.8836 (t)
REVERT: D4  108 MET cc_start: 0.8861 (mmp) cc_final: 0.8186 (mmp)
REVERT: D4  121 MET cc_start: 0.8206 (mmt) cc_final: 0.7606 (mmm)
REVERT: D4  147 LEU cc_start: 0.9171 (tp) cc_final: 0.8827 (tp)
REVERT: D4  285 LEU cc_start: 0.8661 (mt) cc_final: 0.8265 (tp)
REVERT: D4  310 MET cc_start: 0.6978 (mtm) cc_final: 0.6735 (mtp)
REVERT: D4  349 GLN cc_start: 0.8120 (mm110) cc_final: 0.7596 (mm110)
REVERT: D4  378 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6863 (mt-10)
REVERT: D4  383 MET cc_start: 0.8433 (mmp) cc_final: 0.8213 (mmp)
REVERT: D4  414 THR cc_start: 0.8720 (p) cc_final: 0.8486 (t)
REVERT: D4  431 THR cc_start: 0.8750 (p) cc_final: 0.8139 (t)
REVERT: D2   17 THR cc_start: 0.9104 (m) cc_final: 0.7192 (p)
REVERT: D2   35 MET cc_start: 0.7854 (ttm) cc_final: 0.7631 (ttt)
REVERT: D2   36 ASN cc_start: 0.8839 (t160) cc_final: 0.8584 (t0)
REVERT: D2  174 GLN cc_start: 0.8871 (mm110) cc_final: 0.8530 (mm-40)
REVERT: D2  190 MET cc_start: 0.8765 (mtm) cc_final: 0.8322 (mtm)
REVERT: D2  204 ASN cc_start: 0.9168 (t160) cc_final: 0.8736 (t0)
REVERT: D2  213 SER cc_start: 0.9401 (m) cc_final: 0.9137 (p)
REVERT: D2  219 PHE cc_start: 0.8724 (m-80) cc_final: 0.8207 (m-10)
REVERT: D2  239 ILE cc_start: 0.8958 (mm) cc_final: 0.8681 (mt)
REVERT: D2  248 LEU cc_start: 0.9188 (mm) cc_final: 0.8807 (mt)
REVERT: D2  250 SER cc_start: 0.8899 (t) cc_final: 0.8687 (p)
REVERT: D2  269 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6936 (mt-10)
REVERT: D2  270 MET cc_start: 0.8469 (tpp) cc_final: 0.8257 (tpp)
REVERT: D2  291 TYR cc_start: 0.7760 (t80) cc_final: 0.7375 (t80)
REVERT: AK   22 TYR cc_start: 0.8181 (t80) cc_final: 0.7744 (t80)
REVERT: AK   36 SER cc_start: 0.9147 (p) cc_final: 0.8898 (p)
REVERT: AK   57 ARG cc_start: 0.7144 (ttp-170) cc_final: 0.6661 (tpp-160)
REVERT: AK   65 ILE cc_start: 0.9254 (mt) cc_final: 0.8966 (mm)
REVERT: B5  108 LEU cc_start: 0.9264 (pp) cc_final: 0.8954 (mp)
REVERT: AB    8 LEU cc_start: 0.8817 (mm) cc_final: 0.8389 (mm)
REVERT: AB   79 TYR cc_start: 0.7766 (t80) cc_final: 0.7456 (t80)
REVERT: A8   25 LYS cc_start: 0.8984 (tttt) cc_final: 0.8693 (mmtp)
REVERT: A8   43 MET cc_start: 0.7677 (tpp) cc_final: 0.7319 (tpp)
REVERT: A8  112 ASP cc_start: 0.7510 (m-30) cc_final: 0.7306 (t0)
REVERT: BJ   67 PHE cc_start: 0.6504 (m-10) cc_final: 0.5855 (m-10)
REVERT: BJ  110 LYS cc_start: 0.8242 (mttp) cc_final: 0.8001 (mttt)
REVERT: AJ  173 ASP cc_start: 0.8168 (t0) cc_final: 0.7570 (p0)
REVERT: AJ  185 LYS cc_start: 0.8286 (mttt) cc_final: 0.8076 (tppt)
REVERT: AJ  294 GLN cc_start: 0.8497 (mm110) cc_final: 0.8267 (tp40)
REVERT: S5   72 MET cc_start: 0.7920 (mtp) cc_final: 0.7352 (mtm)
REVERT: A3   15 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7023 (mt-10)
REVERT: A3   31 LEU cc_start: 0.9228 (tp) cc_final: 0.9022 (tp)
REVERT: A3   39 LYS cc_start: 0.8842 (ptmm) cc_final: 0.7124 (mmtm)
REVERT: A3   42 LEU cc_start: 0.8638 (tt) cc_final: 0.8148 (tp)
REVERT: C2    2 MET cc_start: 0.7427 (tmm) cc_final: 0.6545 (tmm)
REVERT: C2   25 LYS cc_start: 0.8514 (mptp) cc_final: 0.8020 (pttp)
REVERT: C2   33 TYR cc_start: 0.8965 (t80) cc_final: 0.8740 (t80)
REVERT: C2   37 LEU cc_start: 0.9123 (tt) cc_final: 0.8831 (tp)
REVERT: C2   63 LEU cc_start: 0.9208 (tp) cc_final: 0.8854 (tp)
REVERT: C2   92 SER cc_start: 0.8986 (t) cc_final: 0.8291 (p)
REVERT: B4   47 GLN cc_start: 0.8761 (mm110) cc_final: 0.8416 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7633 (t160) cc_final: 0.7178 (t0)
REVERT: B4  100 TRP cc_start: 0.8305 (m100) cc_final: 0.7950 (m-90)
REVERT: B6   19 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.6928 (mtt-85)
REVERT: B6   20 ARG cc_start: 0.8672 (mtp-110) cc_final: 0.8352 (mtm110)
REVERT: B6   27 LEU cc_start: 0.8750 (pt) cc_final: 0.8280 (pt)
REVERT: B6   28 SER cc_start: 0.7881 (t) cc_final: 0.7338 (p)
REVERT: B6  120 LYS cc_start: 0.8310 (mmpt) cc_final: 0.7947 (ttmt)
REVERT: B7   51 VAL cc_start: 0.8068 (t) cc_final: 0.7419 (t)
REVERT: B7   57 TYR cc_start: 0.7035 (m-10) cc_final: 0.6824 (m-80)
REVERT: B9   12 GLN cc_start: 0.8503 (tt0) cc_final: 0.8171 (pp30)
REVERT: B2   42 HIS cc_start: 0.7679 (t-90) cc_final: 0.6654 (t-90)
REVERT: B2   55 ASP cc_start: 0.7634 (p0) cc_final: 0.7281 (p0)
REVERT: B8  113 LEU cc_start: 0.9128 (mt) cc_final: 0.8757 (tt)
REVERT: BK  123 ASP cc_start: 0.5157 (t0) cc_final: 0.4849 (m-30)
REVERT: C1   11 SER cc_start: 0.8803 (m) cc_final: 0.8513 (t)
REVERT: A1   36 LYS cc_start: 0.8222 (ttpt) cc_final: 0.8012 (ttpt)
  outliers start: 39
  outliers final: 4
  residues processed: 3282
  average time/residue: 0.6376
  time to fit residues: 3462.1114
Evaluate side-chains
  1888 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 1881
  time to evaluate  : 5.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 664 optimal weight:    3.9990
   chunk 596 optimal weight:   10.0000
   chunk 330 optimal weight:    0.8980
   chunk 203 optimal weight:    2.9990
   chunk 402 optimal weight:    0.9980
   chunk 318 optimal weight:    0.0070
   chunk 616 optimal weight:    6.9990
   chunk 238 optimal weight:    9.9990
   chunk 375 optimal weight:    0.1980
   chunk 459 optimal weight:    9.9990
   chunk 714 optimal weight:    5.9990
   overall best weight:    1.0200

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

Flipped N/Q/H residues before XYZ refinement:
** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 293 ASN
V1 361 GLN
V2  42 HIS
** V2  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S1  36 GLN
** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S1 255 HIS
S1 259 ASN
S1 365 ASN
** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S1 682 GLN
S2  50 ASN
S2  79 HIS
S2  84 HIS
S2 116 GLN
S2 135 GLN
S2 316 ASN
S2 347 HIS
S3  95 ASN
S7  38 ASN
** S8  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S8 150 ASN
V3  44 HIS
V3  75 HIS
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  29 HIS
S4  44 ASN
** S4  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
A9   3 HIS
A9 203 GLN
A9 288 HIS
A2  61 GLN
A5  82 GLN
A6 125 HIS
A7  20 GLN
** A7  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A7  50 ASN
AL  17 HIS
** AL  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D3  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D3 108 GLN
** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1 194 ASN
** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5  23 ASN
D5 115 ASN
** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 205 ASN
** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 309 GLN
** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 534 HIS
D5 570 GLN
D4  82 HIS
D4  83 HIS
D4 103 GLN
D4 293 HIS
** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D2  63 GLN
D2 232 HIS
D2 316 GLN
AK   6 HIS
AK  78 GLN
B5 143 ASN
A8  29 HIS
A8 162 HIS
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
BJ 113 GLN
** BJ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
AJ  76 ASN
AJ  97 GLN
** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
AJ 200 GLN
AJ 204 ASN
AJ 251 GLN
** S5  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S5  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S5  96 HIS
A3  51 ASN
A3  68 HIS
AM  23 ASN
AM  84 GLN
B6  73 HIS
** B7  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B9 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B9 168 HIS
B2  24 GLN
** BK  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
BK 103 HIS

Total number of N/Q/H flips: 67

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.263  67000  Z= 0.572
  Angle     :  1.678  50.994  90856  Z= 1.063
  Chirality :  0.312   6.516   9986
  Planarity :  0.006   0.104  11476
  Dihedral  :  8.718 122.188   9098
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  9.90 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.00 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.63 %
    Twisted General : 0.21 %

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: -2.66 (0.09), residues: 7979
  helix: -0.53 (0.07), residues: 4204
  sheet: -1.89 (0.27), residues: 332
  loop : -3.42 (0.09), residues: 3443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRPD2 234 
 HIS   0.024   0.001   HISD1 287 
 PHE   0.049   0.002   PHEB5 123 
 TYR   0.028   0.002   TYRAJ 240 
 ARG   0.010   0.001   ARGB8  88 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  2372 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 2356
  time to evaluate  : 5.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V1  102 PRO cc_start: 0.8824 (Cg_exo) cc_final: 0.8530 (Cg_endo)
REVERT: S1  200 ILE cc_start: 0.9212 (pt) cc_final: 0.8932 (mt)
REVERT: S1  222 THR cc_start: 0.8067 (p) cc_final: 0.7666 (t)
REVERT: S1  283 MET cc_start: 0.8067 (mtt) cc_final: 0.7853 (mtt)
REVERT: S1  307 LEU cc_start: 0.8829 (tt) cc_final: 0.8506 (mt)
REVERT: S1  419 TYR cc_start: 0.7833 (p90) cc_final: 0.7386 (p90)
REVERT: S1  490 MET cc_start: 0.7880 (tmm) cc_final: 0.7372 (tmm)
REVERT: S1  521 MET cc_start: 0.7697 (ttm) cc_final: 0.7421 (ttp)
REVERT: S1  549 HIS cc_start: 0.7906 (p90) cc_final: 0.7657 (p-80)
REVERT: S2  155 THR cc_start: 0.9021 (p) cc_final: 0.8711 (t)
REVERT: S2  338 MET cc_start: 0.8400 (tmm) cc_final: 0.8001 (tmm)
REVERT: S2  349 PHE cc_start: 0.8533 (t80) cc_final: 0.8142 (t80)
REVERT: S2  413 ASP cc_start: 0.8820 (m-30) cc_final: 0.8477 (m-30)
REVERT: S3  177 ASP cc_start: 0.7357 (p0) cc_final: 0.7118 (p0)
REVERT: S3  200 ASN cc_start: 0.7826 (m-40) cc_final: 0.7211 (p0)
REVERT: S7   62 MET cc_start: 0.9260 (tmm) cc_final: 0.8553 (tmm)
REVERT: S7   82 GLN cc_start: 0.8018 (pt0) cc_final: 0.7139 (tm-30)
REVERT: S7   92 LEU cc_start: 0.9390 (tp) cc_final: 0.9182 (tp)
REVERT: S7  118 SER cc_start: 0.9363 (m) cc_final: 0.9044 (p)
REVERT: S7  142 VAL cc_start: 0.8727 (t) cc_final: 0.8396 (t)
REVERT: S7  170 GLU cc_start: 0.8025 (tp30) cc_final: 0.7816 (tp30)
REVERT: S7  173 LEU cc_start: 0.8991 (mt) cc_final: 0.8621 (mt)
REVERT: S8   23 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8455 (tm-30)
REVERT: S8   61 PHE cc_start: 0.7971 (t80) cc_final: 0.7761 (t80)
REVERT: S8   92 ILE cc_start: 0.9496 (mm) cc_final: 0.9254 (mm)
REVERT: S8  113 MET cc_start: 0.8637 (tpp) cc_final: 0.8414 (mmm)
REVERT: S6   36 ASN cc_start: 0.8591 (t0) cc_final: 0.8241 (t0)
REVERT: A9  121 SER cc_start: 0.9264 (m) cc_final: 0.8964 (p)
REVERT: A9  154 LYS cc_start: 0.9162 (tttt) cc_final: 0.8815 (ttpt)
REVERT: A9  184 ASN cc_start: 0.8803 (t0) cc_final: 0.8548 (m-40)
REVERT: A9  282 ASP cc_start: 0.7463 (p0) cc_final: 0.7258 (p0)
REVERT: A9  310 LEU cc_start: 0.8731 (tp) cc_final: 0.8478 (pt)
REVERT: A2   80 ASN cc_start: 0.8020 (m-40) cc_final: 0.7398 (m110)
REVERT: A6   41 GLU cc_start: 0.7861 (tp30) cc_final: 0.7606 (tp30)
REVERT: A6   53 ILE cc_start: 0.8501 (mm) cc_final: 0.8244 (mm)
REVERT: A6   57 GLN cc_start: 0.8123 (tt0) cc_final: 0.7776 (tp40)
REVERT: A7   50 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7676 (t0)
REVERT: AL   56 PHE cc_start: 0.8453 (t80) cc_final: 0.7887 (t80)
REVERT: AL  135 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7834 (tm-30)
REVERT: AA    9 GLU cc_start: 0.8108 (tt0) cc_final: 0.7589 (tt0)
REVERT: AA   37 MET cc_start: 0.7447 (tpt) cc_final: 0.7238 (tpt)
REVERT: AA   48 VAL cc_start: 0.9327 (p) cc_final: 0.9072 (p)
REVERT: AA   74 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8452 (tp40)
REVERT: D3    4 MET cc_start: 0.7091 (ttt) cc_final: 0.6481 (tmm)
REVERT: D3   66 ASP cc_start: 0.9005 (t70) cc_final: 0.8795 (t0)
REVERT: D3   86 THR cc_start: 0.8390 (p) cc_final: 0.8040 (t)
REVERT: D1   26 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9196 (mmmm)
REVERT: D1   43 TYR cc_start: 0.9096 (m-10) cc_final: 0.8645 (m-10)
REVERT: D1   73 LEU cc_start: 0.9264 (tt) cc_final: 0.8988 (mm)
REVERT: D1  271 LEU cc_start: 0.8993 (tt) cc_final: 0.8735 (tt)
REVERT: D1  272 TRP cc_start: 0.8844 (t60) cc_final: 0.8284 (t60)
REVERT: D1  283 ASP cc_start: 0.8285 (m-30) cc_final: 0.7974 (m-30)
REVERT: D1  286 MET cc_start: 0.8743 (mmt) cc_final: 0.8343 (mmm)
REVERT: D6    1 MET cc_start: 0.5879 (tmm) cc_final: 0.5085 (tmm)
REVERT: D6    5 ILE cc_start: 0.8714 (pt) cc_final: 0.8457 (pt)
REVERT: D6   20 PHE cc_start: 0.8251 (p90) cc_final: 0.7605 (p90)
REVERT: D6   57 PHE cc_start: 0.8187 (t80) cc_final: 0.7412 (t80)
REVERT: D6   64 MET cc_start: 0.8774 (tpp) cc_final: 0.8388 (tpp)
REVERT: D6   65 MET cc_start: 0.8429 (mmp) cc_final: 0.7515 (tpt)
REVERT: D6  100 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7782 (tm-30)
REVERT: D6  124 ASP cc_start: 0.7170 (m-30) cc_final: 0.6818 (m-30)
REVERT: D6  169 MET cc_start: 0.8479 (mmt) cc_final: 0.8222 (tpp)
REVERT: 4L    9 MET cc_start: 0.8346 (mmm) cc_final: 0.7100 (tmm)
REVERT: 4L   10 MET cc_start: 0.7896 (ttt) cc_final: 0.7655 (ttt)
REVERT: 4L   24 SER cc_start: 0.8603 (p) cc_final: 0.8268 (t)
REVERT: 4L   25 HIS cc_start: 0.8721 (m-70) cc_final: 0.7858 (m-70)
REVERT: 4L   36 MET cc_start: 0.8515 (tmm) cc_final: 0.8296 (tmm)
REVERT: 4L   47 MET cc_start: 0.8890 (ttm) cc_final: 0.8669 (ttm)
REVERT: 4L   49 LEU cc_start: 0.8640 (mp) cc_final: 0.8004 (tt)
REVERT: 4L   63 LEU cc_start: 0.8325 (tt) cc_final: 0.8073 (tt)
REVERT: 4L   66 PHE cc_start: 0.8438 (m-80) cc_final: 0.8157 (m-80)
REVERT: D5   12 LEU cc_start: 0.8544 (tt) cc_final: 0.8228 (mm)
REVERT: D5   48 MET cc_start: 0.7691 (ttt) cc_final: 0.7090 (ttp)
REVERT: D5   61 MET cc_start: 0.7833 (ppp) cc_final: 0.7422 (ppp)
REVERT: D5  102 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7608 (tp30)
REVERT: D5  136 ASN cc_start: 0.8072 (t0) cc_final: 0.7696 (t0)
REVERT: D5  221 THR cc_start: 0.9300 (t) cc_final: 0.8896 (p)
REVERT: D5  243 VAL cc_start: 0.9164 (t) cc_final: 0.8578 (t)
REVERT: D5  326 PHE cc_start: 0.8346 (t80) cc_final: 0.8040 (t80)
REVERT: D5  355 ASP cc_start: 0.7890 (m-30) cc_final: 0.7321 (t70)
REVERT: D5  366 MET cc_start: 0.7568 (pmm) cc_final: 0.7294 (pmm)
REVERT: D5  370 THR cc_start: 0.8778 (p) cc_final: 0.8381 (t)
REVERT: D5  393 ASP cc_start: 0.7951 (t70) cc_final: 0.7730 (t0)
REVERT: D5  495 ILE cc_start: 0.8140 (mm) cc_final: 0.7820 (pt)
REVERT: D5  506 ASN cc_start: 0.8037 (m-40) cc_final: 0.7668 (m110)
REVERT: D5  573 MET cc_start: 0.7322 (mmm) cc_final: 0.6976 (mmt)
REVERT: D5  604 PHE cc_start: 0.8103 (m-10) cc_final: 0.7865 (m-80)
REVERT: D4   12 MET cc_start: 0.7823 (tmm) cc_final: 0.7564 (tmm)
REVERT: D4  119 TYR cc_start: 0.8125 (t80) cc_final: 0.7830 (t80)
REVERT: D4  141 GLU cc_start: 0.8679 (tt0) cc_final: 0.8440 (tt0)
REVERT: D4  147 LEU cc_start: 0.9133 (tp) cc_final: 0.8895 (tp)
REVERT: D4  414 THR cc_start: 0.8711 (p) cc_final: 0.8454 (t)
REVERT: D4  431 THR cc_start: 0.8767 (p) cc_final: 0.8211 (t)
REVERT: D4  441 MET cc_start: 0.8197 (mmt) cc_final: 0.7929 (mmt)
REVERT: D4  447 LEU cc_start: 0.8978 (mt) cc_final: 0.8587 (mt)
REVERT: D2   36 ASN cc_start: 0.8890 (t0) cc_final: 0.8545 (t0)
REVERT: D2   63 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8724 (mm110)
REVERT: D2   85 THR cc_start: 0.7823 (p) cc_final: 0.7604 (p)
REVERT: D2  120 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8395 (tp40)
REVERT: D2  174 GLN cc_start: 0.8719 (mm110) cc_final: 0.8479 (mm-40)
REVERT: D2  179 MET cc_start: 0.7866 (tpt) cc_final: 0.7392 (tpp)
REVERT: D2  190 MET cc_start: 0.8852 (mtm) cc_final: 0.8449 (mtm)
REVERT: D2  213 SER cc_start: 0.9443 (m) cc_final: 0.9034 (p)
REVERT: D2  248 LEU cc_start: 0.9101 (mm) cc_final: 0.8433 (mt)
REVERT: D2  268 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8895 (tm-30)
REVERT: D2  334 THR cc_start: 0.9386 (t) cc_final: 0.8975 (t)
REVERT: D2  335 MET cc_start: 0.7685 (mmt) cc_final: 0.7172 (mpp)
REVERT: AK   22 TYR cc_start: 0.8034 (t80) cc_final: 0.7752 (t80)
REVERT: AK   57 ARG cc_start: 0.7036 (ttp-170) cc_final: 0.6514 (tpp-160)
REVERT: AK   78 GLN cc_start: 0.8642 (mm110) cc_final: 0.8316 (mm-40)
REVERT: B5   44 ASN cc_start: 0.7984 (t0) cc_final: 0.7760 (t0)
REVERT: AB   43 ASP cc_start: 0.7930 (p0) cc_final: 0.7675 (p0)
REVERT: AB   68 GLU cc_start: 0.6659 (pm20) cc_final: 0.6297 (pm20)
REVERT: AB   79 TYR cc_start: 0.7745 (t80) cc_final: 0.7332 (t80)
REVERT: A8   25 LYS cc_start: 0.9017 (tttt) cc_final: 0.8731 (tppt)
REVERT: BJ   30 THR cc_start: 0.7354 (p) cc_final: 0.7114 (p)
REVERT: BJ   37 ASP cc_start: 0.9085 (t0) cc_final: 0.8819 (t0)
REVERT: BJ  134 VAL cc_start: 0.8540 (t) cc_final: 0.8239 (p)
REVERT: BJ  163 LEU cc_start: 0.9298 (mp) cc_final: 0.9085 (mm)
REVERT: AJ   20 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7685 (tp30)
REVERT: AJ  106 LEU cc_start: 0.9127 (mm) cc_final: 0.8878 (mm)
REVERT: AJ  110 ASP cc_start: 0.8798 (m-30) cc_final: 0.8157 (m-30)
REVERT: AJ  173 ASP cc_start: 0.8071 (t0) cc_final: 0.7692 (p0)
REVERT: AJ  185 LYS cc_start: 0.8320 (mttt) cc_final: 0.8102 (tppt)
REVERT: AJ  256 LEU cc_start: 0.8597 (mt) cc_final: 0.8370 (mt)
REVERT: A3   15 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6986 (mt-10)
REVERT: A3   31 LEU cc_start: 0.9110 (tp) cc_final: 0.8800 (tp)
REVERT: A3   50 TYR cc_start: 0.6948 (m-80) cc_final: 0.6690 (m-10)
REVERT: C2    2 MET cc_start: 0.7610 (tmm) cc_final: 0.7267 (tmm)
REVERT: C2   62 PHE cc_start: 0.8593 (m-10) cc_final: 0.8368 (m-10)
REVERT: B4   74 ASN cc_start: 0.7804 (t0) cc_final: 0.7397 (t0)
REVERT: AM   78 LYS cc_start: 0.8571 (tppt) cc_final: 0.8261 (tppt)
REVERT: B6   27 LEU cc_start: 0.8675 (pt) cc_final: 0.8376 (pt)
REVERT: B6   28 SER cc_start: 0.7949 (t) cc_final: 0.7585 (p)
REVERT: B6  119 MET cc_start: 0.6866 (tmm) cc_final: 0.6623 (tmm)
REVERT: B7   67 LYS cc_start: 0.9154 (tptm) cc_final: 0.8250 (mtmt)
REVERT: B9  103 LEU cc_start: 0.8799 (tp) cc_final: 0.8389 (tt)
REVERT: B2   16 GLN cc_start: 0.6780 (pt0) cc_final: 0.6341 (pm20)
REVERT: B2   42 HIS cc_start: 0.7565 (t-90) cc_final: 0.6671 (t-90)
REVERT: B2   61 ASP cc_start: 0.7365 (t0) cc_final: 0.7032 (t0)
REVERT: B8   69 LEU cc_start: 0.8472 (mt) cc_final: 0.8212 (mt)
REVERT: B8   77 MET cc_start: 0.8161 (mmp) cc_final: 0.7770 (mmm)
REVERT: B8  113 LEU cc_start: 0.9123 (mt) cc_final: 0.8667 (tt)
REVERT: BK   29 ASP cc_start: 0.8938 (t70) cc_final: 0.8603 (t0)
REVERT: BK   53 VAL cc_start: 0.6869 (m) cc_final: 0.6531 (p)
REVERT: BK   86 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8518 (mm-40)
REVERT: BK  108 MET cc_start: 0.6647 (ttm) cc_final: 0.5935 (ttt)
REVERT: C1   11 SER cc_start: 0.8799 (m) cc_final: 0.8598 (t)
REVERT: C1   37 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6877 (tm-30)
REVERT: A1   29 PHE cc_start: 0.8055 (t80) cc_final: 0.7668 (t80)
REVERT: A1   55 SER cc_start: 0.9163 (t) cc_final: 0.8629 (p)
  outliers start: 16
  outliers final: 2
  residues processed: 2366
  average time/residue: 0.5988
  time to fit residues: 2399.5704
Evaluate side-chains
  1714 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 1711
  time to evaluate  : 5.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 397 optimal weight:    7.9990
   chunk 221 optimal weight:    3.9990
   chunk 594 optimal weight:    9.9990
   chunk 486 optimal weight:    2.9990
   chunk 197 optimal weight:    5.9990
   chunk 715 optimal weight:    9.9990
   chunk 773 optimal weight:   10.0000
   chunk 637 optimal weight:   10.0000
   chunk 710 optimal weight:    4.9990
   chunk 244 optimal weight:    8.9990
   chunk 574 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 293 ASN
V1 356 HIS
V2 101 GLN
** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S1 119 GLN
S1 401 HIS
S1 430 GLN
S1 494 HIS
S1 653 ASN
S1 682 GLN
S2 135 GLN
S2 252 ASN
S8 123 GLN
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S6  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  44 ASN
S4  50 ASN
** A9  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A9  87 HIS
A9 288 HIS
** A2  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A5  20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A5  85 ASN
A6 107 HIS
** A7  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AL  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AA  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D3  10 ASN
D1   5 ASN
** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 4L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5  59 GLN
D5 175 ASN
** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
** D5 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D4  51 ASN
** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D4 440 HIS
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B5 124 GLN
BJ  64 HIS
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** BJ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
AJ 151 HIS
AJ 184 GLN
AJ 200 GLN
AJ 264 GLN
S5  96 HIS
A3  68 HIS
** B4  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4  49 GLN
AM  23 ASN
** B7  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B9  25 HIS
B9  32 HIS
B9 138 GLN
** B2  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B8  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
BK 103 HIS
C1  36 ASN

Total number of N/Q/H flips: 40

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.235  67000  Z= 0.663
  Angle     :  1.752  51.264  90856  Z= 1.099
  Chirality :  0.313   6.423   9986
  Planarity :  0.007   0.122  11476
  Dihedral  :  8.441 117.984   9098
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 11.77 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.97 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.33 %
    Twisted Proline : 0.84 %
    Twisted General : 0.25 %

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: -2.23 (0.09), residues: 7979
  helix: -0.12 (0.08), residues: 4179
  sheet: -1.86 (0.26), residues: 366
  loop : -3.27 (0.10), residues: 3434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRPB4 100 
 HIS   0.019   0.002   HISS2 150 
 PHE   0.038   0.003   PHED5 385 
 TYR   0.032   0.003   TYRS7 125 
 ARG   0.012   0.001   ARGS1 253 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  2031 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 2018
  time to evaluate  : 5.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S1   94 MET cc_start: 0.8309 (tpp) cc_final: 0.7961 (mmt)
REVERT: S1  226 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8000 (tm-30)
REVERT: S1  253 ARG cc_start: 0.7337 (ptt-90) cc_final: 0.7085 (ptt90)
REVERT: S1  283 MET cc_start: 0.8049 (mtt) cc_final: 0.7763 (mtt)
REVERT: S1  419 TYR cc_start: 0.7887 (p90) cc_final: 0.7407 (p90)
REVERT: S1  490 MET cc_start: 0.7782 (tmm) cc_final: 0.7178 (tmm)
REVERT: S1  549 HIS cc_start: 0.7980 (p90) cc_final: 0.7605 (p-80)
REVERT: S2  137 ILE cc_start: 0.9443 (mt) cc_final: 0.9047 (tt)
REVERT: S2  152 MET cc_start: 0.9135 (tpp) cc_final: 0.8894 (tpp)
REVERT: S2  174 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8166 (ptm160)
REVERT: S2  199 VAL cc_start: 0.8716 (t) cc_final: 0.8415 (p)
REVERT: S2  208 MET cc_start: 0.7835 (mmm) cc_final: 0.7511 (mmm)
REVERT: S2  338 MET cc_start: 0.8546 (tmm) cc_final: 0.8333 (tmm)
REVERT: S2  404 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8602 (mmmt)
REVERT: S2  413 ASP cc_start: 0.8952 (m-30) cc_final: 0.8719 (m-30)
REVERT: S3   38 GLN cc_start: 0.8433 (mp10) cc_final: 0.8197 (mp10)
REVERT: S3  200 ASN cc_start: 0.7952 (m-40) cc_final: 0.7160 (p0)
REVERT: S7   62 MET cc_start: 0.9243 (tmm) cc_final: 0.8574 (tmm)
REVERT: S7  128 TYR cc_start: 0.8225 (m-80) cc_final: 0.7752 (m-80)
REVERT: S7  173 LEU cc_start: 0.9218 (mt) cc_final: 0.8949 (mt)
REVERT: S8   23 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8652 (tm-30)
REVERT: S8   58 SER cc_start: 0.9362 (t) cc_final: 0.7938 (t)
REVERT: S8   92 ILE cc_start: 0.9624 (mm) cc_final: 0.9286 (mm)
REVERT: S6   36 ASN cc_start: 0.8970 (t0) cc_final: 0.8609 (t0)
REVERT: S6   78 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7459 (tm-30)
REVERT: S4   22 LEU cc_start: 0.9340 (mm) cc_final: 0.9035 (mp)
REVERT: S4   46 GLN cc_start: 0.7598 (tp40) cc_final: 0.7394 (mm110)
REVERT: A9   67 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8095 (tp-100)
REVERT: A9   74 ASN cc_start: 0.8483 (p0) cc_final: 0.8087 (p0)
REVERT: A9   99 TRP cc_start: 0.9217 (p90) cc_final: 0.8996 (p90)
REVERT: A9  184 ASN cc_start: 0.8773 (t0) cc_final: 0.8571 (m-40)
REVERT: A9  216 ASN cc_start: 0.8577 (t0) cc_final: 0.8357 (t0)
REVERT: A9  306 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7337 (tm-30)
REVERT: A9  310 LEU cc_start: 0.8914 (tp) cc_final: 0.8569 (tp)
REVERT: A6   20 PHE cc_start: 0.8330 (m-10) cc_final: 0.8037 (m-10)
REVERT: A6   41 GLU cc_start: 0.8179 (tp30) cc_final: 0.7876 (tp30)
REVERT: A7   31 SER cc_start: 0.7980 (m) cc_final: 0.7749 (m)
REVERT: A7   34 THR cc_start: 0.7813 (p) cc_final: 0.7416 (p)
REVERT: A7   47 ARG cc_start: 0.7448 (ptm160) cc_final: 0.6936 (ptm160)
REVERT: A7   69 MET cc_start: 0.7550 (tpp) cc_final: 0.6649 (tpt)
REVERT: AL   56 PHE cc_start: 0.8613 (t80) cc_final: 0.8220 (t80)
REVERT: AL   59 HIS cc_start: 0.7488 (m-70) cc_final: 0.7061 (m-70)
REVERT: AL  117 LEU cc_start: 0.8171 (pt) cc_final: 0.7860 (pt)
REVERT: AL  122 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: AA   37 MET cc_start: 0.7462 (tpt) cc_final: 0.6977 (tpp)
REVERT: AA   48 VAL cc_start: 0.9555 (p) cc_final: 0.9264 (p)
REVERT: D3    4 MET cc_start: 0.7309 (ttt) cc_final: 0.6709 (tmm)
REVERT: D3   57 LEU cc_start: 0.8987 (mm) cc_final: 0.8639 (mt)
REVERT: D3   66 ASP cc_start: 0.9122 (t70) cc_final: 0.8816 (t0)
REVERT: D3   80 GLN cc_start: 0.8147 (pm20) cc_final: 0.7812 (pm20)
REVERT: D3   86 THR cc_start: 0.8603 (p) cc_final: 0.8300 (t)
REVERT: D3   96 PHE cc_start: 0.8366 (t80) cc_final: 0.8040 (t80)
REVERT: D1   73 LEU cc_start: 0.9289 (tt) cc_final: 0.8849 (pp)
REVERT: D1   98 MET cc_start: 0.7589 (mmm) cc_final: 0.7342 (mmm)
REVERT: D1  272 TRP cc_start: 0.9138 (t60) cc_final: 0.8819 (t60)
REVERT: D1  282 TYR cc_start: 0.8788 (t80) cc_final: 0.7465 (t80)
REVERT: D1  283 ASP cc_start: 0.8490 (m-30) cc_final: 0.8239 (m-30)
REVERT: D1  286 MET cc_start: 0.9011 (mmt) cc_final: 0.8637 (mmm)
REVERT: D6    1 MET cc_start: 0.6223 (tmm) cc_final: 0.5998 (ttm)
REVERT: D6   57 PHE cc_start: 0.8383 (t80) cc_final: 0.8001 (t80)
REVERT: D6   70 TYR cc_start: 0.8703 (t80) cc_final: 0.8190 (t80)
REVERT: D6   74 MET cc_start: 0.7476 (mmm) cc_final: 0.7083 (mtm)
REVERT: D6   99 MET cc_start: 0.7118 (ttt) cc_final: 0.6759 (tpp)
REVERT: D6  100 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: 4L    9 MET cc_start: 0.8413 (mmm) cc_final: 0.7589 (tpt)
REVERT: 4L   24 SER cc_start: 0.8579 (p) cc_final: 0.8154 (t)
REVERT: 4L   25 HIS cc_start: 0.8704 (m-70) cc_final: 0.7820 (m-70)
REVERT: 4L   36 MET cc_start: 0.8579 (tmm) cc_final: 0.8306 (tmm)
REVERT: D5   12 LEU cc_start: 0.8776 (tt) cc_final: 0.8431 (mm)
REVERT: D5   87 MET cc_start: 0.7282 (mmp) cc_final: 0.7028 (mmm)
REVERT: D5  102 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7560 (tp30)
REVERT: D5  277 MET cc_start: 0.8270 (tpp) cc_final: 0.8056 (tpp)
REVERT: D5  283 MET cc_start: 0.8022 (ptm) cc_final: 0.7799 (ptp)
REVERT: D5  326 PHE cc_start: 0.8499 (t80) cc_final: 0.8137 (t80)
REVERT: D5  355 ASP cc_start: 0.8168 (m-30) cc_final: 0.7771 (t0)
REVERT: D5  370 THR cc_start: 0.8909 (p) cc_final: 0.8624 (t)
REVERT: D5  604 PHE cc_start: 0.8189 (m-10) cc_final: 0.7773 (m-80)
REVERT: D4    5 ILE cc_start: 0.9086 (mm) cc_final: 0.8880 (mm)
REVERT: D4    9 MET cc_start: 0.8170 (tmm) cc_final: 0.7792 (tmm)
REVERT: D4   12 MET cc_start: 0.7798 (tmm) cc_final: 0.7486 (tmm)
REVERT: D4  108 MET cc_start: 0.8874 (mmm) cc_final: 0.8300 (mmm)
REVERT: D4  141 GLU cc_start: 0.8808 (tt0) cc_final: 0.8560 (tt0)
REVERT: D4  147 LEU cc_start: 0.9051 (tp) cc_final: 0.8851 (tp)
REVERT: D4  238 LEU cc_start: 0.8691 (tt) cc_final: 0.8371 (tp)
REVERT: D4  250 LEU cc_start: 0.8317 (mm) cc_final: 0.7966 (mm)
REVERT: D4  263 MET cc_start: 0.9062 (mmp) cc_final: 0.8774 (mmp)
REVERT: D4  294 MET cc_start: 0.8807 (mmm) cc_final: 0.8513 (mmp)
REVERT: D4  447 LEU cc_start: 0.9082 (mt) cc_final: 0.8750 (mt)
REVERT: D2   72 MET cc_start: 0.9078 (tpt) cc_final: 0.8474 (tpt)
REVERT: D2   85 THR cc_start: 0.8186 (p) cc_final: 0.7941 (p)
REVERT: D2  120 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8352 (tm-30)
REVERT: D2  135 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8608 (mmtm)
REVERT: D2  167 TRP cc_start: 0.8615 (m-10) cc_final: 0.8317 (m-10)
REVERT: D2  174 GLN cc_start: 0.8743 (mm110) cc_final: 0.8404 (mm-40)
REVERT: D2  178 ILE cc_start: 0.8893 (mt) cc_final: 0.8651 (mm)
REVERT: D2  213 SER cc_start: 0.9459 (m) cc_final: 0.9122 (p)
REVERT: D2  248 LEU cc_start: 0.9208 (mm) cc_final: 0.8954 (mt)
REVERT: D2  263 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8551 (mttt)
REVERT: D2  268 GLN cc_start: 0.9351 (tm-30) cc_final: 0.8812 (tm-30)
REVERT: D2  334 THR cc_start: 0.9320 (t) cc_final: 0.9024 (t)
REVERT: D2  335 MET cc_start: 0.7646 (mmt) cc_final: 0.7246 (mpp)
REVERT: D2  344 SER cc_start: 0.9070 (p) cc_final: 0.8626 (m)
REVERT: AK   22 TYR cc_start: 0.7986 (t80) cc_final: 0.7655 (t80)
REVERT: AK   57 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6770 (tpp-160)
REVERT: B5   97 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7057 (tt0)
REVERT: B5  115 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8125 (tpp80)
REVERT: AB   68 GLU cc_start: 0.6794 (pm20) cc_final: 0.6261 (pm20)
REVERT: AB   71 MET cc_start: 0.5964 (tmm) cc_final: 0.5560 (tmm)
REVERT: AB   79 TYR cc_start: 0.7907 (t80) cc_final: 0.7642 (t80)
REVERT: A8   25 LYS cc_start: 0.9252 (tttt) cc_final: 0.8786 (mmtp)
REVERT: A8   64 GLN cc_start: 0.7978 (pp30) cc_final: 0.7679 (tm-30)
REVERT: AJ   20 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7554 (tp30)
REVERT: AJ  185 LYS cc_start: 0.8553 (mttt) cc_final: 0.8191 (tppt)
REVERT: S5   72 MET cc_start: 0.7506 (mmp) cc_final: 0.7272 (mmp)
REVERT: A3   14 LYS cc_start: 0.5659 (mtmt) cc_final: 0.5419 (mtmm)
REVERT: A3   15 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7175 (mt-10)
REVERT: A3   29 VAL cc_start: 0.9016 (t) cc_final: 0.8719 (m)
REVERT: C2    2 MET cc_start: 0.7794 (tmm) cc_final: 0.7069 (tmm)
REVERT: C2   62 PHE cc_start: 0.8681 (m-10) cc_final: 0.8322 (m-10)
REVERT: C2   65 ILE cc_start: 0.9283 (mt) cc_final: 0.9066 (tp)
REVERT: B4   26 SER cc_start: 0.7871 (t) cc_final: 0.7618 (p)
REVERT: B4   47 GLN cc_start: 0.8949 (mm110) cc_final: 0.8562 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7763 (t0) cc_final: 0.7257 (t0)
REVERT: AM    9 MET cc_start: 0.7275 (tpt) cc_final: 0.6957 (tpt)
REVERT: B6   15 ARG cc_start: 0.8771 (tpp-160) cc_final: 0.8545 (mmm160)
REVERT: B6   28 SER cc_start: 0.7981 (t) cc_final: 0.7554 (p)
REVERT: B7   76 PHE cc_start: 0.7815 (t80) cc_final: 0.7356 (p90)
REVERT: B7   88 TYR cc_start: 0.8084 (t80) cc_final: 0.7816 (t80)
REVERT: B9   27 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8153 (mt-10)
REVERT: B9   43 LEU cc_start: 0.8519 (mm) cc_final: 0.8237 (mm)
REVERT: B9   50 HIS cc_start: 0.7331 (p-80) cc_final: 0.6728 (p-80)
REVERT: B2   16 GLN cc_start: 0.7081 (pt0) cc_final: 0.6529 (pm20)
REVERT: B2   32 MET cc_start: 0.8914 (tmm) cc_final: 0.8692 (tmm)
REVERT: B2   61 ASP cc_start: 0.7117 (t0) cc_final: 0.6894 (t0)
REVERT: B8   63 ASP cc_start: 0.8851 (m-30) cc_final: 0.8645 (m-30)
REVERT: B8   83 MET cc_start: 0.8165 (tmm) cc_final: 0.7950 (tmm)
REVERT: B8   86 ARG cc_start: 0.8048 (ptp90) cc_final: 0.7793 (ptp90)
REVERT: B8  113 LEU cc_start: 0.9226 (mt) cc_final: 0.8757 (tt)
REVERT: BK   43 ASP cc_start: 0.8566 (p0) cc_final: 0.8178 (p0)
REVERT: BK   53 VAL cc_start: 0.6892 (m) cc_final: 0.6485 (p)
REVERT: BK   66 PHE cc_start: 0.8412 (m-10) cc_final: 0.8081 (m-10)
REVERT: C1   11 SER cc_start: 0.8791 (m) cc_final: 0.8470 (t)
REVERT: C1   37 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7068 (tm-30)
  outliers start: 13
  outliers final: 1
  residues processed: 2026
  average time/residue: 0.5992
  time to fit residues: 2073.7456
Evaluate side-chains
  1531 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 1529
  time to evaluate  : 5.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 707 optimal weight:    4.9990
   chunk 538 optimal weight:    0.9990
   chunk 371 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 341 optimal weight:    0.9980
   chunk 480 optimal weight:    6.9990
   chunk 718 optimal weight:    1.9990
   chunk 760 optimal weight:    8.9990
   chunk 375 optimal weight:    3.9990
   chunk 680 optimal weight:   10.0000
   chunk 205 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 431 GLN
V2  37 ASN
V2  99 HIS
V2 101 GLN
S1  51 ASN
** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S3 160 HIS
** S7  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S7  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S8  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S6  94 GLN
** S4  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
A9  37 HIS
** A9  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A9 288 HIS
A5  20 HIS
A6 125 HIS
** A7  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A7  50 ASN
** AL  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AA  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D3  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 4L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5  23 ASN
** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 194 ASN
** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2 235 ASN
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B5  44 ASN
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S5  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S5  96 HIS
** C2  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4  47 GLN
B4  49 GLN
AM  23 ASN
** B9  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B9  25 HIS
B9  32 HIS
B2  24 GLN
B8  56 GLN
B8  72 ASN
** B8  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
BK  86 GLN
A1  31 ASN

Total number of N/Q/H flips: 29

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.242  67000  Z= 0.559
  Angle     :  1.677  50.720  90856  Z= 1.063
  Chirality :  0.312   6.378   9986
  Planarity :  0.006   0.155  11476
  Dihedral  :  7.962 112.136   9098
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 10.31 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.58 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.63 %
    Twisted General : 0.23 %

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: -1.84 (0.09), residues: 7979
  helix:  0.23 (0.08), residues: 4156
  sheet: -1.65 (0.26), residues: 373
  loop : -3.12 (0.10), residues: 3450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRPB4 100 
 HIS   0.020   0.001   HISA9  87 
 PHE   0.031   0.002   PHED5 385 
 TYR   0.031   0.002   TYRS8 118 
 ARG   0.009   0.001   ARGBJ 141 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  2055 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 2050
  time to evaluate  : 5.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V1  102 PRO cc_start: 0.8821 (Cg_exo) cc_final: 0.8423 (Cg_endo)
REVERT: S1   20 VAL cc_start: 0.8727 (p) cc_final: 0.8398 (p)
REVERT: S1  190 MET cc_start: 0.8267 (ttp) cc_final: 0.8001 (ptm)
REVERT: S1  200 ILE cc_start: 0.9261 (pt) cc_final: 0.8896 (mt)
REVERT: S1  283 MET cc_start: 0.8199 (mtt) cc_final: 0.7947 (mtt)
REVERT: S1  419 TYR cc_start: 0.7818 (p90) cc_final: 0.7379 (p90)
REVERT: S1  490 MET cc_start: 0.7743 (tmm) cc_final: 0.7161 (tmm)
REVERT: S1  549 HIS cc_start: 0.7918 (p90) cc_final: 0.7664 (p-80)
REVERT: S2  137 ILE cc_start: 0.9376 (mt) cc_final: 0.9002 (tt)
REVERT: S2  148 LEU cc_start: 0.8803 (tt) cc_final: 0.8602 (tt)
REVERT: S2  152 MET cc_start: 0.9153 (tpp) cc_final: 0.8918 (tpp)
REVERT: S2  155 THR cc_start: 0.8900 (p) cc_final: 0.8502 (t)
REVERT: S2  199 VAL cc_start: 0.8680 (t) cc_final: 0.8386 (p)
REVERT: S2  242 ILE cc_start: 0.8193 (pt) cc_final: 0.7980 (pt)
REVERT: S2  302 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7868 (mm-30)
REVERT: S2  338 MET cc_start: 0.8615 (tmm) cc_final: 0.8404 (tmm)
REVERT: S2  379 VAL cc_start: 0.9532 (t) cc_final: 0.9208 (p)
REVERT: S2  404 LYS cc_start: 0.8816 (mmpt) cc_final: 0.8588 (mmmt)
REVERT: S2  413 ASP cc_start: 0.8932 (m-30) cc_final: 0.8731 (m-30)
REVERT: S3  200 ASN cc_start: 0.7825 (m-40) cc_final: 0.7100 (p0)
REVERT: S7   62 MET cc_start: 0.9152 (tmm) cc_final: 0.8940 (tmm)
REVERT: S7   69 MET cc_start: 0.8512 (mpp) cc_final: 0.8006 (mpp)
REVERT: S7  128 TYR cc_start: 0.8051 (m-80) cc_final: 0.7559 (m-80)
REVERT: S7  172 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7253 (tmt170)
REVERT: S7  173 LEU cc_start: 0.9075 (mt) cc_final: 0.8855 (mt)
REVERT: S8   23 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8679 (tm-30)
REVERT: S8   58 SER cc_start: 0.8982 (t) cc_final: 0.8338 (t)
REVERT: S8   92 ILE cc_start: 0.9492 (mm) cc_final: 0.9275 (mm)
REVERT: S8  118 TYR cc_start: 0.8469 (m-80) cc_final: 0.8240 (m-80)
REVERT: S8  136 ASN cc_start: 0.8054 (p0) cc_final: 0.7692 (p0)
REVERT: S8  169 ILE cc_start: 0.9188 (mt) cc_final: 0.8930 (tt)
REVERT: S6   36 ASN cc_start: 0.8822 (t0) cc_final: 0.8570 (t0)
REVERT: S4   46 GLN cc_start: 0.7625 (tp40) cc_final: 0.7416 (mm110)
REVERT: S4   77 ASP cc_start: 0.8297 (t0) cc_final: 0.8021 (t0)
REVERT: A9   74 ASN cc_start: 0.8407 (p0) cc_final: 0.8066 (p0)
REVERT: A9  216 ASN cc_start: 0.8475 (t0) cc_final: 0.8210 (t0)
REVERT: A9  306 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7546 (tm-30)
REVERT: A9  310 LEU cc_start: 0.8824 (tp) cc_final: 0.8479 (tp)
REVERT: A6   41 GLU cc_start: 0.8136 (tp30) cc_final: 0.7867 (tp30)
REVERT: A6   90 GLU cc_start: 0.8130 (tp30) cc_final: 0.7795 (tp30)
REVERT: A7   47 ARG cc_start: 0.7531 (ptm160) cc_final: 0.6975 (ptm160)
REVERT: A7   50 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.6908 (t160)
REVERT: A7   69 MET cc_start: 0.7498 (tpp) cc_final: 0.6446 (tpt)
REVERT: AL   25 ARG cc_start: 0.8414 (ttp80) cc_final: 0.7862 (ttp80)
REVERT: AL   56 PHE cc_start: 0.8536 (t80) cc_final: 0.8230 (t80)
REVERT: AL   59 HIS cc_start: 0.7601 (m-70) cc_final: 0.7278 (m-70)
REVERT: D3    4 MET cc_start: 0.7285 (ttt) cc_final: 0.6612 (tmm)
REVERT: D3   57 LEU cc_start: 0.8906 (mm) cc_final: 0.8518 (mt)
REVERT: D3   86 THR cc_start: 0.8526 (p) cc_final: 0.8192 (t)
REVERT: D3   96 PHE cc_start: 0.8221 (t80) cc_final: 0.7956 (t80)
REVERT: D1   26 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9208 (mmmm)
REVERT: D1   47 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: D1   66 SER cc_start: 0.8246 (m) cc_final: 0.7839 (p)
REVERT: D1   70 MET cc_start: 0.7719 (ttm) cc_final: 0.7354 (mtm)
REVERT: D1  272 TRP cc_start: 0.9025 (t60) cc_final: 0.8793 (t60)
REVERT: D1  285 LEU cc_start: 0.9528 (tp) cc_final: 0.9074 (tp)
REVERT: D1  286 MET cc_start: 0.8754 (mmt) cc_final: 0.8384 (mmm)
REVERT: D6    1 MET cc_start: 0.6098 (tmm) cc_final: 0.5579 (tmm)
REVERT: D6  124 ASP cc_start: 0.7183 (m-30) cc_final: 0.6765 (m-30)
REVERT: 4L    9 MET cc_start: 0.8495 (mmm) cc_final: 0.7633 (tpt)
REVERT: 4L   36 MET cc_start: 0.8441 (tmm) cc_final: 0.8111 (tmm)
REVERT: 4L   40 LEU cc_start: 0.8899 (tt) cc_final: 0.8697 (tp)
REVERT: 4L   47 MET cc_start: 0.8998 (ttm) cc_final: 0.8785 (ttm)
REVERT: D5   12 LEU cc_start: 0.8632 (tt) cc_final: 0.8370 (mm)
REVERT: D5   48 MET cc_start: 0.7974 (ttt) cc_final: 0.7348 (ttp)
REVERT: D5   88 MET cc_start: 0.7597 (tpp) cc_final: 0.7342 (tpp)
REVERT: D5  102 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7539 (tp30)
REVERT: D5  201 ILE cc_start: 0.9140 (pt) cc_final: 0.8894 (pt)
REVERT: D5  283 MET cc_start: 0.8100 (ptm) cc_final: 0.7898 (ptp)
REVERT: D5  313 MET cc_start: 0.8782 (ptp) cc_final: 0.8429 (ptt)
REVERT: D5  326 PHE cc_start: 0.8303 (t80) cc_final: 0.7997 (t80)
REVERT: D5  355 ASP cc_start: 0.8057 (m-30) cc_final: 0.7764 (t70)
REVERT: D5  370 THR cc_start: 0.8718 (p) cc_final: 0.8478 (t)
REVERT: D5  573 MET cc_start: 0.7700 (mmt) cc_final: 0.7322 (mmt)
REVERT: D5  604 PHE cc_start: 0.8383 (m-10) cc_final: 0.7898 (m-80)
REVERT: D4    9 MET cc_start: 0.8242 (tmm) cc_final: 0.7805 (tmm)
REVERT: D4   59 ASP cc_start: 0.8514 (p0) cc_final: 0.8264 (p0)
REVERT: D4   66 LEU cc_start: 0.9161 (tt) cc_final: 0.8792 (tp)
REVERT: D4  119 TYR cc_start: 0.8192 (t80) cc_final: 0.7960 (t80)
REVERT: D4  141 GLU cc_start: 0.8813 (tt0) cc_final: 0.8592 (tt0)
REVERT: D4  147 LEU cc_start: 0.9075 (tp) cc_final: 0.8866 (tp)
REVERT: D4  200 MET cc_start: 0.7770 (mmp) cc_final: 0.7490 (mmm)
REVERT: D4  263 MET cc_start: 0.9020 (mmp) cc_final: 0.8767 (mmp)
REVERT: D4  278 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7699 (ttt-90)
REVERT: D4  294 MET cc_start: 0.8726 (mmm) cc_final: 0.8244 (mmp)
REVERT: D4  369 LEU cc_start: 0.8372 (tp) cc_final: 0.8114 (tt)
REVERT: D4  447 LEU cc_start: 0.8942 (mt) cc_final: 0.8501 (mt)
REVERT: D2   36 ASN cc_start: 0.8941 (t0) cc_final: 0.8632 (t0)
REVERT: D2   85 THR cc_start: 0.8239 (p) cc_final: 0.8026 (p)
REVERT: D2  135 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8495 (mmtm)
REVERT: D2  151 LEU cc_start: 0.8775 (tt) cc_final: 0.8403 (tt)
REVERT: D2  167 TRP cc_start: 0.8600 (m-10) cc_final: 0.8067 (m-10)
REVERT: D2  178 ILE cc_start: 0.8810 (mt) cc_final: 0.8474 (mm)
REVERT: D2  213 SER cc_start: 0.9491 (m) cc_final: 0.9084 (p)
REVERT: D2  248 LEU cc_start: 0.9180 (mm) cc_final: 0.8605 (mt)
REVERT: D2  263 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8512 (mttt)
REVERT: D2  268 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8714 (tm-30)
REVERT: D2  344 SER cc_start: 0.8920 (p) cc_final: 0.8305 (m)
REVERT: AK   22 TYR cc_start: 0.7779 (t80) cc_final: 0.7449 (t80)
REVERT: AK   57 ARG cc_start: 0.7169 (ttp-170) cc_final: 0.6730 (tpp-160)
REVERT: AK   80 ARG cc_start: 0.7466 (ttp-170) cc_final: 0.6840 (ttp-170)
REVERT: B5  115 ARG cc_start: 0.8357 (tpp80) cc_final: 0.7855 (tpp80)
REVERT: AB   56 ASP cc_start: 0.8519 (p0) cc_final: 0.8226 (p0)
REVERT: AB   68 GLU cc_start: 0.6670 (pm20) cc_final: 0.6295 (pm20)
REVERT: A8   25 LYS cc_start: 0.9152 (tttt) cc_final: 0.8744 (mmtp)
REVERT: A8   64 GLN cc_start: 0.8025 (pp30) cc_final: 0.7795 (tm-30)
REVERT: A8   89 ASP cc_start: 0.8118 (t0) cc_final: 0.7322 (t0)
REVERT: BJ   76 CYS cc_start: 0.6337 (m) cc_final: 0.6135 (m)
REVERT: BJ  140 ASP cc_start: 0.8841 (m-30) cc_final: 0.8578 (m-30)
REVERT: AJ   20 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7511 (tp30)
REVERT: AJ  106 LEU cc_start: 0.9091 (mm) cc_final: 0.8824 (mm)
REVERT: AJ  110 ASP cc_start: 0.8671 (m-30) cc_final: 0.8434 (m-30)
REVERT: AJ  185 LYS cc_start: 0.8439 (mttt) cc_final: 0.8067 (tppt)
REVERT: AJ  241 LEU cc_start: 0.8374 (tp) cc_final: 0.8170 (tp)
REVERT: A3   15 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7005 (mt-10)
REVERT: A3   29 VAL cc_start: 0.9048 (t) cc_final: 0.8789 (m)
REVERT: C2    2 MET cc_start: 0.7800 (tmm) cc_final: 0.6564 (tmm)
REVERT: C2   37 LEU cc_start: 0.9217 (tp) cc_final: 0.8775 (tt)
REVERT: C2   62 PHE cc_start: 0.8613 (m-10) cc_final: 0.8260 (m-10)
REVERT: C2   83 TYR cc_start: 0.8652 (m-80) cc_final: 0.7964 (m-80)
REVERT: C2   95 LYS cc_start: 0.8577 (pttm) cc_final: 0.8286 (mmtm)
REVERT: B4   47 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8517 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7761 (t0) cc_final: 0.7305 (t0)
REVERT: B4   99 PHE cc_start: 0.7735 (t80) cc_final: 0.7223 (m-10)
REVERT: AM   50 MET cc_start: 0.7401 (tmm) cc_final: 0.7163 (tmm)
REVERT: B6   28 SER cc_start: 0.7975 (t) cc_final: 0.7567 (p)
REVERT: B6   85 LEU cc_start: 0.8767 (mp) cc_final: 0.8452 (tt)
REVERT: B6   99 LYS cc_start: 0.8408 (tmtt) cc_final: 0.7754 (tmtt)
REVERT: B7   50 LEU cc_start: 0.8609 (tp) cc_final: 0.8364 (tp)
REVERT: B7   88 TYR cc_start: 0.7724 (t80) cc_final: 0.7491 (t80)
REVERT: B9   27 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7840 (mt-10)
REVERT: B9   50 HIS cc_start: 0.7393 (p-80) cc_final: 0.6888 (p-80)
REVERT: B2   42 HIS cc_start: 0.7461 (t-90) cc_final: 0.6627 (t-90)
REVERT: B8    6 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8301 (pttm)
REVERT: B8   20 ARG cc_start: 0.8406 (mmt90) cc_final: 0.8037 (mmm-85)
REVERT: B8   68 ASP cc_start: 0.7368 (m-30) cc_final: 0.7036 (m-30)
REVERT: B8  113 LEU cc_start: 0.9182 (mt) cc_final: 0.8696 (tt)
REVERT: BK   28 GLU cc_start: 0.8459 (pm20) cc_final: 0.8096 (pm20)
REVERT: BK   33 GLU cc_start: 0.6549 (mp0) cc_final: 0.5987 (mp0)
REVERT: BK   43 ASP cc_start: 0.8516 (p0) cc_final: 0.8022 (p0)
REVERT: BK   53 VAL cc_start: 0.6700 (m) cc_final: 0.6248 (p)
REVERT: BK   66 PHE cc_start: 0.8200 (m-10) cc_final: 0.7899 (m-10)
REVERT: C1   11 SER cc_start: 0.8768 (m) cc_final: 0.8470 (t)
REVERT: C1   37 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7123 (tm-30)
REVERT: C1   38 ASP cc_start: 0.8540 (t0) cc_final: 0.8292 (t0)
REVERT: A1   36 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7950 (ttpt)
  outliers start: 5
  outliers final: 2
  residues processed: 2054
  average time/residue: 0.5843
  time to fit residues: 2048.5957
Evaluate side-chains
  1612 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 1609
  time to evaluate  : 5.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 633 optimal weight:    9.9990
   chunk 431 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 566 optimal weight:    7.9990
   chunk 313 optimal weight:    0.7980
   chunk 649 optimal weight:    0.8980
   chunk 525 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 388 optimal weight:    6.9990
   chunk 682 optimal weight:    6.9990
   chunk 191 optimal weight:    4.9990
   overall best weight:    1.6582

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V2  37 ASN
V2  99 HIS
S1  51 ASN
** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S2 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S7  38 ASN
** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S4  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
A9 288 HIS
A5  20 HIS
A5 110 GLN
A7  24 GLN
A7  50 ASN
AL  31 ASN
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AA  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D3  10 ASN
** D1   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 4L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5  23 ASN
** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 199 GLN
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
D5 580 GLN
** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D4 279 GLN
D2  48 HIS
** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2 235 ASN
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
BJ 103 ASN
** S5  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S5  69 GLN
S5  96 HIS
B4  49 GLN
AM  23 ASN
** B7  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B7  75 ASN
** B8  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.240  67000  Z= 0.549
  Angle     :  1.668  50.998  90856  Z= 1.059
  Chirality :  0.312   6.718   9986
  Planarity :  0.006   0.120  11476
  Dihedral  :  7.694 107.452   9098
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  : 10.43 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.03 %
    Allowed  :  3.27 %
    Favored  : 96.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.63 %
    Twisted General : 0.20 %

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: -1.63 (0.09), residues: 7979
  helix:  0.41 (0.08), residues: 4152
  sheet: -1.63 (0.26), residues: 380
  loop : -3.02 (0.10), residues: 3447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRPD2  30 
 HIS   0.013   0.001   HISS2 150 
 PHE   0.033   0.002   PHED5 340 
 TYR   0.036   0.002   TYRS8  40 
 ARG   0.010   0.000   ARGS8  43 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  2023 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 2021
  time to evaluate  : 6.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V1   82 MET cc_start: 0.8445 (tpp) cc_final: 0.8070 (tpp)
REVERT: V1  102 PRO cc_start: 0.8873 (Cg_exo) cc_final: 0.8511 (Cg_endo)
REVERT: S1  190 MET cc_start: 0.7793 (ttp) cc_final: 0.7552 (ptm)
REVERT: S1  192 MET cc_start: 0.7733 (mmm) cc_final: 0.7402 (mmm)
REVERT: S1  200 ILE cc_start: 0.9255 (pt) cc_final: 0.8970 (mt)
REVERT: S1  222 THR cc_start: 0.8438 (p) cc_final: 0.7879 (t)
REVERT: S1  419 TYR cc_start: 0.7799 (p90) cc_final: 0.7368 (p90)
REVERT: S1  490 MET cc_start: 0.7851 (tmm) cc_final: 0.7358 (tmm)
REVERT: S1  549 HIS cc_start: 0.7939 (p90) cc_final: 0.7716 (p-80)
REVERT: S1  617 ASP cc_start: 0.8364 (p0) cc_final: 0.7718 (t70)
REVERT: S2   72 MET cc_start: 0.6286 (ttt) cc_final: 0.5856 (ttt)
REVERT: S2   75 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7367 (tttp)
REVERT: S2  137 ILE cc_start: 0.9370 (mt) cc_final: 0.8972 (tt)
REVERT: S2  148 LEU cc_start: 0.8901 (tt) cc_final: 0.7723 (tt)
REVERT: S2  152 MET cc_start: 0.9078 (tpp) cc_final: 0.8635 (tpp)
REVERT: S2  155 THR cc_start: 0.8881 (p) cc_final: 0.8645 (t)
REVERT: S2  174 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.6444 (ttm-80)
REVERT: S2  242 ILE cc_start: 0.8163 (pt) cc_final: 0.7927 (pt)
REVERT: S2  302 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7941 (mm-30)
REVERT: S2  338 MET cc_start: 0.8626 (tmm) cc_final: 0.8400 (tmm)
REVERT: S2  371 LYS cc_start: 0.9113 (mptt) cc_final: 0.8907 (mmtm)
REVERT: S2  379 VAL cc_start: 0.9479 (t) cc_final: 0.9122 (p)
REVERT: S2  413 ASP cc_start: 0.9002 (m-30) cc_final: 0.8648 (m-30)
REVERT: S3  131 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7383 (mt-10)
REVERT: S3  200 ASN cc_start: 0.7772 (m-40) cc_final: 0.7079 (p0)
REVERT: S7   62 MET cc_start: 0.9098 (tmm) cc_final: 0.8872 (tmm)
REVERT: S7  128 TYR cc_start: 0.8134 (m-80) cc_final: 0.7692 (m-80)
REVERT: S7  152 THR cc_start: 0.8628 (m) cc_final: 0.8217 (p)
REVERT: S7  172 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7258 (tmt170)
REVERT: S7  173 LEU cc_start: 0.8994 (mt) cc_final: 0.8724 (mt)
REVERT: S8   23 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8721 (tm-30)
REVERT: S8   58 SER cc_start: 0.9162 (t) cc_final: 0.8441 (t)
REVERT: S8   92 ILE cc_start: 0.9440 (mm) cc_final: 0.9186 (mm)
REVERT: S8  136 ASN cc_start: 0.8172 (p0) cc_final: 0.7914 (p0)
REVERT: S8  169 ILE cc_start: 0.9149 (mt) cc_final: 0.8899 (tt)
REVERT: S6   36 ASN cc_start: 0.8858 (t0) cc_final: 0.8382 (t0)
REVERT: S4   77 ASP cc_start: 0.8181 (t0) cc_final: 0.7958 (t0)
REVERT: A9  216 ASN cc_start: 0.8470 (t0) cc_final: 0.8194 (t0)
REVERT: A9  306 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7532 (tm-30)
REVERT: A9  310 LEU cc_start: 0.8953 (tp) cc_final: 0.8716 (tp)
REVERT: A6   34 LEU cc_start: 0.9147 (tp) cc_final: 0.8753 (tp)
REVERT: A6   41 GLU cc_start: 0.8140 (tp30) cc_final: 0.7202 (tp30)
REVERT: A6   90 GLU cc_start: 0.8170 (tp30) cc_final: 0.7830 (tp30)
REVERT: A6   93 ILE cc_start: 0.9278 (tt) cc_final: 0.8890 (tp)
REVERT: A7   31 SER cc_start: 0.7663 (m) cc_final: 0.7461 (m)
REVERT: A7   34 THR cc_start: 0.7375 (p) cc_final: 0.7163 (p)
REVERT: AL   25 ARG cc_start: 0.8469 (ttp80) cc_final: 0.7899 (ttp80)
REVERT: AL   56 PHE cc_start: 0.8370 (t80) cc_final: 0.7842 (t80)
REVERT: AL   59 HIS cc_start: 0.7582 (m-70) cc_final: 0.7374 (m-70)
REVERT: AL   89 TRP cc_start: 0.8953 (t60) cc_final: 0.8638 (t60)
REVERT: AL  136 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: D3    4 MET cc_start: 0.7297 (ttt) cc_final: 0.6611 (tmm)
REVERT: D3   57 LEU cc_start: 0.8972 (mm) cc_final: 0.8664 (mt)
REVERT: D3   86 THR cc_start: 0.8424 (p) cc_final: 0.8087 (t)
REVERT: D3   96 PHE cc_start: 0.8074 (t80) cc_final: 0.7866 (t80)
REVERT: D1   26 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9170 (mmmm)
REVERT: D1   47 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: D1   66 SER cc_start: 0.8300 (m) cc_final: 0.7901 (p)
REVERT: D1   70 MET cc_start: 0.7681 (ttm) cc_final: 0.7440 (mtm)
REVERT: D1  145 THR cc_start: 0.9161 (m) cc_final: 0.8720 (p)
REVERT: D1  183 MET cc_start: 0.9093 (ppp) cc_final: 0.8725 (ppp)
REVERT: D1  283 ASP cc_start: 0.8430 (m-30) cc_final: 0.7975 (m-30)
REVERT: D1  285 LEU cc_start: 0.9544 (tp) cc_final: 0.9179 (tp)
REVERT: D1  286 MET cc_start: 0.8755 (mmt) cc_final: 0.8400 (mmm)
REVERT: D1  287 HIS cc_start: 0.8183 (t70) cc_final: 0.7780 (m-70)
REVERT: D6    1 MET cc_start: 0.6220 (tmm) cc_final: 0.5962 (ttm)
REVERT: D6   57 PHE cc_start: 0.8635 (t80) cc_final: 0.8255 (t80)
REVERT: D6  124 ASP cc_start: 0.7402 (m-30) cc_final: 0.7126 (m-30)
REVERT: 4L    9 MET cc_start: 0.8529 (mmm) cc_final: 0.7664 (tpt)
REVERT: 4L   10 MET cc_start: 0.8432 (ttt) cc_final: 0.7795 (tpp)
REVERT: 4L   24 SER cc_start: 0.8497 (p) cc_final: 0.8218 (t)
REVERT: 4L   25 HIS cc_start: 0.8601 (m-70) cc_final: 0.7704 (m-70)
REVERT: 4L   36 MET cc_start: 0.8589 (tmm) cc_final: 0.8140 (tmm)
REVERT: D5   48 MET cc_start: 0.7956 (ttt) cc_final: 0.7416 (ttp)
REVERT: D5   88 MET cc_start: 0.7576 (tpp) cc_final: 0.7273 (tpp)
REVERT: D5  102 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7453 (tp30)
REVERT: D5  315 VAL cc_start: 0.9116 (t) cc_final: 0.8815 (t)
REVERT: D5  326 PHE cc_start: 0.8316 (t80) cc_final: 0.7947 (t80)
REVERT: D5  355 ASP cc_start: 0.7983 (m-30) cc_final: 0.7704 (t70)
REVERT: D5  370 THR cc_start: 0.8604 (p) cc_final: 0.8396 (t)
REVERT: D5  495 ILE cc_start: 0.8247 (mm) cc_final: 0.7854 (pt)
REVERT: D5  573 MET cc_start: 0.7569 (mmt) cc_final: 0.7281 (mmt)
REVERT: D5  604 PHE cc_start: 0.7914 (m-10) cc_final: 0.7654 (m-80)
REVERT: D4    9 MET cc_start: 0.8302 (tmm) cc_final: 0.7903 (tmm)
REVERT: D4   66 LEU cc_start: 0.9204 (tt) cc_final: 0.8772 (tp)
REVERT: D4  147 LEU cc_start: 0.9117 (tp) cc_final: 0.8915 (tp)
REVERT: D4  174 LEU cc_start: 0.9365 (mt) cc_final: 0.9156 (mt)
REVERT: D4  204 MET cc_start: 0.8954 (mtt) cc_final: 0.8578 (mtt)
REVERT: D4  220 HIS cc_start: 0.7988 (m90) cc_final: 0.7723 (m90)
REVERT: D4  400 MET cc_start: 0.6369 (mmp) cc_final: 0.5993 (mmm)
REVERT: D4  409 TYR cc_start: 0.8830 (t80) cc_final: 0.8600 (t80)
REVERT: D4  447 LEU cc_start: 0.8939 (mt) cc_final: 0.8570 (mt)
REVERT: D2   36 ASN cc_start: 0.8941 (t0) cc_final: 0.8620 (t0)
REVERT: D2   63 GLN cc_start: 0.9006 (mm110) cc_final: 0.8673 (mm110)
REVERT: D2   85 THR cc_start: 0.8274 (p) cc_final: 0.8019 (p)
REVERT: D2   96 MET cc_start: 0.8678 (ttm) cc_final: 0.8424 (ttm)
REVERT: D2   98 MET cc_start: 0.8040 (tpp) cc_final: 0.7778 (tpp)
REVERT: D2  167 TRP cc_start: 0.8522 (m-10) cc_final: 0.7960 (m-10)
REVERT: D2  176 ARG cc_start: 0.8153 (mpp80) cc_final: 0.7876 (mtm-85)
REVERT: D2  210 ILE cc_start: 0.8927 (tt) cc_final: 0.8613 (tt)
REVERT: D2  213 SER cc_start: 0.9488 (m) cc_final: 0.9131 (p)
REVERT: D2  248 LEU cc_start: 0.9054 (mm) cc_final: 0.8641 (mt)
REVERT: D2  263 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8514 (mttt)
REVERT: D2  268 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8748 (tm-30)
REVERT: D2  332 LEU cc_start: 0.9376 (tp) cc_final: 0.8867 (pp)
REVERT: D2  334 THR cc_start: 0.9104 (t) cc_final: 0.8866 (t)
REVERT: D2  344 SER cc_start: 0.8989 (p) cc_final: 0.8269 (m)
REVERT: AK   57 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6690 (tpp-160)
REVERT: AK  117 MET cc_start: 0.7431 (ttm) cc_final: 0.7212 (ttm)
REVERT: B5  115 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7694 (tpp80)
REVERT: AB   68 GLU cc_start: 0.6812 (pm20) cc_final: 0.6435 (pm20)
REVERT: A8   25 LYS cc_start: 0.9162 (tttt) cc_final: 0.8806 (mmtp)
REVERT: A8   64 GLN cc_start: 0.8047 (pp30) cc_final: 0.7815 (tm-30)
REVERT: BJ  140 ASP cc_start: 0.8877 (m-30) cc_final: 0.8589 (m-30)
REVERT: AJ   20 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7552 (tp30)
REVERT: AJ  106 LEU cc_start: 0.9051 (mm) cc_final: 0.8734 (mm)
REVERT: AJ  110 ASP cc_start: 0.8668 (m-30) cc_final: 0.8430 (m-30)
REVERT: AJ  157 LYS cc_start: 0.9177 (ttpt) cc_final: 0.8965 (ptpt)
REVERT: AJ  185 LYS cc_start: 0.8477 (mttt) cc_final: 0.8084 (tppt)
REVERT: A3   15 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7178 (mt-10)
REVERT: C2    2 MET cc_start: 0.7818 (tmm) cc_final: 0.6891 (tmm)
REVERT: C2   36 PHE cc_start: 0.9120 (t80) cc_final: 0.8866 (t80)
REVERT: C2   37 LEU cc_start: 0.9164 (tp) cc_final: 0.8720 (tt)
REVERT: C2   62 PHE cc_start: 0.8446 (m-10) cc_final: 0.8220 (m-10)
REVERT: C2   83 TYR cc_start: 0.8671 (m-80) cc_final: 0.7963 (m-80)
REVERT: C2   95 LYS cc_start: 0.8610 (pttm) cc_final: 0.8403 (mmpt)
REVERT: B4   47 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8558 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7760 (t0) cc_final: 0.7335 (t0)
REVERT: AM   71 MET cc_start: 0.8015 (ppp) cc_final: 0.7809 (ppp)
REVERT: B6   28 SER cc_start: 0.7842 (t) cc_final: 0.7555 (p)
REVERT: B6   85 LEU cc_start: 0.8657 (mp) cc_final: 0.8367 (tt)
REVERT: B6   99 LYS cc_start: 0.8177 (tmtt) cc_final: 0.7480 (tmtt)
REVERT: B6  100 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7931 (mtmt)
REVERT: B7   51 VAL cc_start: 0.7952 (t) cc_final: 0.7717 (t)
REVERT: B7   77 LEU cc_start: 0.8970 (mp) cc_final: 0.8611 (pt)
REVERT: B7   88 TYR cc_start: 0.7716 (t80) cc_final: 0.7419 (t80)
REVERT: B9   36 TYR cc_start: 0.7336 (t80) cc_final: 0.6823 (t80)
REVERT: B9   43 LEU cc_start: 0.8411 (mm) cc_final: 0.8076 (mm)
REVERT: B9   50 HIS cc_start: 0.7396 (p-80) cc_final: 0.6863 (p-80)
REVERT: B9   74 GLN cc_start: 0.7968 (pp30) cc_final: 0.7738 (pp30)
REVERT: B2   42 HIS cc_start: 0.7465 (t-90) cc_final: 0.6632 (t-90)
REVERT: B8    6 LYS cc_start: 0.8676 (mmmm) cc_final: 0.8191 (pttm)
REVERT: B8   20 ARG cc_start: 0.8387 (mmt90) cc_final: 0.8042 (mmm-85)
REVERT: B8  113 LEU cc_start: 0.9121 (mt) cc_final: 0.8598 (tt)
REVERT: BK   28 GLU cc_start: 0.8424 (pm20) cc_final: 0.8142 (pm20)
REVERT: BK   33 GLU cc_start: 0.6263 (mp0) cc_final: 0.5863 (mp0)
REVERT: BK   43 ASP cc_start: 0.8552 (p0) cc_final: 0.8053 (p0)
REVERT: BK   53 VAL cc_start: 0.6735 (m) cc_final: 0.6250 (p)
REVERT: BK   66 PHE cc_start: 0.8347 (m-10) cc_final: 0.7887 (m-10)
REVERT: C1   11 SER cc_start: 0.8761 (m) cc_final: 0.8490 (t)
REVERT: C1   37 GLU cc_start: 0.7247 (tm-30) cc_final: 0.7019 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 2022
  average time/residue: 0.6087
  time to fit residues: 2110.3694
Evaluate side-chains
  1597 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 1597
  time to evaluate  : 5.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 255 optimal weight:   10.0000
   chunk 685 optimal weight:    9.9990
   chunk 150 optimal weight:   10.0000
   chunk 446 optimal weight:    2.9990
   chunk 187 optimal weight:    0.9990
   chunk 761 optimal weight:    2.9990
   chunk 632 optimal weight:    2.9990
   chunk 352 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 251 optimal weight:   10.0000
   chunk 399 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V2  37 ASN
S1 100 ASN
S1 259 ASN
S1 430 GLN
** S2 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S7  38 ASN
S8 123 GLN
S8 168 ASN
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
** A9  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A7  24 GLN
A7  50 ASN
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AA  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 194 ASN
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D4 279 GLN
D4 440 HIS
** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D2 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2 235 ASN
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
AK  78 GLN
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S5  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C2  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4  49 GLN
AM  23 ASN
BK 103 HIS

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.5217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.237  67000  Z= 0.562
  Angle     :  1.676  50.766  90856  Z= 1.062
  Chirality :  0.313   6.435   9986
  Planarity :  0.006   0.129  11476
  Dihedral  :  7.584 107.149   9098
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  : 10.78 %
    Favored  : 89.20 %
  Rotamer:
    Outliers :  0.03 %
    Allowed  :  2.91 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.63 %
    Twisted General : 0.19 %

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: -1.58 (0.09), residues: 7979
  helix:  0.44 (0.08), residues: 4163
  sheet: -1.61 (0.26), residues: 371
  loop : -2.98 (0.10), residues: 3445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.075   0.002   TRPD2  30 
 HIS   0.019   0.001   HISA9  87 
 PHE   0.039   0.002   PHE4L  53 
 TYR   0.036   0.002   TYRS8 118 
 ARG   0.011   0.001   ARGB6  19 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1980 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 1978
  time to evaluate  : 5.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V1   82 MET cc_start: 0.8496 (tpp) cc_final: 0.8108 (tpp)
REVERT: V1  102 PRO cc_start: 0.8865 (Cg_exo) cc_final: 0.8464 (Cg_endo)
REVERT: S1  200 ILE cc_start: 0.9297 (pt) cc_final: 0.9023 (mt)
REVERT: S1  222 THR cc_start: 0.8445 (p) cc_final: 0.7902 (t)
REVERT: S1  248 MET cc_start: 0.7576 (mmt) cc_final: 0.7353 (mmm)
REVERT: S1  253 ARG cc_start: 0.7141 (ptt-90) cc_final: 0.6829 (ptm160)
REVERT: S1  419 TYR cc_start: 0.7841 (p90) cc_final: 0.7397 (p90)
REVERT: S1  490 MET cc_start: 0.7743 (tmm) cc_final: 0.7135 (tmm)
REVERT: S1  549 HIS cc_start: 0.8023 (p90) cc_final: 0.7782 (p-80)
REVERT: S1  617 ASP cc_start: 0.8486 (p0) cc_final: 0.7890 (t70)
REVERT: S2   72 MET cc_start: 0.6898 (ttt) cc_final: 0.6053 (ttt)
REVERT: S2   75 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8174 (tttp)
REVERT: S2  137 ILE cc_start: 0.9387 (mt) cc_final: 0.8982 (tt)
REVERT: S2  152 MET cc_start: 0.8978 (tpp) cc_final: 0.8710 (tpp)
REVERT: S2  155 THR cc_start: 0.8941 (p) cc_final: 0.8720 (t)
REVERT: S2  174 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.6582 (ttm-80)
REVERT: S2  242 ILE cc_start: 0.8245 (pt) cc_final: 0.8014 (pt)
REVERT: S2  302 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7920 (mm-30)
REVERT: S2  371 LYS cc_start: 0.9129 (mptt) cc_final: 0.8765 (mptt)
REVERT: S2  379 VAL cc_start: 0.9486 (t) cc_final: 0.9161 (p)
REVERT: S2  413 ASP cc_start: 0.9034 (m-30) cc_final: 0.8600 (m-30)
REVERT: S3  131 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7467 (mt-10)
REVERT: S3  200 ASN cc_start: 0.7836 (m-40) cc_final: 0.7071 (p0)
REVERT: S7   57 VAL cc_start: 0.8761 (t) cc_final: 0.8394 (t)
REVERT: S7   62 MET cc_start: 0.9092 (tmm) cc_final: 0.8651 (tmm)
REVERT: S7   66 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7597 (ptm160)
REVERT: S7  109 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7797 (mm-30)
REVERT: S7  128 TYR cc_start: 0.8149 (m-80) cc_final: 0.7732 (m-80)
REVERT: S7  172 ARG cc_start: 0.7730 (ttm-80) cc_final: 0.7213 (tmt170)
REVERT: S7  173 LEU cc_start: 0.9051 (mt) cc_final: 0.8799 (mt)
REVERT: S8   23 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8743 (tm-30)
REVERT: S8   36 MET cc_start: 0.8094 (tmm) cc_final: 0.7846 (tmm)
REVERT: S8   92 ILE cc_start: 0.9466 (mm) cc_final: 0.9234 (mm)
REVERT: S8  136 ASN cc_start: 0.8317 (p0) cc_final: 0.8067 (p0)
REVERT: S6   36 ASN cc_start: 0.8662 (t0) cc_final: 0.8383 (t0)
REVERT: S6   78 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7580 (tm-30)
REVERT: S4   77 ASP cc_start: 0.8265 (t0) cc_final: 0.8001 (t0)
REVERT: S4   81 ASN cc_start: 0.8281 (p0) cc_final: 0.8056 (p0)
REVERT: A9  216 ASN cc_start: 0.8518 (t0) cc_final: 0.8235 (t0)
REVERT: A9  306 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: A9  310 LEU cc_start: 0.8769 (tp) cc_final: 0.8552 (tp)
REVERT: A6   41 GLU cc_start: 0.8286 (tp30) cc_final: 0.7958 (tp30)
REVERT: A6   90 GLU cc_start: 0.8164 (tp30) cc_final: 0.7862 (tp30)
REVERT: AL   25 ARG cc_start: 0.8569 (ttp80) cc_final: 0.7901 (ttp80)
REVERT: AL   56 PHE cc_start: 0.8341 (t80) cc_final: 0.7835 (t80)
REVERT: AL   59 HIS cc_start: 0.7627 (m-70) cc_final: 0.7374 (m-70)
REVERT: AA   46 ASP cc_start: 0.8635 (m-30) cc_final: 0.8392 (m-30)
REVERT: D3    4 MET cc_start: 0.7408 (ttt) cc_final: 0.6687 (tmm)
REVERT: D3   57 LEU cc_start: 0.9013 (mm) cc_final: 0.8693 (mt)
REVERT: D3   66 ASP cc_start: 0.8981 (t70) cc_final: 0.8729 (t0)
REVERT: D3   86 THR cc_start: 0.8433 (p) cc_final: 0.8111 (t)
REVERT: D3   96 PHE cc_start: 0.8281 (t80) cc_final: 0.8013 (t80)
REVERT: D1   66 SER cc_start: 0.8318 (m) cc_final: 0.7899 (p)
REVERT: D1   70 MET cc_start: 0.7788 (ttm) cc_final: 0.7404 (mtm)
REVERT: D1   98 MET cc_start: 0.7955 (tpp) cc_final: 0.7214 (tpt)
REVERT: D1  108 MET cc_start: 0.7788 (mmt) cc_final: 0.7399 (mmt)
REVERT: D1  145 THR cc_start: 0.9227 (m) cc_final: 0.9015 (p)
REVERT: D1  183 MET cc_start: 0.9051 (ppp) cc_final: 0.8718 (ppp)
REVERT: D1  283 ASP cc_start: 0.8399 (m-30) cc_final: 0.7968 (m-30)
REVERT: D1  286 MET cc_start: 0.8767 (mmt) cc_final: 0.8387 (mmm)
REVERT: D1  287 HIS cc_start: 0.8076 (t70) cc_final: 0.7814 (m-70)
REVERT: D6    1 MET cc_start: 0.6166 (tmm) cc_final: 0.5950 (ttm)
REVERT: 4L    9 MET cc_start: 0.8484 (mmm) cc_final: 0.7576 (tpt)
REVERT: 4L   21 MET cc_start: 0.6799 (ppp) cc_final: 0.6389 (ppp)
REVERT: 4L   24 SER cc_start: 0.8475 (p) cc_final: 0.8224 (t)
REVERT: 4L   25 HIS cc_start: 0.8590 (m-70) cc_final: 0.7702 (m-70)
REVERT: 4L   31 LEU cc_start: 0.9003 (tt) cc_final: 0.8576 (tt)
REVERT: 4L   36 MET cc_start: 0.8569 (tmm) cc_final: 0.8139 (tmm)
REVERT: 4L   73 LEU cc_start: 0.9522 (tp) cc_final: 0.9172 (tt)
REVERT: D5   48 MET cc_start: 0.7912 (ttt) cc_final: 0.7324 (ttp)
REVERT: D5   88 MET cc_start: 0.7655 (tpp) cc_final: 0.7334 (tpp)
REVERT: D5  102 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7573 (tp30)
REVERT: D5  283 MET cc_start: 0.8196 (ptm) cc_final: 0.7984 (ptp)
REVERT: D5  313 MET cc_start: 0.8458 (ptt) cc_final: 0.8120 (ptp)
REVERT: D5  326 PHE cc_start: 0.8349 (t80) cc_final: 0.7948 (t80)
REVERT: D5  355 ASP cc_start: 0.8031 (m-30) cc_final: 0.7823 (t70)
REVERT: D5  370 THR cc_start: 0.8686 (p) cc_final: 0.8414 (t)
REVERT: D5  495 ILE cc_start: 0.8082 (mm) cc_final: 0.7764 (pt)
REVERT: D5  573 MET cc_start: 0.7627 (mmt) cc_final: 0.7371 (mmt)
REVERT: D5  604 PHE cc_start: 0.7930 (m-80) cc_final: 0.7639 (m-80)
REVERT: D4    9 MET cc_start: 0.8272 (tmm) cc_final: 0.7853 (tmm)
REVERT: D4  141 GLU cc_start: 0.8675 (tt0) cc_final: 0.8393 (tt0)
REVERT: D4  174 LEU cc_start: 0.9365 (mt) cc_final: 0.9160 (mt)
REVERT: D4  207 MET cc_start: 0.8296 (tpp) cc_final: 0.7577 (tpp)
REVERT: D4  220 HIS cc_start: 0.7992 (m90) cc_final: 0.7776 (m90)
REVERT: D4  447 LEU cc_start: 0.8871 (mt) cc_final: 0.8413 (mt)
REVERT: D2   36 ASN cc_start: 0.8986 (t0) cc_final: 0.8737 (t0)
REVERT: D2   60 PHE cc_start: 0.9044 (t80) cc_final: 0.8835 (t80)
REVERT: D2   63 GLN cc_start: 0.9060 (mm110) cc_final: 0.8793 (mm110)
REVERT: D2   76 ILE cc_start: 0.9348 (mm) cc_final: 0.9052 (pt)
REVERT: D2   85 THR cc_start: 0.8301 (p) cc_final: 0.8064 (p)
REVERT: D2   96 MET cc_start: 0.8797 (ttm) cc_final: 0.8483 (ttm)
REVERT: D2   98 MET cc_start: 0.7908 (tpp) cc_final: 0.7506 (tpp)
REVERT: D2  108 MET cc_start: 0.7791 (mmm) cc_final: 0.7567 (mmm)
REVERT: D2  167 TRP cc_start: 0.8607 (m-10) cc_final: 0.7979 (m-10)
REVERT: D2  190 MET cc_start: 0.9264 (mtt) cc_final: 0.8716 (mtt)
REVERT: D2  210 ILE cc_start: 0.8917 (tt) cc_final: 0.8571 (tt)
REVERT: D2  213 SER cc_start: 0.9462 (m) cc_final: 0.9124 (p)
REVERT: D2  232 HIS cc_start: 0.8904 (m-70) cc_final: 0.8661 (m170)
REVERT: D2  248 LEU cc_start: 0.8922 (mm) cc_final: 0.8149 (mt)
REVERT: D2  263 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8525 (mttt)
REVERT: D2  268 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8737 (tm-30)
REVERT: D2  293 TYR cc_start: 0.8071 (m-10) cc_final: 0.7306 (m-10)
REVERT: D2  332 LEU cc_start: 0.9338 (tp) cc_final: 0.8883 (pp)
REVERT: D2  334 THR cc_start: 0.9043 (t) cc_final: 0.8814 (t)
REVERT: D2  335 MET cc_start: 0.8461 (mpp) cc_final: 0.8180 (mpp)
REVERT: D2  344 SER cc_start: 0.8979 (p) cc_final: 0.8188 (m)
REVERT: AK   57 ARG cc_start: 0.7242 (ttp-170) cc_final: 0.6711 (tpp-160)
REVERT: AK   80 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7276 (ttm-80)
REVERT: AB   68 GLU cc_start: 0.6908 (pm20) cc_final: 0.6426 (pm20)
REVERT: A8   25 LYS cc_start: 0.9215 (tttt) cc_final: 0.8838 (mmtp)
REVERT: A8   64 GLN cc_start: 0.8032 (pp30) cc_final: 0.7827 (tm-30)
REVERT: BJ   76 CYS cc_start: 0.6560 (m) cc_final: 0.6303 (m)
REVERT: BJ   98 ASP cc_start: 0.8608 (m-30) cc_final: 0.8028 (m-30)
REVERT: BJ  140 ASP cc_start: 0.8892 (m-30) cc_final: 0.8620 (m-30)
REVERT: AJ   20 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7485 (tp30)
REVERT: AJ  185 LYS cc_start: 0.8564 (mttt) cc_final: 0.8172 (tppt)
REVERT: A3   14 LYS cc_start: 0.6285 (mttp) cc_final: 0.6047 (mtmm)
REVERT: A3   15 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7043 (mt-10)
REVERT: B3   18 TYR cc_start: 0.6487 (p90) cc_final: 0.6259 (p90)
REVERT: C2    2 MET cc_start: 0.8003 (tmm) cc_final: 0.7523 (ttp)
REVERT: C2    3 THR cc_start: 0.8585 (m) cc_final: 0.8328 (m)
REVERT: C2   36 PHE cc_start: 0.9176 (t80) cc_final: 0.8861 (t80)
REVERT: C2   37 LEU cc_start: 0.9193 (tp) cc_final: 0.8684 (tt)
REVERT: C2   62 PHE cc_start: 0.8456 (m-10) cc_final: 0.8186 (m-10)
REVERT: C2   83 TYR cc_start: 0.8730 (m-80) cc_final: 0.7972 (m-80)
REVERT: B4   47 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8600 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7736 (t0) cc_final: 0.7525 (t0)
REVERT: B6   85 LEU cc_start: 0.8704 (mp) cc_final: 0.8383 (tt)
REVERT: B7   51 VAL cc_start: 0.8089 (t) cc_final: 0.7806 (t)
REVERT: B7   57 TYR cc_start: 0.7275 (m-10) cc_final: 0.6794 (m-10)
REVERT: B9   43 LEU cc_start: 0.8569 (mm) cc_final: 0.8230 (mm)
REVERT: B9   50 HIS cc_start: 0.7496 (p-80) cc_final: 0.6729 (p-80)
REVERT: B9   74 GLN cc_start: 0.7879 (pp30) cc_final: 0.7579 (pp30)
REVERT: B9  103 LEU cc_start: 0.8846 (tp) cc_final: 0.8623 (tp)
REVERT: B2   16 GLN cc_start: 0.6792 (pt0) cc_final: 0.6365 (pm20)
REVERT: B2   44 SER cc_start: 0.7751 (m) cc_final: 0.7523 (m)
REVERT: B8    6 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8374 (pttm)
REVERT: B8   68 ASP cc_start: 0.7482 (m-30) cc_final: 0.6781 (m-30)
REVERT: B8  113 LEU cc_start: 0.9134 (mt) cc_final: 0.8609 (tt)
REVERT: BK   28 GLU cc_start: 0.8416 (pm20) cc_final: 0.8129 (pm20)
REVERT: BK   43 ASP cc_start: 0.8601 (p0) cc_final: 0.8089 (p0)
REVERT: BK   66 PHE cc_start: 0.8344 (m-10) cc_final: 0.7904 (m-10)
REVERT: BK   90 ARG cc_start: 0.9038 (tpp-160) cc_final: 0.8705 (tpt170)
REVERT: BK  108 MET cc_start: 0.7255 (tpt) cc_final: 0.6424 (tpt)
REVERT: C1   11 SER cc_start: 0.8783 (m) cc_final: 0.8467 (t)
REVERT: C1   38 ASP cc_start: 0.8443 (t0) cc_final: 0.8217 (t0)
REVERT: B1   25 TYR cc_start: 0.8508 (t80) cc_final: 0.8229 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 1979
  average time/residue: 0.5928
  time to fit residues: 2019.0745
Evaluate side-chains
  1569 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 1569
  time to evaluate  : 5.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 734 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 433 optimal weight:    5.9990
   chunk 556 optimal weight:    8.9990
   chunk 430 optimal weight:    0.9980
   chunk 640 optimal weight:    7.9990
   chunk 425 optimal weight:    7.9990
   chunk 758 optimal weight:    0.9980
   chunk 474 optimal weight:    0.7980
   chunk 462 optimal weight:    7.9990
   chunk 350 optimal weight:    2.9990
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 148 ASN
** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 373 ASN
V2  37 ASN
S1 100 ASN
S1 259 ASN
S1 430 GLN
S3 192 GLN
S7  38 ASN
S8 123 GLN
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A7  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A7  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A7  50 ASN
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AA  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 332 HIS
** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
D5 446 ASN
D4 279 GLN
D4 440 HIS
** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2 235 ASN
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
BJ 103 ASN
** S5  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S5  69 GLN
** C2  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4  49 GLN
AM  23 ASN
AM  75 GLN
** B7  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B9  25 HIS
** B8  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
BK  86 GLN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.5355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.238  67000  Z= 0.557
  Angle     :  1.679  50.741  90856  Z= 1.062
  Chirality :  0.312   6.374   9986
  Planarity :  0.006   0.165  11476
  Dihedral  :  7.503 104.494   9098
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  : 10.68 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  0.03 %
    Allowed  :  1.92 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.63 %
    Twisted General : 0.20 %

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 (0.09), residues: 7979
  helix:  0.48 (0.08), residues: 4160
  sheet: -1.62 (0.26), residues: 395
  loop : -2.92 (0.10), residues: 3424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.082   0.002   TRPD2  30 
 HIS   0.009   0.001   HISS2 150 
 PHE   0.036   0.002   PHED5 385 
 TYR   0.032   0.002   TYRB9  90 
 ARG   0.016   0.001   ARGA1  34 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1964 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 1962
  time to evaluate  : 6.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V1   32 ARG cc_start: 0.8111 (mpt180) cc_final: 0.7768 (mmt90)
REVERT: V1   82 MET cc_start: 0.8359 (tpp) cc_final: 0.7941 (tpp)
REVERT: V1  102 PRO cc_start: 0.8903 (Cg_exo) cc_final: 0.8507 (Cg_endo)
REVERT: V2  155 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7385 (tm-30)
REVERT: S1  222 THR cc_start: 0.8381 (p) cc_final: 0.7880 (t)
REVERT: S1  248 MET cc_start: 0.7698 (mmt) cc_final: 0.7376 (mmm)
REVERT: S1  419 TYR cc_start: 0.7822 (p90) cc_final: 0.7360 (p90)
REVERT: S1  490 MET cc_start: 0.7700 (tmm) cc_final: 0.7097 (tmm)
REVERT: S1  549 HIS cc_start: 0.8034 (p90) cc_final: 0.7805 (p-80)
REVERT: S1  566 TYR cc_start: 0.8605 (p90) cc_final: 0.8402 (p90)
REVERT: S1  609 MET cc_start: 0.7095 (pmm) cc_final: 0.6886 (pmm)
REVERT: S2   72 MET cc_start: 0.6957 (ttt) cc_final: 0.5959 (ttt)
REVERT: S2   75 LYS cc_start: 0.8632 (ttpp) cc_final: 0.8163 (tttp)
REVERT: S2  137 ILE cc_start: 0.9416 (mt) cc_final: 0.8990 (tt)
REVERT: S2  152 MET cc_start: 0.9004 (tpp) cc_final: 0.8761 (tpp)
REVERT: S2  155 THR cc_start: 0.8949 (p) cc_final: 0.8693 (t)
REVERT: S2  174 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7126 (ttm-80)
REVERT: S2  242 ILE cc_start: 0.8313 (pt) cc_final: 0.8092 (pt)
REVERT: S2  302 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7903 (mm-30)
REVERT: S2  371 LYS cc_start: 0.9123 (mptt) cc_final: 0.8735 (mptt)
REVERT: S2  379 VAL cc_start: 0.9485 (t) cc_final: 0.9202 (p)
REVERT: S2  404 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8331 (mmmm)
REVERT: S2  413 ASP cc_start: 0.9001 (m-30) cc_final: 0.8605 (m-30)
REVERT: S3  131 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7460 (mt-10)
REVERT: S3  152 LEU cc_start: 0.8335 (mt) cc_final: 0.8123 (mt)
REVERT: S3  200 ASN cc_start: 0.7795 (m-40) cc_final: 0.6919 (p0)
REVERT: S7   66 ARG cc_start: 0.8040 (mtp-110) cc_final: 0.7774 (ptm160)
REVERT: S7   69 MET cc_start: 0.8686 (mpp) cc_final: 0.8124 (mpp)
REVERT: S7  152 THR cc_start: 0.8593 (m) cc_final: 0.8037 (p)
REVERT: S7  172 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7079 (tmt170)
REVERT: S7  173 LEU cc_start: 0.9036 (mt) cc_final: 0.8822 (mt)
REVERT: S8   23 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8734 (tm-30)
REVERT: S8   58 SER cc_start: 0.9171 (t) cc_final: 0.8840 (t)
REVERT: S8   92 ILE cc_start: 0.9430 (mm) cc_final: 0.9198 (mm)
REVERT: S6   78 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7552 (tm-30)
REVERT: S4   77 ASP cc_start: 0.8152 (t0) cc_final: 0.7936 (t0)
REVERT: S4   81 ASN cc_start: 0.8309 (p0) cc_final: 0.8021 (p0)
REVERT: A9   71 MET cc_start: 0.7812 (mmm) cc_final: 0.7566 (mmm)
REVERT: A9  216 ASN cc_start: 0.8518 (t0) cc_final: 0.8240 (t0)
REVERT: A9  231 VAL cc_start: 0.7708 (m) cc_final: 0.7504 (p)
REVERT: A9  306 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: A6   23 ASP cc_start: 0.8339 (p0) cc_final: 0.8127 (p0)
REVERT: A6   90 GLU cc_start: 0.8230 (tp30) cc_final: 0.7831 (tp30)
REVERT: A6  103 MET cc_start: 0.8451 (mmp) cc_final: 0.8217 (tpp)
REVERT: A7   34 THR cc_start: 0.7741 (p) cc_final: 0.7530 (p)
REVERT: A7   69 MET cc_start: 0.8062 (tpp) cc_final: 0.7068 (tpt)
REVERT: AL   56 PHE cc_start: 0.8276 (t80) cc_final: 0.7804 (t80)
REVERT: AL   59 HIS cc_start: 0.7597 (m-70) cc_final: 0.7364 (m-70)
REVERT: AA    9 GLU cc_start: 0.8019 (tp30) cc_final: 0.7662 (tp30)
REVERT: AA   12 LYS cc_start: 0.8865 (ptmm) cc_final: 0.8322 (ptpp)
REVERT: AA   46 ASP cc_start: 0.8615 (m-30) cc_final: 0.8374 (m-30)
REVERT: D3    4 MET cc_start: 0.7499 (ttt) cc_final: 0.6644 (tmm)
REVERT: D3   57 LEU cc_start: 0.9131 (mm) cc_final: 0.8806 (mt)
REVERT: D3   86 THR cc_start: 0.8355 (p) cc_final: 0.8104 (t)
REVERT: D3   96 PHE cc_start: 0.8235 (t80) cc_final: 0.7988 (t80)
REVERT: D1   66 SER cc_start: 0.8364 (m) cc_final: 0.7915 (p)
REVERT: D1   70 MET cc_start: 0.7693 (ttm) cc_final: 0.7318 (mtm)
REVERT: D1  145 THR cc_start: 0.9272 (m) cc_final: 0.8878 (p)
REVERT: D1  283 ASP cc_start: 0.8376 (m-30) cc_final: 0.7920 (m-30)
REVERT: D1  285 LEU cc_start: 0.9524 (tp) cc_final: 0.9073 (tp)
REVERT: D1  286 MET cc_start: 0.8771 (mmt) cc_final: 0.8375 (mmm)
REVERT: D1  287 HIS cc_start: 0.8150 (t70) cc_final: 0.7946 (m-70)
REVERT: D6   20 PHE cc_start: 0.8078 (p90) cc_final: 0.7075 (p90)
REVERT: D6  110 ASP cc_start: 0.5444 (t0) cc_final: 0.5027 (t0)
REVERT: D6  124 ASP cc_start: 0.7366 (m-30) cc_final: 0.7159 (m-30)
REVERT: 4L    9 MET cc_start: 0.8445 (mmm) cc_final: 0.7536 (tpt)
REVERT: 4L   10 MET cc_start: 0.8824 (ttt) cc_final: 0.8394 (tpp)
REVERT: 4L   21 MET cc_start: 0.6801 (ppp) cc_final: 0.6362 (ppp)
REVERT: 4L   24 SER cc_start: 0.8450 (p) cc_final: 0.8213 (t)
REVERT: 4L   25 HIS cc_start: 0.8560 (m-70) cc_final: 0.7717 (m-70)
REVERT: 4L   31 LEU cc_start: 0.8881 (tt) cc_final: 0.8398 (tt)
REVERT: 4L   36 MET cc_start: 0.8554 (tmm) cc_final: 0.8120 (tmm)
REVERT: 4L   73 LEU cc_start: 0.9531 (tp) cc_final: 0.9193 (tt)
REVERT: D5   13 ILE cc_start: 0.8726 (tp) cc_final: 0.8153 (tp)
REVERT: D5   48 MET cc_start: 0.7859 (ttt) cc_final: 0.7322 (ttp)
REVERT: D5   88 MET cc_start: 0.7646 (tpp) cc_final: 0.7326 (tpp)
REVERT: D5  102 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7577 (tp30)
REVERT: D5  283 MET cc_start: 0.8287 (ptm) cc_final: 0.7964 (ptp)
REVERT: D5  326 PHE cc_start: 0.8262 (t80) cc_final: 0.7890 (t80)
REVERT: D5  355 ASP cc_start: 0.8064 (m-30) cc_final: 0.7809 (t70)
REVERT: D5  370 THR cc_start: 0.8615 (p) cc_final: 0.8333 (t)
REVERT: D5  393 ASP cc_start: 0.8201 (t70) cc_final: 0.7910 (t0)
REVERT: D5  495 ILE cc_start: 0.8383 (mm) cc_final: 0.8027 (pt)
REVERT: D5  573 MET cc_start: 0.7612 (mmt) cc_final: 0.7316 (mmt)
REVERT: D4    9 MET cc_start: 0.8220 (tmm) cc_final: 0.7813 (tmm)
REVERT: D4   76 MET cc_start: 0.7223 (ttm) cc_final: 0.7015 (ttm)
REVERT: D4  141 GLU cc_start: 0.8736 (tt0) cc_final: 0.8404 (tt0)
REVERT: D4  147 LEU cc_start: 0.9167 (tp) cc_final: 0.8932 (tp)
REVERT: D4  174 LEU cc_start: 0.9382 (mt) cc_final: 0.9146 (mt)
REVERT: D4  200 MET cc_start: 0.7876 (mmp) cc_final: 0.7488 (mmm)
REVERT: D4  204 MET cc_start: 0.8559 (mtm) cc_final: 0.8145 (mtm)
REVERT: D4  220 HIS cc_start: 0.8091 (m90) cc_final: 0.7767 (m90)
REVERT: D4  229 MET cc_start: 0.8023 (mtp) cc_final: 0.7801 (mtm)
REVERT: D4  278 ARG cc_start: 0.8028 (ttt-90) cc_final: 0.7666 (ttt90)
REVERT: D4  400 MET cc_start: 0.7431 (mmm) cc_final: 0.6090 (mmm)
REVERT: D4  447 LEU cc_start: 0.8829 (mt) cc_final: 0.8400 (mt)
REVERT: D2   30 TRP cc_start: 0.8327 (t60) cc_final: 0.7788 (t60)
REVERT: D2   36 ASN cc_start: 0.8990 (t0) cc_final: 0.8749 (t0)
REVERT: D2   63 GLN cc_start: 0.9023 (mm110) cc_final: 0.8791 (mm110)
REVERT: D2   71 MET cc_start: 0.8338 (mmm) cc_final: 0.7272 (mmm)
REVERT: D2   76 ILE cc_start: 0.9268 (mm) cc_final: 0.8994 (pt)
REVERT: D2   85 THR cc_start: 0.8162 (p) cc_final: 0.7921 (p)
REVERT: D2   96 MET cc_start: 0.8693 (ttm) cc_final: 0.8431 (ttm)
REVERT: D2   98 MET cc_start: 0.7973 (tpp) cc_final: 0.7657 (tpp)
REVERT: D2  167 TRP cc_start: 0.8638 (m-10) cc_final: 0.7977 (m-10)
REVERT: D2  176 ARG cc_start: 0.8248 (mpp80) cc_final: 0.8004 (mtm-85)
REVERT: D2  210 ILE cc_start: 0.8891 (tt) cc_final: 0.8604 (tt)
REVERT: D2  213 SER cc_start: 0.9499 (m) cc_final: 0.9096 (p)
REVERT: D2  232 HIS cc_start: 0.8945 (m-70) cc_final: 0.8675 (m170)
REVERT: D2  248 LEU cc_start: 0.8997 (mm) cc_final: 0.8733 (mt)
REVERT: D2  251 MET cc_start: 0.7946 (mtp) cc_final: 0.7735 (mtm)
REVERT: D2  263 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8565 (mttt)
REVERT: D2  268 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8762 (tm-30)
REVERT: D2  293 TYR cc_start: 0.7857 (m-10) cc_final: 0.7527 (m-10)
REVERT: D2  332 LEU cc_start: 0.9326 (tp) cc_final: 0.8894 (pp)
REVERT: D2  334 THR cc_start: 0.8958 (t) cc_final: 0.8711 (t)
REVERT: D2  335 MET cc_start: 0.8249 (mpp) cc_final: 0.7959 (mpp)
REVERT: D2  344 SER cc_start: 0.8966 (p) cc_final: 0.8269 (m)
REVERT: AK   57 ARG cc_start: 0.7242 (ttp-170) cc_final: 0.6712 (tpp-160)
REVERT: AK   80 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7249 (ttm-80)
REVERT: AK  117 MET cc_start: 0.7280 (ttm) cc_final: 0.7065 (ttm)
REVERT: AK  139 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8439 (tptt)
REVERT: AB   68 GLU cc_start: 0.7080 (pm20) cc_final: 0.6582 (pm20)
REVERT: A8   25 LYS cc_start: 0.9196 (tttt) cc_final: 0.8848 (mmtp)
REVERT: A8   64 GLN cc_start: 0.7978 (pp30) cc_final: 0.7774 (tm-30)
REVERT: BJ   98 ASP cc_start: 0.8554 (m-30) cc_final: 0.7946 (m-30)
REVERT: AJ   20 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7363 (tp30)
REVERT: AJ  185 LYS cc_start: 0.8549 (mttt) cc_final: 0.8152 (tppt)
REVERT: AJ  261 MET cc_start: 0.8344 (tpp) cc_final: 0.8116 (tpp)
REVERT: A3   14 LYS cc_start: 0.6395 (mttp) cc_final: 0.6135 (mtmm)
REVERT: A3   15 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7191 (mt-10)
REVERT: C2    2 MET cc_start: 0.7966 (tmm) cc_final: 0.7413 (ttp)
REVERT: C2    3 THR cc_start: 0.8661 (m) cc_final: 0.8449 (m)
REVERT: C2   36 PHE cc_start: 0.9108 (t80) cc_final: 0.8844 (t80)
REVERT: C2   37 LEU cc_start: 0.9182 (tp) cc_final: 0.8720 (tt)
REVERT: C2   62 PHE cc_start: 0.8403 (m-10) cc_final: 0.8134 (m-10)
REVERT: C2   83 TYR cc_start: 0.8731 (m-80) cc_final: 0.7953 (m-80)
REVERT: B4   47 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8627 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7791 (t0) cc_final: 0.7460 (t0)
REVERT: AM    6 LYS cc_start: 0.8415 (tppt) cc_final: 0.6719 (tppt)
REVERT: AM   71 MET cc_start: 0.8050 (ppp) cc_final: 0.7840 (ppp)
REVERT: B6   85 LEU cc_start: 0.8616 (mp) cc_final: 0.8301 (tt)
REVERT: B7   51 VAL cc_start: 0.8139 (t) cc_final: 0.7846 (t)
REVERT: B7   57 TYR cc_start: 0.7255 (m-10) cc_final: 0.6824 (m-10)
REVERT: B9   43 LEU cc_start: 0.8563 (mm) cc_final: 0.8234 (mm)
REVERT: B9   50 HIS cc_start: 0.7490 (p-80) cc_final: 0.6745 (p-80)
REVERT: B9  103 LEU cc_start: 0.8833 (tp) cc_final: 0.8590 (tp)
REVERT: B2   44 SER cc_start: 0.7681 (m) cc_final: 0.7470 (m)
REVERT: B8    6 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8233 (pttm)
REVERT: B8   68 ASP cc_start: 0.7353 (m-30) cc_final: 0.6902 (m-30)
REVERT: B8  113 LEU cc_start: 0.9121 (mt) cc_final: 0.8609 (tt)
REVERT: BK   28 GLU cc_start: 0.8436 (pm20) cc_final: 0.8116 (pm20)
REVERT: BK   43 ASP cc_start: 0.8463 (p0) cc_final: 0.7939 (p0)
REVERT: BK   66 PHE cc_start: 0.8442 (m-10) cc_final: 0.7950 (m-10)
REVERT: BK   99 TYR cc_start: 0.8339 (t80) cc_final: 0.8004 (t80)
REVERT: BK  108 MET cc_start: 0.7140 (tpt) cc_final: 0.6083 (tpt)
REVERT: C1   11 SER cc_start: 0.8771 (m) cc_final: 0.8476 (t)
REVERT: B1   25 TYR cc_start: 0.8507 (t80) cc_final: 0.8219 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 1963
  average time/residue: 0.6404
  time to fit residues: 2198.8546
Evaluate side-chains
  1578 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 1578
  time to evaluate  : 5.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 469 optimal weight:    1.9990
   chunk 302 optimal weight:    1.9990
   chunk 453 optimal weight:    0.3980
   chunk 228 optimal weight:    7.9990
   chunk 149 optimal weight:    1.9990
   chunk 146 optimal weight:    4.9990
   chunk 482 optimal weight:    9.9990
   chunk 516 optimal weight:    0.9990
   chunk 375 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0670
   chunk 596 optimal weight:    0.2980
   overall best weight:    0.7522

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 373 ASN
V2  37 ASN
S1 237 ASN
** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S1 430 GLN
** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S7  38 ASN
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2  80 ASN
** A7  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A7  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A7  50 ASN
AL  59 HIS
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AA  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
4L   7 ASN
D5  23 ASN
** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 194 ASN
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 332 HIS
** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
D4 180 GLN
D4 279 GLN
D4 415 GLN
D4 440 HIS
** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2 235 ASN
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B5  69 HIS
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S5  44 HIS
C2  61 GLN
B4  49 GLN
AM  23 ASN
** B2  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B8  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.5482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.244  67000  Z= 0.545
  Angle     :  1.673  50.629  90856  Z= 1.058
  Chirality :  0.312   6.347   9986
  Planarity :  0.005   0.091  11476
  Dihedral  :  7.295  96.222   9098
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  9.91 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  0.04 %
    Allowed  :  1.32 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.63 %
    Twisted General : 0.17 %

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: -1.40 (0.09), residues: 7979
  helix:  0.57 (0.08), residues: 4165
  sheet: -1.62 (0.26), residues: 388
  loop : -2.86 (0.10), residues: 3426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.002   TRPD2  30 
 HIS   0.016   0.001   HISD5 332 
 PHE   0.035   0.002   PHED1 270 
 TYR   0.030   0.002   TYRS8 118 
 ARG   0.012   0.000   ARGB9  33 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  2004 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 2001
  time to evaluate  : 5.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V1  102 PRO cc_start: 0.8838 (Cg_exo) cc_final: 0.8466 (Cg_endo)
REVERT: V2  155 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7372 (tm-30)
REVERT: S1  222 THR cc_start: 0.8397 (p) cc_final: 0.7826 (t)
REVERT: S1  246 GLU cc_start: 0.6169 (pt0) cc_final: 0.5961 (pt0)
REVERT: S1  248 MET cc_start: 0.7657 (mmt) cc_final: 0.7345 (mmm)
REVERT: S1  490 MET cc_start: 0.7629 (tmm) cc_final: 0.7141 (tmm)
REVERT: S1  617 ASP cc_start: 0.8355 (p0) cc_final: 0.7758 (t70)
REVERT: S2   72 MET cc_start: 0.6963 (ttt) cc_final: 0.6747 (ttp)
REVERT: S2   75 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8156 (tttp)
REVERT: S2  152 MET cc_start: 0.9119 (tpp) cc_final: 0.8907 (tpp)
REVERT: S2  242 ILE cc_start: 0.8125 (pt) cc_final: 0.7907 (pt)
REVERT: S2  302 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7702 (mm-30)
REVERT: S2  379 VAL cc_start: 0.9398 (t) cc_final: 0.9087 (p)
REVERT: S2  404 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8152 (mmmm)
REVERT: S2  413 ASP cc_start: 0.9005 (m-30) cc_final: 0.8711 (m-30)
REVERT: S3  131 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7205 (mt-10)
REVERT: S3  200 ASN cc_start: 0.7664 (m-40) cc_final: 0.6823 (p0)
REVERT: S7   92 LEU cc_start: 0.9153 (tt) cc_final: 0.8945 (tt)
REVERT: S7   96 MET cc_start: 0.8605 (mmm) cc_final: 0.8109 (mmm)
REVERT: S7  107 MET cc_start: 0.8715 (ttt) cc_final: 0.8368 (ttt)
REVERT: S7  109 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7889 (mm-30)
REVERT: S7  128 TYR cc_start: 0.8015 (m-80) cc_final: 0.7475 (m-80)
REVERT: S7  152 THR cc_start: 0.8531 (m) cc_final: 0.8063 (p)
REVERT: S7  156 LEU cc_start: 0.9010 (tp) cc_final: 0.8763 (tp)
REVERT: S7  172 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7116 (tmt170)
REVERT: S8   92 ILE cc_start: 0.9429 (mm) cc_final: 0.9163 (mm)
REVERT: S6   36 ASN cc_start: 0.8620 (t0) cc_final: 0.8407 (t0)
REVERT: S6   78 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7441 (tm-30)
REVERT: S4   81 ASN cc_start: 0.8205 (p0) cc_final: 0.7972 (p0)
REVERT: A9   71 MET cc_start: 0.7857 (mmm) cc_final: 0.7625 (mmm)
REVERT: A9  216 ASN cc_start: 0.8454 (t0) cc_final: 0.8145 (t0)
REVERT: A9  306 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7553 (tm-30)
REVERT: A2   80 ASN cc_start: 0.7152 (m-40) cc_final: 0.6464 (p0)
REVERT: A2   86 VAL cc_start: 0.7620 (t) cc_final: 0.7420 (t)
REVERT: A5   57 ILE cc_start: 0.6657 (mt) cc_final: 0.6202 (mt)
REVERT: A6   60 ASP cc_start: 0.8026 (m-30) cc_final: 0.7500 (m-30)
REVERT: A6   90 GLU cc_start: 0.8198 (tp30) cc_final: 0.7639 (tp30)
REVERT: A6  103 MET cc_start: 0.8370 (mmp) cc_final: 0.7951 (tpp)
REVERT: AL   25 ARG cc_start: 0.8522 (ttp80) cc_final: 0.7971 (ttp80)
REVERT: AA    9 GLU cc_start: 0.8217 (tp30) cc_final: 0.7810 (tp30)
REVERT: AA   12 LYS cc_start: 0.8945 (ptmm) cc_final: 0.8437 (ptpp)
REVERT: AA   46 ASP cc_start: 0.8594 (m-30) cc_final: 0.8368 (m-30)
REVERT: D3    4 MET cc_start: 0.7453 (ttt) cc_final: 0.6563 (tmm)
REVERT: D3   57 LEU cc_start: 0.9060 (mm) cc_final: 0.8716 (mt)
REVERT: D3   62 PHE cc_start: 0.9053 (t80) cc_final: 0.8839 (t80)
REVERT: D3   86 THR cc_start: 0.8292 (p) cc_final: 0.8041 (t)
REVERT: D1   66 SER cc_start: 0.8246 (m) cc_final: 0.7812 (p)
REVERT: D1  133 LEU cc_start: 0.9323 (tp) cc_final: 0.8870 (tp)
REVERT: D1  145 THR cc_start: 0.9151 (m) cc_final: 0.8949 (p)
REVERT: D1  183 MET cc_start: 0.8982 (ppp) cc_final: 0.8577 (ppp)
REVERT: D1  188 SER cc_start: 0.9046 (m) cc_final: 0.8583 (t)
REVERT: D1  283 ASP cc_start: 0.8299 (m-30) cc_final: 0.7803 (m-30)
REVERT: D1  285 LEU cc_start: 0.9487 (tp) cc_final: 0.9229 (tp)
REVERT: D1  286 MET cc_start: 0.8715 (mmt) cc_final: 0.8443 (mmm)
REVERT: D6  110 ASP cc_start: 0.5390 (t0) cc_final: 0.5090 (t0)
REVERT: D6  124 ASP cc_start: 0.7571 (m-30) cc_final: 0.7137 (m-30)
REVERT: 4L    9 MET cc_start: 0.8358 (mmm) cc_final: 0.7495 (tpt)
REVERT: 4L   21 MET cc_start: 0.6760 (ppp) cc_final: 0.6322 (ppp)
REVERT: 4L   25 HIS cc_start: 0.8563 (m-70) cc_final: 0.7740 (m-70)
REVERT: 4L   36 MET cc_start: 0.8433 (tmm) cc_final: 0.7950 (tmm)
REVERT: D5   13 ILE cc_start: 0.8679 (tp) cc_final: 0.8095 (tp)
REVERT: D5   48 MET cc_start: 0.7778 (ttt) cc_final: 0.7074 (tmm)
REVERT: D5   87 MET cc_start: 0.6955 (mmm) cc_final: 0.6676 (mmm)
REVERT: D5   88 MET cc_start: 0.7588 (tpp) cc_final: 0.7302 (tpp)
REVERT: D5  102 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7457 (tp30)
REVERT: D5  154 LEU cc_start: 0.8876 (tp) cc_final: 0.8623 (tp)
REVERT: D5  283 MET cc_start: 0.8220 (ptm) cc_final: 0.7922 (ptp)
REVERT: D5  326 PHE cc_start: 0.8028 (t80) cc_final: 0.7781 (t80)
REVERT: D5  336 LYS cc_start: 0.8628 (mppt) cc_final: 0.8116 (mptt)
REVERT: D5  355 ASP cc_start: 0.7944 (m-30) cc_final: 0.7653 (t0)
REVERT: D5  370 THR cc_start: 0.8545 (p) cc_final: 0.8227 (t)
REVERT: D5  393 ASP cc_start: 0.8054 (t70) cc_final: 0.7350 (t70)
REVERT: D5  495 ILE cc_start: 0.8372 (mm) cc_final: 0.7993 (pt)
REVERT: D5  559 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7396 (mt-10)
REVERT: D5  573 MET cc_start: 0.7560 (mmt) cc_final: 0.7249 (mmt)
REVERT: D4    9 MET cc_start: 0.8213 (tmm) cc_final: 0.7981 (tmm)
REVERT: D4  141 GLU cc_start: 0.8826 (tt0) cc_final: 0.8429 (tt0)
REVERT: D4  200 MET cc_start: 0.7747 (mmp) cc_final: 0.7432 (mmm)
REVERT: D4  204 MET cc_start: 0.8520 (mtm) cc_final: 0.8020 (mtm)
REVERT: D4  229 MET cc_start: 0.7891 (mtp) cc_final: 0.7671 (mtp)
REVERT: D4  400 MET cc_start: 0.7121 (mmp) cc_final: 0.6886 (mmp)
REVERT: D4  431 THR cc_start: 0.8835 (p) cc_final: 0.8291 (t)
REVERT: D4  447 LEU cc_start: 0.8759 (mt) cc_final: 0.8310 (mt)
REVERT: D2   36 ASN cc_start: 0.8912 (t0) cc_final: 0.8618 (t0)
REVERT: D2   76 ILE cc_start: 0.9271 (mm) cc_final: 0.8833 (pt)
REVERT: D2   96 MET cc_start: 0.8595 (ttm) cc_final: 0.8377 (ttm)
REVERT: D2  167 TRP cc_start: 0.8515 (m-10) cc_final: 0.7883 (m-10)
REVERT: D2  176 ARG cc_start: 0.8195 (mpp80) cc_final: 0.7937 (mtm-85)
REVERT: D2  210 ILE cc_start: 0.8770 (tt) cc_final: 0.8441 (tt)
REVERT: D2  213 SER cc_start: 0.9484 (m) cc_final: 0.9260 (p)
REVERT: D2  248 LEU cc_start: 0.8837 (mm) cc_final: 0.8432 (mt)
REVERT: D2  263 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8416 (mttt)
REVERT: D2  268 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8691 (tm-30)
REVERT: D2  332 LEU cc_start: 0.9336 (tp) cc_final: 0.8893 (pp)
REVERT: D2  334 THR cc_start: 0.8776 (t) cc_final: 0.8392 (t)
REVERT: D2  344 SER cc_start: 0.9107 (p) cc_final: 0.8586 (m)
REVERT: AK   57 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6593 (tpp-160)
REVERT: AK   80 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7392 (ttm-80)
REVERT: B5  114 MET cc_start: 0.8396 (ttt) cc_final: 0.7835 (ttt)
REVERT: AB   12 LYS cc_start: 0.9109 (tmmt) cc_final: 0.8878 (tmmt)
REVERT: AB   68 GLU cc_start: 0.7161 (pm20) cc_final: 0.6659 (pm20)
REVERT: A8   25 LYS cc_start: 0.9142 (tttt) cc_final: 0.8838 (mmtp)
REVERT: BJ   98 ASP cc_start: 0.8491 (m-30) cc_final: 0.8269 (m-30)
REVERT: AJ   20 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7515 (tp30)
REVERT: AJ  185 LYS cc_start: 0.8550 (mttt) cc_final: 0.8163 (tppt)
REVERT: S5   91 TYR cc_start: 0.6320 (p90) cc_final: 0.6083 (p90)
REVERT: S5   95 PRO cc_start: 0.5880 (Cg_exo) cc_final: 0.3535 (Cg_endo)
REVERT: A3   14 LYS cc_start: 0.6402 (mttp) cc_final: 0.6088 (mtmm)
REVERT: A3   15 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7053 (mt-10)
REVERT: C2    2 MET cc_start: 0.7486 (tmm) cc_final: 0.7126 (tmm)
REVERT: C2   36 PHE cc_start: 0.9140 (t80) cc_final: 0.8812 (t80)
REVERT: C2   37 LEU cc_start: 0.9196 (tp) cc_final: 0.8774 (tp)
REVERT: C2   61 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8116 (mm110)
REVERT: C2   83 TYR cc_start: 0.8675 (m-80) cc_final: 0.7948 (m-80)
REVERT: B4   47 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8586 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7793 (t0) cc_final: 0.7421 (t0)
REVERT: AM   71 MET cc_start: 0.7974 (ppp) cc_final: 0.7748 (ppp)
REVERT: B6    9 LEU cc_start: 0.8513 (tt) cc_final: 0.7956 (tt)
REVERT: B6   85 LEU cc_start: 0.8655 (mp) cc_final: 0.8349 (tt)
REVERT: B6  119 MET cc_start: 0.6787 (tmm) cc_final: 0.6544 (tmm)
REVERT: B7   51 VAL cc_start: 0.8206 (t) cc_final: 0.7999 (t)
REVERT: B7   67 LYS cc_start: 0.9273 (tptm) cc_final: 0.8246 (mtmt)
REVERT: B9   43 LEU cc_start: 0.8463 (mm) cc_final: 0.8189 (mm)
REVERT: B9   50 HIS cc_start: 0.7202 (p-80) cc_final: 0.6812 (p-80)
REVERT: B2   44 SER cc_start: 0.7489 (m) cc_final: 0.7268 (m)
REVERT: B8    6 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8192 (pttm)
REVERT: B8   68 ASP cc_start: 0.7272 (m-30) cc_final: 0.6983 (m-30)
REVERT: B8  113 LEU cc_start: 0.9019 (mt) cc_final: 0.8570 (tt)
REVERT: BK   29 ASP cc_start: 0.8578 (t0) cc_final: 0.8301 (t0)
REVERT: BK   43 ASP cc_start: 0.8405 (p0) cc_final: 0.7849 (p0)
REVERT: BK   81 PRO cc_start: 0.9333 (Cg_exo) cc_final: 0.9103 (Cg_endo)
REVERT: BK   99 TYR cc_start: 0.8059 (t80) cc_final: 0.7620 (t80)
REVERT: BK  108 MET cc_start: 0.7097 (tpt) cc_final: 0.6410 (tpt)
REVERT: C1   11 SER cc_start: 0.8737 (m) cc_final: 0.8433 (t)
REVERT: C1   21 LEU cc_start: 0.7981 (mm) cc_final: 0.7746 (pp)
REVERT: A1   43 TYR cc_start: 0.8465 (t80) cc_final: 0.8231 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 2003
  average time/residue: 0.5852
  time to fit residues: 2005.8557
Evaluate side-chains
  1598 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 1597
  time to evaluate  : 5.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 690 optimal weight:    0.0040
   chunk 726 optimal weight:    4.9990
   chunk 663 optimal weight:   10.0000
   chunk 706 optimal weight:    0.0050
   chunk 425 optimal weight:    0.0870
   chunk 307 optimal weight:    7.9990
   chunk 555 optimal weight:    5.9990
   chunk 216 optimal weight:    5.9990
   chunk 638 optimal weight:    6.9990
   chunk 668 optimal weight:    8.9990
   chunk 704 optimal weight:    0.7980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 373 ASN
V2  37 ASN
S1 401 HIS
S1 430 GLN
** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S7  38 ASN
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
A9  87 HIS
** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A7  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A7  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A7  50 ASN
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AA  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1 138 GLN
D5  23 ASN
** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
D4 279 GLN
D4 415 GLN
D4 440 HIS
D2  63 GLN
D2 235 ASN
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
AJ 107 GLN
S5  44 HIS
B4  49 GLN
AM  23 ASN
AM  53 ASN
B9  25 HIS
** B2  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B8  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
BK 103 HIS

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.5616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.242  67000  Z= 0.547
  Angle     :  1.675  50.626  90856  Z= 1.059
  Chirality :  0.312   6.350   9986
  Planarity :  0.005   0.115  11476
  Dihedral  :  7.194  91.494   9098
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  9.85 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  0.03 %
    Allowed  :  1.07 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.42 %
    Twisted General : 0.20 %

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: -1.35 (0.09), residues: 7979
  helix:  0.59 (0.08), residues: 4158
  sheet: -1.59 (0.25), residues: 405
  loop : -2.80 (0.10), residues: 3416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRPD2 234 
 HIS   0.010   0.001   HISA9 288 
 PHE   0.033   0.002   PHED5 385 
 TYR   0.030   0.002   TYRD4 152 
 ARG   0.016   0.000   ARGV3  74 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1956 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 1954
  time to evaluate  : 5.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V1  102 PRO cc_start: 0.8822 (Cg_exo) cc_final: 0.8434 (Cg_endo)
REVERT: V2  136 LEU cc_start: 0.6270 (pt) cc_final: 0.5993 (pt)
REVERT: V2  155 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7418 (tm-30)
REVERT: S1  222 THR cc_start: 0.8304 (p) cc_final: 0.7865 (t)
REVERT: S1  490 MET cc_start: 0.7619 (tmm) cc_final: 0.7105 (tmm)
REVERT: S1  549 HIS cc_start: 0.7984 (p-80) cc_final: 0.7738 (p-80)
REVERT: S1  609 MET cc_start: 0.6917 (pmm) cc_final: 0.6362 (pmm)
REVERT: S1  617 ASP cc_start: 0.8342 (p0) cc_final: 0.7743 (t70)
REVERT: S2   72 MET cc_start: 0.6995 (ttt) cc_final: 0.6785 (ttp)
REVERT: S2   75 LYS cc_start: 0.8647 (ttpp) cc_final: 0.8289 (tttp)
REVERT: S2  242 ILE cc_start: 0.8109 (pt) cc_final: 0.7888 (pt)
REVERT: S2  302 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7663 (mm-30)
REVERT: S2  379 VAL cc_start: 0.9426 (t) cc_final: 0.9099 (p)
REVERT: S2  404 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8210 (mmmm)
REVERT: S2  413 ASP cc_start: 0.9037 (m-30) cc_final: 0.8749 (m-30)
REVERT: S3  131 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7202 (mt-10)
REVERT: S3  200 ASN cc_start: 0.7703 (m-40) cc_final: 0.6824 (p0)
REVERT: S7   96 MET cc_start: 0.8631 (mmm) cc_final: 0.8341 (mmm)
REVERT: S7  107 MET cc_start: 0.8689 (ttt) cc_final: 0.8348 (ttt)
REVERT: S7  109 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7885 (mm-30)
REVERT: S7  112 TYR cc_start: 0.7744 (m-80) cc_final: 0.7319 (m-80)
REVERT: S7  152 THR cc_start: 0.8606 (m) cc_final: 0.8100 (p)
REVERT: S7  166 LYS cc_start: 0.8816 (tttp) cc_final: 0.8610 (tttm)
REVERT: S7  172 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7127 (tmt170)
REVERT: S8   92 ILE cc_start: 0.9426 (mm) cc_final: 0.9193 (mm)
REVERT: S6   36 ASN cc_start: 0.8707 (t0) cc_final: 0.8378 (t0)
REVERT: S4   81 ASN cc_start: 0.8206 (p0) cc_final: 0.7795 (p0)
REVERT: A9   71 MET cc_start: 0.7829 (mmm) cc_final: 0.7591 (mmm)
REVERT: A9  216 ASN cc_start: 0.8462 (t0) cc_final: 0.8193 (t0)
REVERT: A9  306 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7548 (tm-30)
REVERT: A2   80 ASN cc_start: 0.7290 (m-40) cc_final: 0.6589 (p0)
REVERT: A5   57 ILE cc_start: 0.6633 (mt) cc_final: 0.6194 (mt)
REVERT: A6   90 GLU cc_start: 0.8185 (tp30) cc_final: 0.7632 (tp30)
REVERT: A6   97 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8366 (tmtt)
REVERT: A7   34 THR cc_start: 0.7634 (p) cc_final: 0.7430 (p)
REVERT: A7   69 MET cc_start: 0.7917 (tpp) cc_final: 0.6812 (tpp)
REVERT: AL   25 ARG cc_start: 0.8588 (ttp80) cc_final: 0.7989 (ttp80)
REVERT: AA    9 GLU cc_start: 0.8234 (tp30) cc_final: 0.7765 (tp30)
REVERT: AA   12 LYS cc_start: 0.8941 (ptmm) cc_final: 0.8454 (ptpp)
REVERT: AA   54 MET cc_start: 0.7969 (mmp) cc_final: 0.7751 (mmp)
REVERT: AA   75 GLU cc_start: 0.8505 (tp30) cc_final: 0.8254 (tp30)
REVERT: D3    4 MET cc_start: 0.7461 (ttt) cc_final: 0.6555 (tmm)
REVERT: D3   86 THR cc_start: 0.8443 (p) cc_final: 0.7959 (t)
REVERT: D1   51 ASP cc_start: 0.8594 (p0) cc_final: 0.8331 (p0)
REVERT: D1   66 SER cc_start: 0.8318 (m) cc_final: 0.7886 (p)
REVERT: D1  188 SER cc_start: 0.9081 (m) cc_final: 0.8566 (t)
REVERT: D1  189 THR cc_start: 0.9261 (p) cc_final: 0.7711 (p)
REVERT: D1  283 ASP cc_start: 0.8264 (m-30) cc_final: 0.7881 (m-30)
REVERT: D1  286 MET cc_start: 0.8549 (mmt) cc_final: 0.8289 (mmm)
REVERT: D6   20 PHE cc_start: 0.7921 (p90) cc_final: 0.6846 (p90)
REVERT: D6   65 MET cc_start: 0.9237 (mpp) cc_final: 0.8894 (mpp)
REVERT: D6  110 ASP cc_start: 0.5324 (t0) cc_final: 0.5000 (t0)
REVERT: D6  124 ASP cc_start: 0.7276 (m-30) cc_final: 0.6936 (m-30)
REVERT: 4L    4 VAL cc_start: 0.8704 (m) cc_final: 0.8463 (p)
REVERT: 4L    7 ASN cc_start: 0.7310 (m-40) cc_final: 0.7022 (t0)
REVERT: 4L    9 MET cc_start: 0.8369 (mmm) cc_final: 0.7574 (tpt)
REVERT: 4L   10 MET cc_start: 0.8825 (ttt) cc_final: 0.8018 (tpp)
REVERT: 4L   21 MET cc_start: 0.6762 (ppp) cc_final: 0.6343 (ppp)
REVERT: 4L   31 LEU cc_start: 0.8782 (tt) cc_final: 0.8479 (tt)
REVERT: D5   13 ILE cc_start: 0.8674 (tp) cc_final: 0.8128 (tp)
REVERT: D5   48 MET cc_start: 0.7778 (ttt) cc_final: 0.7073 (tmm)
REVERT: D5   82 MET cc_start: 0.7430 (ptp) cc_final: 0.7129 (mtm)
REVERT: D5   87 MET cc_start: 0.7156 (mmm) cc_final: 0.6924 (mmm)
REVERT: D5   88 MET cc_start: 0.7622 (tpp) cc_final: 0.7353 (tpp)
REVERT: D5  102 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7439 (tp30)
REVERT: D5  283 MET cc_start: 0.8266 (ptm) cc_final: 0.8018 (ptp)
REVERT: D5  326 PHE cc_start: 0.8149 (t80) cc_final: 0.7787 (t80)
REVERT: D5  336 LYS cc_start: 0.8678 (mppt) cc_final: 0.8110 (mptt)
REVERT: D5  355 ASP cc_start: 0.7891 (m-30) cc_final: 0.7632 (t0)
REVERT: D5  370 THR cc_start: 0.8432 (p) cc_final: 0.8186 (t)
REVERT: D5  393 ASP cc_start: 0.7916 (t70) cc_final: 0.7138 (t70)
REVERT: D5  397 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7339 (mt-10)
REVERT: D5  559 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7355 (mt-10)
REVERT: D5  573 MET cc_start: 0.7404 (mmt) cc_final: 0.7134 (mmt)
REVERT: D5  604 PHE cc_start: 0.7957 (m-80) cc_final: 0.7438 (m-80)
REVERT: D4    9 MET cc_start: 0.8202 (tmm) cc_final: 0.7941 (tmm)
REVERT: D4  157 SER cc_start: 0.8920 (p) cc_final: 0.8695 (p)
REVERT: D4  200 MET cc_start: 0.7634 (mmp) cc_final: 0.7396 (mmm)
REVERT: D4  204 MET cc_start: 0.8614 (mtm) cc_final: 0.8130 (mtm)
REVERT: D4  207 MET cc_start: 0.7719 (tpp) cc_final: 0.7037 (tpp)
REVERT: D4  229 MET cc_start: 0.7844 (mtp) cc_final: 0.7576 (mtm)
REVERT: D4  400 MET cc_start: 0.7532 (mmp) cc_final: 0.6602 (mmp)
REVERT: D4  409 TYR cc_start: 0.8562 (t80) cc_final: 0.8292 (t80)
REVERT: D4  431 THR cc_start: 0.8797 (p) cc_final: 0.8312 (t)
REVERT: D4  447 LEU cc_start: 0.8778 (mt) cc_final: 0.8400 (mt)
REVERT: D2   36 ASN cc_start: 0.8807 (t0) cc_final: 0.8607 (t0)
REVERT: D2   63 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8618 (mm110)
REVERT: D2   76 ILE cc_start: 0.9207 (mm) cc_final: 0.8741 (pt)
REVERT: D2   96 MET cc_start: 0.8625 (ttm) cc_final: 0.8340 (ttm)
REVERT: D2  105 LYS cc_start: 0.9065 (tptp) cc_final: 0.8727 (tptp)
REVERT: D2  167 TRP cc_start: 0.8544 (m-10) cc_final: 0.7938 (m-10)
REVERT: D2  210 ILE cc_start: 0.8678 (tt) cc_final: 0.8462 (tt)
REVERT: D2  248 LEU cc_start: 0.8885 (mm) cc_final: 0.8521 (mt)
REVERT: D2  263 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8499 (mtmt)
REVERT: D2  268 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8773 (tm-30)
REVERT: D2  332 LEU cc_start: 0.9320 (tp) cc_final: 0.8947 (pp)
REVERT: AK   57 ARG cc_start: 0.7127 (ttp-170) cc_final: 0.6523 (tpp-160)
REVERT: AK  139 LYS cc_start: 0.8252 (tptt) cc_final: 0.7614 (tptt)
REVERT: B5  113 LEU cc_start: 0.9428 (tp) cc_final: 0.9199 (tp)
REVERT: B5  114 MET cc_start: 0.8307 (ttt) cc_final: 0.7938 (tpp)
REVERT: AB   12 LYS cc_start: 0.9106 (tmmt) cc_final: 0.8851 (tmmt)
REVERT: AB   68 GLU cc_start: 0.6961 (pm20) cc_final: 0.6443 (pm20)
REVERT: A8   25 LYS cc_start: 0.9160 (tttt) cc_final: 0.8862 (mmtp)
REVERT: AJ   20 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7446 (tp30)
REVERT: AJ  185 LYS cc_start: 0.8602 (mttt) cc_final: 0.8233 (tppt)
REVERT: A3   14 LYS cc_start: 0.6383 (mttp) cc_final: 0.6144 (mtmm)
REVERT: A3   15 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7073 (mt-10)
REVERT: C2    2 MET cc_start: 0.7697 (tmm) cc_final: 0.7052 (tmm)
REVERT: C2   36 PHE cc_start: 0.9118 (t80) cc_final: 0.8790 (t80)
REVERT: C2   37 LEU cc_start: 0.9201 (tp) cc_final: 0.8820 (tp)
REVERT: C2   83 TYR cc_start: 0.8703 (m-80) cc_final: 0.8366 (m-80)
REVERT: B4   47 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8608 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7779 (t0) cc_final: 0.7415 (t0)
REVERT: B6   85 LEU cc_start: 0.8626 (mp) cc_final: 0.8355 (tt)
REVERT: B6  102 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7661 (ttp-170)
REVERT: B6  119 MET cc_start: 0.6780 (tmm) cc_final: 0.6533 (tmm)
REVERT: B7   51 VAL cc_start: 0.8448 (t) cc_final: 0.8232 (t)
REVERT: B7   67 LYS cc_start: 0.9226 (tptm) cc_final: 0.8227 (mtmt)
REVERT: B9   43 LEU cc_start: 0.8270 (mm) cc_final: 0.7936 (mm)
REVERT: B9   50 HIS cc_start: 0.7298 (p-80) cc_final: 0.6841 (p-80)
REVERT: B9   94 GLU cc_start: 0.6614 (tm-30) cc_final: 0.5840 (tm-30)
REVERT: B2   44 SER cc_start: 0.7449 (m) cc_final: 0.7227 (m)
REVERT: B8    6 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8161 (pttm)
REVERT: B8   68 ASP cc_start: 0.7619 (m-30) cc_final: 0.7043 (m-30)
REVERT: B8  101 MET cc_start: 0.7196 (mtm) cc_final: 0.6912 (mtm)
REVERT: B8  113 LEU cc_start: 0.9010 (mt) cc_final: 0.8572 (tt)
REVERT: BK   28 GLU cc_start: 0.8400 (pm20) cc_final: 0.8135 (pm20)
REVERT: BK   43 ASP cc_start: 0.8385 (p0) cc_final: 0.7856 (p0)
REVERT: BK   90 ARG cc_start: 0.8961 (tpp-160) cc_final: 0.8686 (tpt170)
REVERT: BK   99 TYR cc_start: 0.7888 (t80) cc_final: 0.7566 (t80)
REVERT: BK  108 MET cc_start: 0.7034 (tpt) cc_final: 0.6831 (tpt)
REVERT: C1   11 SER cc_start: 0.8722 (m) cc_final: 0.8428 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 1955
  average time/residue: 0.5833
  time to fit residues: 1966.2567
Evaluate side-chains
  1588 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 1588
  time to evaluate  : 7.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 464 optimal weight:    4.9990
   chunk 747 optimal weight:    4.9990
   chunk 456 optimal weight:    4.9990
   chunk 354 optimal weight:    5.9990
   chunk 519 optimal weight:    4.9990
   chunk 784 optimal weight:    3.9990
   chunk 721 optimal weight:    0.8980
   chunk 624 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 482 optimal weight:    4.9990
   chunk 382 optimal weight:    7.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 373 ASN
V2  37 ASN
** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S1 430 GLN
** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S3 192 GLN
S7  38 ASN
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A5  82 GLN
A7  28 GLN
A7  50 ASN
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** AA  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D3  83 ASN
** D1   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1 138 GLN
** D1 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 199 GLN
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
D4 180 GLN
** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2 204 ASN
D2 235 ASN
AK   6 HIS
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S5  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S5  69 GLN
AM  23 ASN
** B2  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B8  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B8  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B8 132 GLN
BK 103 HIS
A1  31 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.5736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.238  67000  Z= 0.565
  Angle     :  1.692  50.882  90856  Z= 1.068
  Chirality :  0.312   6.493   9986
  Planarity :  0.006   0.133  11476
  Dihedral  :  7.244  89.977   9098
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 18.15
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.45 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  0.04 %
    Allowed  :  0.54 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.42 %
    Twisted General : 0.17 %

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: -1.40 (0.09), residues: 7979
  helix:  0.54 (0.08), residues: 4159
  sheet: -1.51 (0.26), residues: 396
  loop : -2.83 (0.10), residues: 3424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRPD2 234 
 HIS   0.010   0.001   HISA9 288 
 PHE   0.041   0.002   PHED2 216 
 TYR   0.029   0.002   TYRS8 118 
 ARG   0.010   0.001   ARGV3  74 

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

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

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  15958 Ramachandran restraints generated.
    7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1908 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 1905
  time to evaluate  : 6.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V1  102 PRO cc_start: 0.8777 (Cg_exo) cc_final: 0.8416 (Cg_endo)
REVERT: V2  155 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7416 (tm-30)
REVERT: S1  222 THR cc_start: 0.8456 (p) cc_final: 0.7951 (t)
REVERT: S1  490 MET cc_start: 0.7674 (tmm) cc_final: 0.7081 (tmm)
REVERT: S1  549 HIS cc_start: 0.8137 (p-80) cc_final: 0.7861 (p-80)
REVERT: S2   72 MET cc_start: 0.7183 (ttt) cc_final: 0.6528 (ttt)
REVERT: S2   75 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8294 (tttp)
REVERT: S2  111 MET cc_start: 0.8002 (pmm) cc_final: 0.7552 (pmm)
REVERT: S2  112 MET cc_start: 0.8640 (mmm) cc_final: 0.7402 (mmt)
REVERT: S2  155 THR cc_start: 0.9301 (p) cc_final: 0.8959 (t)
REVERT: S2  242 ILE cc_start: 0.8270 (pt) cc_final: 0.8065 (pt)
REVERT: S2  302 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7714 (mm-30)
REVERT: S2  379 VAL cc_start: 0.9471 (t) cc_final: 0.9182 (p)
REVERT: S2  404 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8243 (mmmm)
REVERT: S2  413 ASP cc_start: 0.9058 (m-30) cc_final: 0.8655 (m-30)
REVERT: S3  131 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7303 (mt-10)
REVERT: S3  147 ASP cc_start: 0.7143 (t0) cc_final: 0.6720 (t70)
REVERT: S3  149 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7752 (mtm110)
REVERT: S3  200 ASN cc_start: 0.7773 (m-40) cc_final: 0.6848 (p0)
REVERT: S7  107 MET cc_start: 0.8660 (ttt) cc_final: 0.8317 (ttt)
REVERT: S7  109 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7847 (mm-30)
REVERT: S7  128 TYR cc_start: 0.8037 (m-80) cc_final: 0.7376 (m-80)
REVERT: S7  152 THR cc_start: 0.8605 (m) cc_final: 0.8215 (p)
REVERT: S7  172 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7228 (tmt170)
REVERT: S8   49 ASN cc_start: 0.7758 (p0) cc_final: 0.7357 (p0)
REVERT: S8   92 ILE cc_start: 0.9486 (mm) cc_final: 0.9214 (mm)
REVERT: V3   54 LEU cc_start: 0.8445 (mt) cc_final: 0.8241 (mt)
REVERT: S6   36 ASN cc_start: 0.8752 (t0) cc_final: 0.8416 (t0)
REVERT: S6   42 ASP cc_start: 0.7633 (p0) cc_final: 0.7264 (p0)
REVERT: S4   81 ASN cc_start: 0.8216 (p0) cc_final: 0.7797 (p0)
REVERT: A9   67 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8119 (tp-100)
REVERT: A9   71 MET cc_start: 0.7865 (mmm) cc_final: 0.7594 (mmm)
REVERT: A9  216 ASN cc_start: 0.8555 (t0) cc_final: 0.8322 (t0)
REVERT: A9  306 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7614 (tm-30)
REVERT: A2   80 ASN cc_start: 0.7415 (m-40) cc_final: 0.6772 (p0)
REVERT: A2   86 VAL cc_start: 0.7638 (t) cc_final: 0.7437 (t)
REVERT: A6   90 GLU cc_start: 0.8250 (tp30) cc_final: 0.7791 (tp30)
REVERT: A6   97 LYS cc_start: 0.8945 (tmtt) cc_final: 0.8376 (tmtt)
REVERT: A6  103 MET cc_start: 0.8236 (mmp) cc_final: 0.8022 (tpp)
REVERT: A7   69 MET cc_start: 0.7978 (tpp) cc_final: 0.6887 (tpp)
REVERT: AA   12 LYS cc_start: 0.8946 (ptmm) cc_final: 0.8718 (ptmt)
REVERT: AA   46 ASP cc_start: 0.8719 (m-30) cc_final: 0.8384 (m-30)
REVERT: AA   68 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7705 (mm-30)
REVERT: AA   75 GLU cc_start: 0.8512 (tp30) cc_final: 0.8226 (tp30)
REVERT: AA   83 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8108 (mtmt)
REVERT: D3    4 MET cc_start: 0.7559 (ttt) cc_final: 0.6689 (tmm)
REVERT: D3   66 ASP cc_start: 0.9062 (t70) cc_final: 0.8792 (t0)
REVERT: D3   67 LEU cc_start: 0.9531 (mt) cc_final: 0.9320 (mt)
REVERT: D3   86 THR cc_start: 0.8523 (p) cc_final: 0.7998 (t)
REVERT: D1   51 ASP cc_start: 0.8530 (p0) cc_final: 0.8317 (p0)
REVERT: D1   66 SER cc_start: 0.8358 (m) cc_final: 0.7918 (p)
REVERT: D1  140 ILE cc_start: 0.9244 (tp) cc_final: 0.8769 (tp)
REVERT: D1  143 GLU cc_start: 0.8566 (mp0) cc_final: 0.8309 (pm20)
REVERT: D1  189 THR cc_start: 0.9053 (p) cc_final: 0.8300 (p)
REVERT: D1  239 THR cc_start: 0.9449 (m) cc_final: 0.9248 (t)
REVERT: D1  283 ASP cc_start: 0.8250 (m-30) cc_final: 0.7945 (m-30)
REVERT: D1  286 MET cc_start: 0.8708 (mmt) cc_final: 0.8279 (mmm)
REVERT: D6   65 MET cc_start: 0.9280 (mpp) cc_final: 0.8909 (mpp)
REVERT: D6   70 TYR cc_start: 0.8258 (t80) cc_final: 0.8036 (t80)
REVERT: D6   99 MET cc_start: 0.8029 (ppp) cc_final: 0.7685 (ppp)
REVERT: D6  100 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7866 (tm-30)
REVERT: D6  110 ASP cc_start: 0.5462 (t0) cc_final: 0.5121 (t0)
REVERT: D6  124 ASP cc_start: 0.7595 (m-30) cc_final: 0.7197 (m-30)
REVERT: 4L    7 ASN cc_start: 0.7116 (m-40) cc_final: 0.6840 (t0)
REVERT: 4L    9 MET cc_start: 0.8400 (mmm) cc_final: 0.7548 (tpt)
REVERT: 4L   21 MET cc_start: 0.6835 (ppp) cc_final: 0.6403 (ppp)
REVERT: 4L   59 MET cc_start: 0.8221 (mmp) cc_final: 0.7971 (mmp)
REVERT: D5   13 ILE cc_start: 0.8661 (tp) cc_final: 0.8188 (tp)
REVERT: D5   48 MET cc_start: 0.7815 (ttt) cc_final: 0.7098 (tmm)
REVERT: D5   87 MET cc_start: 0.7217 (mmm) cc_final: 0.6888 (mmm)
REVERT: D5  102 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7544 (tp30)
REVERT: D5  283 MET cc_start: 0.8311 (ptm) cc_final: 0.8038 (ptp)
REVERT: D5  355 ASP cc_start: 0.7988 (m-30) cc_final: 0.7703 (t0)
REVERT: D5  370 THR cc_start: 0.8550 (p) cc_final: 0.8288 (t)
REVERT: D5  393 ASP cc_start: 0.7943 (t70) cc_final: 0.7151 (t70)
REVERT: D5  397 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7191 (mt-10)
REVERT: D5  498 PHE cc_start: 0.6967 (m-80) cc_final: 0.5996 (m-10)
REVERT: D5  559 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7403 (mt-10)
REVERT: D5  573 MET cc_start: 0.7552 (mmt) cc_final: 0.6907 (mmt)
REVERT: D5  604 PHE cc_start: 0.8038 (m-80) cc_final: 0.7593 (m-80)
REVERT: D4    9 MET cc_start: 0.8329 (tmm) cc_final: 0.7897 (tmm)
REVERT: D4   71 TRP cc_start: 0.9140 (t-100) cc_final: 0.8923 (t-100)
REVERT: D4  108 MET cc_start: 0.9268 (mmm) cc_final: 0.8533 (mtt)
REVERT: D4  147 LEU cc_start: 0.9061 (tp) cc_final: 0.8831 (tp)
REVERT: D4  204 MET cc_start: 0.8706 (mtm) cc_final: 0.8212 (mtm)
REVERT: D4  207 MET cc_start: 0.7907 (tpp) cc_final: 0.7457 (tpp)
REVERT: D4  400 MET cc_start: 0.7552 (mmp) cc_final: 0.7282 (mmp)
REVERT: D4  409 TYR cc_start: 0.8680 (t80) cc_final: 0.8364 (t80)
REVERT: D4  447 LEU cc_start: 0.8767 (mt) cc_final: 0.8374 (mt)
REVERT: D2   60 PHE cc_start: 0.8873 (t80) cc_final: 0.8595 (t80)
REVERT: D2   63 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8783 (mm110)
REVERT: D2   76 ILE cc_start: 0.9156 (mm) cc_final: 0.8656 (pt)
REVERT: D2   96 MET cc_start: 0.8608 (ttm) cc_final: 0.8330 (ttm)
REVERT: D2  167 TRP cc_start: 0.8665 (m-10) cc_final: 0.8087 (m-10)
REVERT: D2  190 MET cc_start: 0.8650 (mmm) cc_final: 0.8397 (mtp)
REVERT: D2  248 LEU cc_start: 0.8983 (mm) cc_final: 0.8441 (mm)
REVERT: D2  263 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8500 (mtmt)
REVERT: D2  268 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8595 (tm-30)
REVERT: D2  332 LEU cc_start: 0.9370 (tp) cc_final: 0.8994 (pp)
REVERT: AK   57 ARG cc_start: 0.7224 (ttp-170) cc_final: 0.6633 (tpp-160)
REVERT: AK   80 ARG cc_start: 0.7693 (mtp180) cc_final: 0.7368 (mtp180)
REVERT: B5   84 GLU cc_start: 0.7604 (mp0) cc_final: 0.7213 (pm20)
REVERT: B5  114 MET cc_start: 0.8303 (ttt) cc_final: 0.7810 (ttt)
REVERT: AB   68 GLU cc_start: 0.7121 (pm20) cc_final: 0.6616 (pm20)
REVERT: A8   25 LYS cc_start: 0.9181 (tttt) cc_final: 0.8876 (mmtp)
REVERT: AJ   20 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7417 (tp30)
REVERT: AJ  185 LYS cc_start: 0.8576 (mttt) cc_final: 0.8232 (tppt)
REVERT: A3   15 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7232 (mt-10)
REVERT: A3   18 LEU cc_start: 0.8994 (mp) cc_final: 0.8776 (mp)
REVERT: A3   29 VAL cc_start: 0.8964 (t) cc_final: 0.8681 (m)
REVERT: C2    2 MET cc_start: 0.7796 (tmm) cc_final: 0.7495 (ttp)
REVERT: C2    3 THR cc_start: 0.8694 (m) cc_final: 0.8271 (m)
REVERT: C2   36 PHE cc_start: 0.9095 (t80) cc_final: 0.8808 (t80)
REVERT: C2   37 LEU cc_start: 0.9219 (tp) cc_final: 0.8845 (tp)
REVERT: C2   83 TYR cc_start: 0.8773 (m-80) cc_final: 0.8441 (m-80)
REVERT: B4   17 LEU cc_start: 0.7142 (pt) cc_final: 0.6565 (pp)
REVERT: B4   26 SER cc_start: 0.8395 (p) cc_final: 0.8102 (p)
REVERT: B4   47 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8670 (mm-40)
REVERT: B4   74 ASN cc_start: 0.7791 (t0) cc_final: 0.7255 (t0)
REVERT: B4  114 LEU cc_start: 0.9086 (tt) cc_final: 0.8857 (mm)
REVERT: AM   71 MET cc_start: 0.8088 (ppp) cc_final: 0.7844 (ppp)
REVERT: B6   85 LEU cc_start: 0.8735 (mp) cc_final: 0.8325 (tt)
REVERT: B6   99 LYS cc_start: 0.8756 (tmtt) cc_final: 0.8468 (tmtt)
REVERT: B6  119 MET cc_start: 0.6826 (tmm) cc_final: 0.6595 (tmm)
REVERT: B7   51 VAL cc_start: 0.8512 (t) cc_final: 0.8298 (t)
REVERT: B7   67 LYS cc_start: 0.9210 (tptm) cc_final: 0.8196 (mtmt)
REVERT: B9   50 HIS cc_start: 0.7572 (p-80) cc_final: 0.6772 (p-80)
REVERT: B9   52 ASN cc_start: 0.8131 (p0) cc_final: 0.7894 (p0)
REVERT: B9   74 GLN cc_start: 0.8147 (pp30) cc_final: 0.7714 (pp30)
REVERT: B2   44 SER cc_start: 0.7512 (m) cc_final: 0.7264 (m)
REVERT: B8    6 LYS cc_start: 0.8842 (tptm) cc_final: 0.8563 (pttm)
REVERT: B8   68 ASP cc_start: 0.7470 (m-30) cc_final: 0.7195 (m-30)
REVERT: B8  113 LEU cc_start: 0.9085 (mt) cc_final: 0.8642 (tt)
REVERT: BK   43 ASP cc_start: 0.8460 (p0) cc_final: 0.7958 (p0)
REVERT: BK   99 TYR cc_start: 0.7899 (t80) cc_final: 0.7588 (t80)
REVERT: C1   11 SER cc_start: 0.8751 (m) cc_final: 0.8449 (t)
  outliers start: 3
  outliers final: 0
  residues processed: 1906
  average time/residue: 0.5867
  time to fit residues: 1932.5504
Evaluate side-chains
  1552 residues out of total 7072 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 1552
  time to evaluate  : 5.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 787
   random chunks:
   chunk 495 optimal weight:    0.9990
   chunk 665 optimal weight:    8.9990
   chunk 191 optimal weight:    2.9990
   chunk 575 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 173 optimal weight:    2.9990
   chunk 625 optimal weight:    2.9990
   chunk 261 optimal weight:    0.8980
   chunk 642 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 115 optimal weight:    5.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V1 373 ASN
V2  37 ASN
** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S1 430 GLN
** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S7  38 ASN
S8 123 GLN
** S6  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S4  50 ASN
** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A5  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A7  50 ASN
** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D5 400 ASN
** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D4 279 GLN
** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2 235 ASN
** AK   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** BJ  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C2  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4  49 GLN
AM  23 ASN
** B2  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B8  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B8  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
BK 103 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.094832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.083650 restraints weight = 210060.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.085458 restraints weight = 120498.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.086807 restraints weight = 81153.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.5833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.240  67000  Z= 0.552
  Angle     :  1.687  50.709  90856  Z= 1.064
  Chirality :  0.312   6.424   9986
  Planarity :  0.006   0.115  11476
  Dihedral  :  7.178  85.712   9098
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  : 10.20 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  0.01 %
    Allowed  :  0.61 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.71 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.42 %
    Twisted General : 0.17 %

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: -1.35 (0.09), residues: 7979
  helix:  0.58 (0.08), residues: 4137
  sheet: -1.41 (0.26), residues: 378
  loop : -2.80 (0.10), residues: 3464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRPD2 234 
 HIS   0.010   0.001   HISA9 288 
 PHE   0.035   0.002   PHED5 385 
 TYR   0.031   0.002   TYRAJ 304 
 ARG   0.010   0.000   ARGV3  74 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 27242.87 seconds
wall clock time: 472 minutes 43.63 seconds (28363.63 seconds total)