Starting phenix.real_space_refine
on Sat Mar 23 22:44:20 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982_neut_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982_neut_trim_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982_neut_trim_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982_neut_trim_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982_neut_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf9_29982/03_2024/8gf9_29982_neut_trim_updated.pdb"
  }
  resolution = 2.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.045
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
     P      36      5.49       5
     S     112      5.16       5
     Na      2      4.78       5
     C   12700      2.51       5
     N    2756      2.21       5
     O    3420      1.98       5
     H   17068      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A PHE  248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  499": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A PHE  516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A PHE  650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ARG  744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B PHE  248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  499": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B PHE  516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B PHE  650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ARG  744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ARG  213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C PHE  248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ARG  281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ARG  421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ARG  429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ARG  433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ARG  499": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C PHE  516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ARG  579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C PHE  650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR  654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ARG  722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ARG  740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ARG  744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ARG  213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D PHE  248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ARG  281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ARG  421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ARG  429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ARG  433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ARG  499": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D PHE  516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ARG  579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D PHE  650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ARG  722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ARG  740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ARG  744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 36094
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 8512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 8512
          Classifications: {'peptide': 523}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 509}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 8512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 8512
          Classifications: {'peptide': 523}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 509}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 8512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 8512
          Classifications: {'peptide': 523}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 509}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 8512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 8512
          Classifications: {'peptide': 523}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 509}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 490
          Unusual residues: {' NA': 2, '8IJ': 1, 'POV': 9}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 488
          Unusual residues: {'8IJ': 1, 'POV': 9}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 488
          Unusual residues: {'8IJ': 1, 'POV': 9}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "D"
      Number of atoms: 488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 488
          Unusual residues: {'8IJ': 1, 'POV': 9}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 23
          Classifications: {'water': 23}
          Link IDs: {None: 22}
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 23
          Classifications: {'water': 23}
          Link IDs: {None: 22}
    Chain: "C"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 23
          Classifications: {'water': 23}
          Link IDs: {None: 22}
    Chain: "D"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 23
          Classifications: {'water': 23}
          Link IDs: {None: 22}
  Time building chain proxies: 15.70, per 1000 atoms: 0.43
  Number of scatterers: 36094
  At special positions: 0
  Unit cell: (116.965, 116.965, 110.685, 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)
     S     112     16.00
     P      36     15.00
     Na      2     11.00
     O    3420      8.00
     N    2756      7.00
     C   12700      6.00
     H   17068      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 387 " - pdb=" SG  CYS A 391 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 387 " - pdb=" SG  CYS B 391 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 387 " - pdb=" SG  CYS C 391 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 387 " - pdb=" SG  CYS D 391 " 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=0, symmetry=0
  Time building additional restraints: 36.61
  Conformation dependent library (CDL) restraints added in 3.1 seconds
  

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3944

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      84 helices and 4 sheets defined
      54.3% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 6.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 211
    Processing helix  chain 'A' and resid 215 through 224
      removed outlier: 3.723A  pdb=" N   THR A 219 " --> pdb=" O   MET A 215 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLU A 223 " --> pdb=" O   THR A 219 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASN A 224 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 252 through 258
    Processing helix  chain 'A' and resid 265 through 269
      removed outlier: 3.745A  pdb=" N   LEU A 269 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 265 through 269'
    Processing helix  chain 'A' and resid 288 through 294
    Processing helix  chain 'A' and resid 300 through 319
      removed outlier: 3.563A  pdb=" N   PHE A 305 " --> pdb=" O   ASP A 301 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU A 314 " --> pdb=" O   TYR A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 347 through 354
    Processing helix  chain 'A' and resid 397 through 400
      No H-bonds generated for 'chain 'A' and resid 397 through 400'
    Processing helix  chain 'A' and resid 419 through 430
    Processing helix  chain 'A' and resid 432 through 454
    Processing helix  chain 'A' and resid 470 through 496
      removed outlier: 3.798A  pdb=" N   THR A 476 " --> pdb=" O   TYR A 472 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLY A 484 " --> pdb=" O   LEU A 480 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TYR A 495 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 506
      No H-bonds generated for 'chain 'A' and resid 504 through 506'
    Processing helix  chain 'A' and resid 511 through 531
      removed outlier: 3.796A  pdb=" N   VAL A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 530 " --> pdb=" O   THR A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 558
      removed outlier: 4.066A  pdb=" N   VAL A 542 " --> pdb=" O   ALA A 539 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A 546 " --> pdb=" O   PHE A 543 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A 547 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TRP A 549 " --> pdb=" O   ALA A 546 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR A 550 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   THR A 556 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY A 558 " --> pdb=" O   TYR A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 573
    Processing helix  chain 'A' and resid 577 through 598
      removed outlier: 3.581A  pdb=" N   LEU A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 657 through 671
    Processing helix  chain 'A' and resid 675 through 711
      removed outlier: 3.836A  pdb=" N   VAL A 687 " --> pdb=" O   MET A 683 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASN A 688 " --> pdb=" O   GLY A 684 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   GLN A 692 " --> pdb=" O   ASN A 688 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   GLU A 693 " --> pdb=" O   LYS A 689 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU A 700 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 211
    Processing helix  chain 'B' and resid 215 through 224
      removed outlier: 3.724A  pdb=" N   THR B 219 " --> pdb=" O   MET B 215 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL B 222 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU B 223 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASN B 224 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 237
      No H-bonds generated for 'chain 'B' and resid 235 through 237'
    Processing helix  chain 'B' and resid 252 through 258
    Processing helix  chain 'B' and resid 265 through 269
      removed outlier: 3.745A  pdb=" N   LEU B 269 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 265 through 269'
    Processing helix  chain 'B' and resid 288 through 294
    Processing helix  chain 'B' and resid 300 through 319
      removed outlier: 3.563A  pdb=" N   PHE B 305 " --> pdb=" O   ASP B 301 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU B 314 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 343
    Processing helix  chain 'B' and resid 347 through 354
    Processing helix  chain 'B' and resid 397 through 400
      No H-bonds generated for 'chain 'B' and resid 397 through 400'
    Processing helix  chain 'B' and resid 419 through 430
    Processing helix  chain 'B' and resid 432 through 454
    Processing helix  chain 'B' and resid 470 through 496
      removed outlier: 3.798A  pdb=" N   THR B 476 " --> pdb=" O   TYR B 472 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLY B 484 " --> pdb=" O   LEU B 480 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   TYR B 495 " --> pdb=" O   ARG B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 506
      No H-bonds generated for 'chain 'B' and resid 504 through 506'
    Processing helix  chain 'B' and resid 511 through 531
      removed outlier: 3.796A  pdb=" N   VAL B 528 " --> pdb=" O   LEU B 524 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR B 530 " --> pdb=" O   THR B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 558
      removed outlier: 4.066A  pdb=" N   VAL B 542 " --> pdb=" O   ALA B 539 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA B 546 " --> pdb=" O   PHE B 543 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B 547 " --> pdb=" O   SER B 544 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   TRP B 549 " --> pdb=" O   ALA B 546 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR B 550 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   THR B 556 " --> pdb=" O   LEU B 553 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY B 558 " --> pdb=" O   TYR B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 573
    Processing helix  chain 'B' and resid 577 through 598
      removed outlier: 3.580A  pdb=" N   LEU B 598 " --> pdb=" O   ALA B 594 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 638
    Processing helix  chain 'B' and resid 657 through 671
    Processing helix  chain 'B' and resid 675 through 711
      removed outlier: 3.836A  pdb=" N   VAL B 687 " --> pdb=" O   MET B 683 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN B 688 " --> pdb=" O   GLY B 684 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   GLN B 692 " --> pdb=" O   ASN B 688 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLU B 693 " --> pdb=" O   LYS B 689 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LYS B 695 " --> pdb=" O   ALA B 691 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU B 700 " --> pdb=" O   ASN B 696 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 211
    Processing helix  chain 'C' and resid 215 through 224
      removed outlier: 3.723A  pdb=" N   THR C 219 " --> pdb=" O   MET C 215 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL C 222 " --> pdb=" O   VAL C 218 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLU C 223 " --> pdb=" O   THR C 219 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASN C 224 " --> pdb=" O   LEU C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 237
      No H-bonds generated for 'chain 'C' and resid 235 through 237'
    Processing helix  chain 'C' and resid 252 through 258
    Processing helix  chain 'C' and resid 265 through 269
      removed outlier: 3.744A  pdb=" N   LEU C 269 " --> pdb=" O   VAL C 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 265 through 269'
    Processing helix  chain 'C' and resid 288 through 294
    Processing helix  chain 'C' and resid 300 through 319
      removed outlier: 3.562A  pdb=" N   PHE C 305 " --> pdb=" O   ASP C 301 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU C 314 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 343
    Processing helix  chain 'C' and resid 347 through 354
    Processing helix  chain 'C' and resid 397 through 400
      No H-bonds generated for 'chain 'C' and resid 397 through 400'
    Processing helix  chain 'C' and resid 419 through 430
    Processing helix  chain 'C' and resid 432 through 454
    Processing helix  chain 'C' and resid 470 through 496
      removed outlier: 3.797A  pdb=" N   THR C 476 " --> pdb=" O   TYR C 472 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLY C 484 " --> pdb=" O   LEU C 480 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TYR C 495 " --> pdb=" O   ARG C 491 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 504 through 506
      No H-bonds generated for 'chain 'C' and resid 504 through 506'
    Processing helix  chain 'C' and resid 511 through 531
      removed outlier: 3.797A  pdb=" N   VAL C 528 " --> pdb=" O   LEU C 524 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR C 530 " --> pdb=" O   THR C 526 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 535 through 558
      removed outlier: 4.066A  pdb=" N   VAL C 542 " --> pdb=" O   ALA C 539 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA C 546 " --> pdb=" O   PHE C 543 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU C 547 " --> pdb=" O   SER C 544 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   TRP C 549 " --> pdb=" O   ALA C 546 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR C 550 " --> pdb=" O   LEU C 547 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   THR C 556 " --> pdb=" O   LEU C 553 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY C 558 " --> pdb=" O   TYR C 555 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 560 through 573
    Processing helix  chain 'C' and resid 577 through 598
      removed outlier: 3.580A  pdb=" N   LEU C 598 " --> pdb=" O   ALA C 594 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 631 through 638
    Processing helix  chain 'C' and resid 657 through 671
    Processing helix  chain 'C' and resid 675 through 711
      removed outlier: 3.835A  pdb=" N   VAL C 687 " --> pdb=" O   MET C 683 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASN C 688 " --> pdb=" O   GLY C 684 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   GLN C 692 " --> pdb=" O   ASN C 688 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLU C 693 " --> pdb=" O   LYS C 689 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LYS C 695 " --> pdb=" O   ALA C 691 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU C 700 " --> pdb=" O   ASN C 696 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 211
    Processing helix  chain 'D' and resid 215 through 224
      removed outlier: 3.723A  pdb=" N   THR D 219 " --> pdb=" O   MET D 215 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL D 222 " --> pdb=" O   VAL D 218 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU D 223 " --> pdb=" O   THR D 219 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASN D 224 " --> pdb=" O   LEU D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 235 through 237
      No H-bonds generated for 'chain 'D' and resid 235 through 237'
    Processing helix  chain 'D' and resid 252 through 258
    Processing helix  chain 'D' and resid 265 through 269
      removed outlier: 3.744A  pdb=" N   LEU D 269 " --> pdb=" O   VAL D 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 265 through 269'
    Processing helix  chain 'D' and resid 288 through 294
    Processing helix  chain 'D' and resid 300 through 319
      removed outlier: 3.563A  pdb=" N   PHE D 305 " --> pdb=" O   ASP D 301 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LEU D 314 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 343
    Processing helix  chain 'D' and resid 347 through 354
    Processing helix  chain 'D' and resid 397 through 400
      No H-bonds generated for 'chain 'D' and resid 397 through 400'
    Processing helix  chain 'D' and resid 419 through 430
    Processing helix  chain 'D' and resid 432 through 454
    Processing helix  chain 'D' and resid 470 through 496
      removed outlier: 3.797A  pdb=" N   THR D 476 " --> pdb=" O   TYR D 472 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLY D 484 " --> pdb=" O   LEU D 480 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TYR D 495 " --> pdb=" O   ARG D 491 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 504 through 506
      No H-bonds generated for 'chain 'D' and resid 504 through 506'
    Processing helix  chain 'D' and resid 511 through 531
      removed outlier: 3.796A  pdb=" N   VAL D 528 " --> pdb=" O   LEU D 524 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR D 530 " --> pdb=" O   THR D 526 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 535 through 558
      removed outlier: 4.066A  pdb=" N   VAL D 542 " --> pdb=" O   ALA D 539 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA D 546 " --> pdb=" O   PHE D 543 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU D 547 " --> pdb=" O   SER D 544 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TRP D 549 " --> pdb=" O   ALA D 546 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR D 550 " --> pdb=" O   LEU D 547 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   THR D 556 " --> pdb=" O   LEU D 553 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY D 558 " --> pdb=" O   TYR D 555 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 560 through 573
    Processing helix  chain 'D' and resid 577 through 598
      removed outlier: 3.580A  pdb=" N   LEU D 598 " --> pdb=" O   ALA D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 631 through 638
    Processing helix  chain 'D' and resid 657 through 671
    Processing helix  chain 'D' and resid 675 through 711
      removed outlier: 3.835A  pdb=" N   VAL D 687 " --> pdb=" O   MET D 683 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN D 688 " --> pdb=" O   GLY D 684 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   GLN D 692 " --> pdb=" O   ASN D 688 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLU D 693 " --> pdb=" O   LYS D 689 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS D 695 " --> pdb=" O   ALA D 691 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU D 700 " --> pdb=" O   ASN D 696 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 378 through 384
    Processing sheet with id=  B, first strand: chain 'B' and resid 378 through 384
    Processing sheet with id=  C, first strand: chain 'C' and resid 378 through 384
    Processing sheet with id=  D, first strand: chain 'D' and resid 378 through 384

    748 hydrogen bonds defined for protein.
    2064 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: 13.35

  Time building geometry restraints manager: 37.23 seconds

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

  Histogram of bond lengths:
        0.82 -     1.40: 24536
        1.40 -     1.99: 11808
        1.99 -     2.57: 4
        2.57 -     3.15: 8
        3.15 -     3.73: 12
  Bond restraints: 36368
  Sorted by residual:
  bond pdb=" CA  ASN A 754 "
       pdb=" HA  ASN A 754 "
    ideal  model  delta    sigma   weight residual
    0.970  3.732 -2.762 2.00e-02 2.50e+03 1.91e+04
  bond pdb=" CA  ASN B 754 "
       pdb=" HA  ASN B 754 "
    ideal  model  delta    sigma   weight residual
    0.970  3.727 -2.757 2.00e-02 2.50e+03 1.90e+04
  bond pdb=" CA  ASN C 754 "
       pdb=" HA  ASN C 754 "
    ideal  model  delta    sigma   weight residual
    0.970  3.726 -2.756 2.00e-02 2.50e+03 1.90e+04
  bond pdb=" CA  ASN D 754 "
       pdb=" HA  ASN D 754 "
    ideal  model  delta    sigma   weight residual
    0.970  3.718 -2.748 2.00e-02 2.50e+03 1.89e+04
  bond pdb=" CB  ASN D 754 "
       pdb=" HB3 ASN D 754 "
    ideal  model  delta    sigma   weight residual
    0.970  3.322 -2.352 2.00e-02 2.50e+03 1.38e+04
  ... (remaining 36363 not shown)

  Histogram of bond angle deviations from ideal:
       91.17 -   100.35: 88
      100.35 -   109.54: 23905
      109.54 -   118.72: 24048
      118.72 -   127.91: 16139
      127.91 -   137.09: 164
  Bond angle restraints: 64344
  Sorted by residual:
  angle pdb="HD21 ASN D 754 "
        pdb=" ND2 ASN D 754 "
        pdb="HD22 ASN D 754 "
      ideal   model   delta    sigma   weight residual
     120.00   93.00   27.00 3.00e+00 1.11e-01 8.10e+01
  angle pdb="HD21 ASN B 754 "
        pdb=" ND2 ASN B 754 "
        pdb="HD22 ASN B 754 "
      ideal   model   delta    sigma   weight residual
     120.00   93.80   26.20 3.00e+00 1.11e-01 7.63e+01
  angle pdb="HD21 ASN A 754 "
        pdb=" ND2 ASN A 754 "
        pdb="HD22 ASN A 754 "
      ideal   model   delta    sigma   weight residual
     120.00   93.91   26.09 3.00e+00 1.11e-01 7.56e+01
  angle pdb="HD21 ASN C 754 "
        pdb=" ND2 ASN C 754 "
        pdb="HD22 ASN C 754 "
      ideal   model   delta    sigma   weight residual
     120.00   94.35   25.65 3.00e+00 1.11e-01 7.31e+01
  angle pdb=" HB2 ASN D 754 "
        pdb=" CB  ASN D 754 "
        pdb=" HB3 ASN D 754 "
      ideal   model   delta    sigma   weight residual
     110.00   91.17   18.83 3.00e+00 1.11e-01 3.94e+01
  ... (remaining 64339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.65: 16972
       35.65 -    71.30: 641
       71.30 -   106.95: 127
      106.95 -   142.60: 32
      142.60 -   178.25: 28
  Dihedral angle restraints: 17800
    sinusoidal: 10148
      harmonic: 7652
  Sorted by residual:
  dihedral pdb=" CA  LEU D 324 "
           pdb=" C   LEU D 324 "
           pdb=" N   LYS D 325 "
           pdb=" CA  LYS D 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -132.85  -47.15     0      5.00e+00 4.00e-02 8.89e+01
  dihedral pdb=" CA  LEU B 324 "
           pdb=" C   LEU B 324 "
           pdb=" N   LYS B 325 "
           pdb=" CA  LYS B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.89  -47.11     0      5.00e+00 4.00e-02 8.88e+01
  dihedral pdb=" CA  LEU C 324 "
           pdb=" C   LEU C 324 "
           pdb=" N   LYS C 325 "
           pdb=" CA  LYS C 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.90  -47.10     0      5.00e+00 4.00e-02 8.87e+01
  ... (remaining 17797 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.000: 2704
       1.000 -    2.001: 0
       2.001 -    3.001: 0
       3.001 -    4.002: 0
       4.002 -    5.002: 4
  Chirality restraints: 2708
  Sorted by residual:
  chirality pdb=" C5  8IJ C1203 "
            pdb=" C14 8IJ C1203 "
            pdb=" C6  8IJ C1203 "
            pdb=" O4  8IJ C1203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50   -2.50    5.00 2.00e-01 2.50e+01 6.26e+02
  chirality pdb=" C5  8IJ A1202 "
            pdb=" C14 8IJ A1202 "
            pdb=" C6  8IJ A1202 "
            pdb=" O4  8IJ A1202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50   -2.50    5.00 2.00e-01 2.50e+01 6.24e+02
  chirality pdb=" C5  8IJ B1203 "
            pdb=" C14 8IJ B1203 "
            pdb=" C6  8IJ B1203 "
            pdb=" O4  8IJ B1203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50   -2.50    5.00 2.00e-01 2.50e+01 6.24e+02
  ... (remaining 2705 not shown)

  Planarity restraints: 5040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 754 "   -0.207 2.00e-02 2.50e+03   1.83e-01 5.03e+02
        pdb=" CG  ASN C 754 "    0.064 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 754 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 754 "    0.352 2.00e-02 2.50e+03
        pdb="HD21 ASN C 754 "   -0.039 2.00e-02 2.50e+03
        pdb="HD22 ASN C 754 "   -0.169 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 754 "   -0.194 2.00e-02 2.50e+03   1.75e-01 4.58e+02
        pdb=" CG  ASN B 754 "    0.061 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 754 "   -0.006 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 754 "    0.339 2.00e-02 2.50e+03
        pdb="HD21 ASN B 754 "   -0.039 2.00e-02 2.50e+03
        pdb="HD22 ASN B 754 "   -0.160 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 754 "    0.195 2.00e-02 2.50e+03   1.73e-01 4.47e+02
        pdb=" CG  ASN D 754 "   -0.059 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 754 "    0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 754 "   -0.333 2.00e-02 2.50e+03
        pdb="HD21 ASN D 754 "    0.036 2.00e-02 2.50e+03
        pdb="HD22 ASN D 754 "    0.160 2.00e-02 2.50e+03
  ... (remaining 5037 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.26: 4099
        2.26 -     2.84: 80615
        2.84 -     3.43: 95581
        3.43 -     4.01: 135380
        4.01 -     4.60: 211309
  Nonbonded interactions: 526984
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 576 "
            pdb="HH21 ARG B 579 "
     model   vdw
     1.671 1.850
  nonbonded pdb=" OD1 ASP D 576 "
            pdb="HH21 ARG D 579 "
     model   vdw
     1.671 1.850
  nonbonded pdb=" OD1 ASP A 576 "
            pdb="HH21 ARG A 579 "
     model   vdw
     1.671 1.850
  nonbonded pdb=" OD1 ASP C 576 "
            pdb="HH21 ARG C 579 "
     model   vdw
     1.671 1.850
  nonbonded pdb=" O   LYS D 640 "
            pdb=" H   MET D 645 "
     model   vdw
     1.688 1.850
  ... (remaining 526979 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 199 through 754 or resid 1201 or (resid 1205 through 1206  \ 
and (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ 
e C310 or name C311 or name C312 or name C313 or name C314 or name C315 or name  \ 
C316)) or resid 1207 through 1210))
  selection = (chain 'B' and (resid 199 through 754 or resid 1201 or (resid 1205 through 1206  \ 
and (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ 
e C310 or name C311 or name C312 or name C313 or name C314 or name C315 or name  \ 
C316)) or resid 1207 through 1210))
  selection = (chain 'C' and (resid 199 through 754 or resid 1201 or (resid 1205 through 1206  \ 
and (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ 
e C310 or name C311 or name C312 or name C313 or name C314 or name C315 or name  \ 
C316)) or resid 1207 through 1210))
  selection = (chain 'D' and (resid 199 through 754 or resid 1201 or (resid 1205 through 1206  \ 
and (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ 
e C310 or name C311 or name C312 or name C313 or name C314 or name C315 or name  \ 
C316)) or resid 1207 through 1210))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  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:             0.500
  Extract box with map and model:          5.470
  Check model and map are aligned:         0.540
  Set scattering table:                    0.330
  Process input model:                     119.470
  Find NCS groups from input model:        1.820
  Set up NCS constraints:                  0.140
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  141.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
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      :  0.012   0.082  19300  Z= 0.762
  Angle     :  1.200  12.838  25744  Z= 0.547
  Chirality :  0.200   5.002   2708
  Planarity :  0.005   0.052   3012
  Dihedral  : 23.039 178.248   7848
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.93 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -5.15 (0.14), residues: 2068
  helix: -3.40 (0.10), residues: 1196
  sheet: -3.71 (0.45), residues: 76
  loop : -3.15 (0.20), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 698 
 HIS   0.015   0.003   HIS D 411 
 PHE   0.022   0.003   PHE A 522 
 TYR   0.017   0.003   TYR D 383 
 ARG   0.012   0.002   ARG D 499 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 358
  time to evaluate  : 2.707 
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: A  201 LYS cc_start: 0.4748 (tptp) cc_final: 0.4422 (mmtm)
REVERT: A  364 ARG cc_start: 0.6041 (ppt-90) cc_final: 0.5040 (ttt-90)
REVERT: A  367 SER cc_start: 0.7378 (m) cc_final: 0.7027 (m)
REVERT: A  446 MET cc_start: 0.8249 (mmp) cc_final: 0.7618 (mmp)
REVERT: A  503 MET cc_start: 0.5588 (mpt) cc_final: 0.5278 (mpm)
REVERT: A  704 ILE cc_start: 0.8054 (mt) cc_final: 0.7706 (mt)
REVERT: B  201 LYS cc_start: 0.4795 (tptp) cc_final: 0.4443 (mptt)
REVERT: B  364 ARG cc_start: 0.6055 (ppt-90) cc_final: 0.5085 (ttt-90)
REVERT: B  367 SER cc_start: 0.7417 (m) cc_final: 0.7064 (m)
REVERT: B  503 MET cc_start: 0.5669 (mpt) cc_final: 0.5430 (mpm)
REVERT: B  704 ILE cc_start: 0.7909 (mt) cc_final: 0.7561 (mt)
REVERT: C  201 LYS cc_start: 0.4816 (tptp) cc_final: 0.4469 (mptt)
REVERT: C  364 ARG cc_start: 0.6103 (ppt-90) cc_final: 0.5134 (ttt-90)
REVERT: C  367 SER cc_start: 0.7405 (m) cc_final: 0.7064 (m)
REVERT: C  503 MET cc_start: 0.5706 (mpt) cc_final: 0.5474 (mpm)
REVERT: C  704 ILE cc_start: 0.7954 (mt) cc_final: 0.7602 (mt)
REVERT: D  201 LYS cc_start: 0.4567 (tptp) cc_final: 0.4099 (mptt)
REVERT: D  235 ASP cc_start: 0.5343 (m-30) cc_final: 0.4943 (m-30)
REVERT: D  332 LYS cc_start: 0.7619 (mmpt) cc_final: 0.7418 (mmpt)
REVERT: D  364 ARG cc_start: 0.5682 (ppt-90) cc_final: 0.5327 (ptm160)
REVERT: D  367 SER cc_start: 0.7306 (m) cc_final: 0.7037 (m)
REVERT: D  503 MET cc_start: 0.5478 (mpt) cc_final: 0.5155 (mpm)
REVERT: D  704 ILE cc_start: 0.7929 (mt) cc_final: 0.7590 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 358
  average time/residue: 2.8397
  time to fit residues: 1138.6643
Evaluate side-chains
  223 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 2.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 175 optimal weight:    0.7980
   chunk 157 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 163 optimal weight:   20.0000
   chunk 63 optimal weight:    9.9990
   chunk 99 optimal weight:    0.8980
   chunk 121 optimal weight:   10.0000
   chunk 188 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 ASN
B 298 ASN
** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 754 ASN
C 298 ASN
** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 420 ASN
C 754 ASN
D 298 ASN
** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 420 ASN
D 754 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6748
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  19300  Z= 0.190
  Angle     :  0.676   9.510  25744  Z= 0.338
  Chirality :  0.039   0.241   2708
  Planarity :  0.005   0.045   3012
  Dihedral  : 27.930 177.914   3880
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  6.53 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.89 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -3.54 (0.16), residues: 2068
  helix: -1.95 (0.12), residues: 1228
  sheet: -2.95 (0.50), residues: 76
  loop : -2.75 (0.21), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 698 
 HIS   0.004   0.001   HIS B 411 
 PHE   0.015   0.002   PHE D 580 
 TYR   0.022   0.001   TYR A 352 
 ARG   0.003   0.000   ARG B 579 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 233
  time to evaluate  : 2.289 
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: A  201 LYS cc_start: 0.4684 (tptp) cc_final: 0.4392 (mmtt)
REVERT: A  364 ARG cc_start: 0.5911 (ppt-90) cc_final: 0.5013 (ttt-90)
REVERT: A  367 SER cc_start: 0.7214 (m) cc_final: 0.6904 (m)
REVERT: A  446 MET cc_start: 0.8217 (mmp) cc_final: 0.7797 (mmp)
REVERT: A  503 MET cc_start: 0.5547 (mpt) cc_final: 0.5277 (mpm)
REVERT: A  708 ASP cc_start: 0.6816 (m-30) cc_final: 0.6591 (m-30)
REVERT: B  201 LYS cc_start: 0.4746 (tptp) cc_final: 0.4384 (mptt)
REVERT: B  364 ARG cc_start: 0.5907 (ppt-90) cc_final: 0.4981 (ttt-90)
REVERT: B  367 SER cc_start: 0.7193 (m) cc_final: 0.6890 (m)
REVERT: B  496 PHE cc_start: 0.6000 (m-80) cc_final: 0.5787 (m-80)
REVERT: B  503 MET cc_start: 0.5677 (mpt) cc_final: 0.5471 (mpm)
REVERT: B  708 ASP cc_start: 0.6813 (m-30) cc_final: 0.6577 (m-30)
REVERT: C  201 LYS cc_start: 0.4773 (tptp) cc_final: 0.4419 (mptt)
REVERT: C  364 ARG cc_start: 0.5962 (ppt-90) cc_final: 0.5084 (ttt-90)
REVERT: C  367 SER cc_start: 0.7199 (m) cc_final: 0.6896 (m)
REVERT: C  503 MET cc_start: 0.5688 (mpt) cc_final: 0.5483 (mpm)
REVERT: C  708 ASP cc_start: 0.6797 (m-30) cc_final: 0.6567 (m-30)
REVERT: C  725 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6050 (mtmm)
REVERT: D  201 LYS cc_start: 0.4432 (tptp) cc_final: 0.3996 (mptt)
REVERT: D  235 ASP cc_start: 0.5344 (m-30) cc_final: 0.4933 (m-30)
REVERT: D  332 LYS cc_start: 0.7624 (mmpt) cc_final: 0.7416 (mmpt)
REVERT: D  364 ARG cc_start: 0.5666 (ppt-90) cc_final: 0.4661 (ttt-90)
REVERT: D  367 SER cc_start: 0.7096 (m) cc_final: 0.6759 (m)
REVERT: D  446 MET cc_start: 0.7946 (mmp) cc_final: 0.7744 (mmp)
REVERT: D  503 MET cc_start: 0.5480 (mpt) cc_final: 0.5194 (mpm)
REVERT: D  708 ASP cc_start: 0.6837 (m-30) cc_final: 0.6597 (m-30)
  outliers start: 13
  outliers final: 4
  residues processed: 243
  average time/residue: 2.3770
  time to fit residues: 661.4072
Evaluate side-chains
  210 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 205
  time to evaluate  : 2.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  651 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 104 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 157 optimal weight:    8.9990
   chunk 128 optimal weight:    0.9990
   chunk 52 optimal weight:   10.0000
   chunk 189 optimal weight:    6.9990
   chunk 204 optimal weight:    5.9990
   chunk 168 optimal weight:    0.7980
   chunk 187 optimal weight:    0.9980
   chunk 64 optimal weight:   20.0000
   chunk 151 optimal weight:    3.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 ASN
A 688 ASN
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 653 ASN
B 688 ASN
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 653 ASN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 653 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  19300  Z= 0.252
  Angle     :  0.608   7.922  25744  Z= 0.309
  Chirality :  0.037   0.120   2708
  Planarity :  0.004   0.041   3012
  Dihedral  : 25.859 173.336   3880
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.29 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.08 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -2.59 (0.17), residues: 2068
  helix: -1.04 (0.13), residues: 1228
  sheet: -2.62 (0.53), residues: 76
  loop : -2.64 (0.22), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 698 
 HIS   0.003   0.001   HIS C 411 
 PHE   0.016   0.002   PHE A 639 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.005   0.000   ARG D 474 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 2.632 
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: A  201 LYS cc_start: 0.4570 (tptp) cc_final: 0.4237 (mmpt)
REVERT: A  235 ASP cc_start: 0.5458 (m-30) cc_final: 0.5043 (m-30)
REVERT: A  364 ARG cc_start: 0.6166 (ppt-90) cc_final: 0.5322 (ttt90)
REVERT: A  367 SER cc_start: 0.7504 (m) cc_final: 0.7252 (m)
REVERT: A  503 MET cc_start: 0.5624 (mpt) cc_final: 0.5353 (mpm)
REVERT: B  201 LYS cc_start: 0.4670 (tptp) cc_final: 0.4298 (mmpt)
REVERT: B  235 ASP cc_start: 0.5458 (m-30) cc_final: 0.5052 (m-30)
REVERT: B  364 ARG cc_start: 0.6174 (ppt-90) cc_final: 0.5352 (ttt90)
REVERT: B  367 SER cc_start: 0.7473 (m) cc_final: 0.7229 (m)
REVERT: B  503 MET cc_start: 0.5774 (mpt) cc_final: 0.5560 (mpm)
REVERT: C  201 LYS cc_start: 0.4694 (tptp) cc_final: 0.4332 (mmpt)
REVERT: C  235 ASP cc_start: 0.5564 (m-30) cc_final: 0.5141 (m-30)
REVERT: C  364 ARG cc_start: 0.6167 (ppt-90) cc_final: 0.5337 (ttt90)
REVERT: C  367 SER cc_start: 0.7506 (m) cc_final: 0.7256 (m)
REVERT: C  503 MET cc_start: 0.5776 (mpt) cc_final: 0.5567 (mpm)
REVERT: C  725 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6084 (mtmm)
REVERT: D  201 LYS cc_start: 0.4328 (tptp) cc_final: 0.3856 (mmpt)
REVERT: D  235 ASP cc_start: 0.5279 (m-30) cc_final: 0.4881 (m-30)
REVERT: D  332 LYS cc_start: 0.7627 (mmpt) cc_final: 0.7382 (mmpt)
REVERT: D  364 ARG cc_start: 0.5813 (ppt-90) cc_final: 0.4909 (ttt90)
REVERT: D  367 SER cc_start: 0.7500 (m) cc_final: 0.7231 (m)
REVERT: D  503 MET cc_start: 0.5551 (mpt) cc_final: 0.5264 (mpm)
  outliers start: 26
  outliers final: 14
  residues processed: 221
  average time/residue: 2.5878
  time to fit residues: 650.4681
Evaluate side-chains
  204 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 2.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain B residue  305 PHE
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain C residue  305 PHE
Chi-restraints excluded: chain C residue  344 THR
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  305 PHE
Chi-restraints excluded: chain D residue  344 THR
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  483 LEU
Chi-restraints excluded: chain D residue  651 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 186 optimal weight:    0.0980
   chunk 142 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9990
   chunk 189 optimal weight:    6.9990
   chunk 201 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 179 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 ASN
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
C 688 ASN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
D 688 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  19300  Z= 0.165
  Angle     :  0.533   6.328  25744  Z= 0.274
  Chirality :  0.035   0.128   2708
  Planarity :  0.004   0.038   3012
  Dihedral  : 24.389 162.867   3880
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.75 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  7.61 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.89 (0.17), residues: 2068
  helix: -0.38 (0.14), residues: 1232
  sheet: -2.55 (0.52), residues: 76
  loop : -2.53 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 698 
 HIS   0.002   0.001   HIS A 290 
 PHE   0.018   0.001   PHE D 248 
 TYR   0.010   0.001   TYR D 383 
 ARG   0.004   0.000   ARG D 474 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 198
  time to evaluate  : 2.719 
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: A  201 LYS cc_start: 0.4545 (tptp) cc_final: 0.4198 (mmpt)
REVERT: A  235 ASP cc_start: 0.5345 (m-30) cc_final: 0.4943 (m-30)
REVERT: A  364 ARG cc_start: 0.6107 (ppt-90) cc_final: 0.5278 (ttt90)
REVERT: A  367 SER cc_start: 0.7415 (m) cc_final: 0.7158 (m)
REVERT: A  478 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6091 (mp0)
REVERT: A  503 MET cc_start: 0.5613 (mpt) cc_final: 0.5332 (mpm)
REVERT: A  725 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5854 (mtmm)
REVERT: B  201 LYS cc_start: 0.4565 (tptp) cc_final: 0.4181 (mmpt)
REVERT: B  235 ASP cc_start: 0.5404 (m-30) cc_final: 0.4980 (m-30)
REVERT: B  364 ARG cc_start: 0.6114 (ppt-90) cc_final: 0.5314 (ttt90)
REVERT: B  367 SER cc_start: 0.7391 (m) cc_final: 0.7142 (m)
REVERT: B  478 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6186 (mp0)
REVERT: B  503 MET cc_start: 0.5747 (mpt) cc_final: 0.5543 (mpm)
REVERT: B  725 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5863 (mtmm)
REVERT: C  201 LYS cc_start: 0.4645 (tptp) cc_final: 0.4266 (mmpt)
REVERT: C  235 ASP cc_start: 0.5441 (m-30) cc_final: 0.5037 (m-30)
REVERT: C  364 ARG cc_start: 0.6131 (ppt-90) cc_final: 0.5341 (ttt90)
REVERT: C  367 SER cc_start: 0.7405 (m) cc_final: 0.7154 (m)
REVERT: C  478 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6208 (mp0)
REVERT: C  725 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.5944 (mtmm)
REVERT: D  201 LYS cc_start: 0.4330 (tptp) cc_final: 0.3896 (mmpt)
REVERT: D  235 ASP cc_start: 0.5235 (m-30) cc_final: 0.4813 (m-30)
REVERT: D  332 LYS cc_start: 0.7658 (mmpt) cc_final: 0.7388 (mmpt)
REVERT: D  364 ARG cc_start: 0.5848 (ppt-90) cc_final: 0.4946 (ttt90)
REVERT: D  367 SER cc_start: 0.7369 (m) cc_final: 0.7108 (m)
REVERT: D  478 GLU cc_start: 0.6561 (mt-10) cc_final: 0.5913 (mp0)
REVERT: D  503 MET cc_start: 0.5594 (mpt) cc_final: 0.5307 (mpm)
REVERT: D  725 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5865 (mtmm)
  outliers start: 48
  outliers final: 23
  residues processed: 236
  average time/residue: 2.4673
  time to fit residues: 666.0464
Evaluate side-chains
  217 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 190
  time to evaluate  : 2.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  500 ARG
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  725 LYS
Chi-restraints excluded: chain B residue  305 PHE
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  483 LEU
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  725 LYS
Chi-restraints excluded: chain C residue  305 PHE
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  305 PHE
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  483 LEU
Chi-restraints excluded: chain D residue  651 THR
Chi-restraints excluded: chain D residue  725 LYS
Chi-restraints excluded: chain D residue  727 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 167 optimal weight:    9.9990
   chunk 114 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 149 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 171 optimal weight:    6.9990
   chunk 138 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 102 optimal weight:    0.4980
   chunk 180 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 ASN
** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  19300  Z= 0.271
  Angle     :  0.569   5.718  25744  Z= 0.291
  Chirality :  0.037   0.124   2708
  Planarity :  0.004   0.038   3012
  Dihedral  : 23.708 149.626   3880
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.58 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  8.26 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.64 (0.18), residues: 2068
  helix: -0.08 (0.14), residues: 1216
  sheet: -2.67 (0.51), residues: 76
  loop : -2.53 (0.21), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 698 
 HIS   0.003   0.001   HIS D 290 
 PHE   0.028   0.002   PHE B 582 
 TYR   0.011   0.002   TYR B 442 
 ARG   0.007   0.001   ARG C 474 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 210
  time to evaluate  : 2.664 
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: A  201 LYS cc_start: 0.4456 (tptp) cc_final: 0.4055 (mmpt)
REVERT: A  235 ASP cc_start: 0.5310 (m-30) cc_final: 0.4908 (m-30)
REVERT: A  364 ARG cc_start: 0.6221 (ppt-90) cc_final: 0.5479 (ttt90)
REVERT: A  367 SER cc_start: 0.7609 (m) cc_final: 0.7390 (m)
REVERT: A  478 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6149 (mp0)
REVERT: A  503 MET cc_start: 0.5641 (mpt) cc_final: 0.5413 (mpm)
REVERT: A  725 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5888 (mtmm)
REVERT: B  201 LYS cc_start: 0.4537 (tptp) cc_final: 0.4128 (mmpt)
REVERT: B  235 ASP cc_start: 0.5454 (m-30) cc_final: 0.5042 (m-30)
REVERT: B  364 ARG cc_start: 0.6149 (ppt-90) cc_final: 0.5416 (ttt90)
REVERT: B  367 SER cc_start: 0.7663 (m) cc_final: 0.7452 (m)
REVERT: B  404 SER cc_start: 0.7350 (m) cc_final: 0.6945 (p)
REVERT: B  478 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6214 (mp0)
REVERT: B  725 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.5881 (mtmm)
REVERT: C  201 LYS cc_start: 0.4570 (tptp) cc_final: 0.4164 (mmpt)
REVERT: C  235 ASP cc_start: 0.5461 (m-30) cc_final: 0.5062 (m-30)
REVERT: C  364 ARG cc_start: 0.6278 (ppt-90) cc_final: 0.5508 (ttt90)
REVERT: C  367 SER cc_start: 0.7671 (m) cc_final: 0.7459 (m)
REVERT: C  404 SER cc_start: 0.7345 (m) cc_final: 0.6947 (p)
REVERT: C  478 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6234 (mp0)
REVERT: C  725 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.5931 (mtmm)
REVERT: D  201 LYS cc_start: 0.4283 (tptp) cc_final: 0.3792 (mmpt)
REVERT: D  235 ASP cc_start: 0.5215 (m-30) cc_final: 0.4816 (m-30)
REVERT: D  332 LYS cc_start: 0.7646 (mmpt) cc_final: 0.7369 (mmpt)
REVERT: D  364 ARG cc_start: 0.5982 (ppt-90) cc_final: 0.5136 (ttt90)
REVERT: D  367 SER cc_start: 0.7700 (m) cc_final: 0.7479 (m)
REVERT: D  404 SER cc_start: 0.7233 (m) cc_final: 0.6721 (p)
REVERT: D  478 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6033 (mp0)
REVERT: D  503 MET cc_start: 0.5630 (mpt) cc_final: 0.5382 (mpm)
REVERT: D  725 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5766 (mtmm)
  outliers start: 44
  outliers final: 16
  residues processed: 242
  average time/residue: 2.3749
  time to fit residues: 658.9712
Evaluate side-chains
  214 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 194
  time to evaluate  : 2.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  725 LYS
Chi-restraints excluded: chain B residue  305 PHE
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  725 LYS
Chi-restraints excluded: chain C residue  305 PHE
Chi-restraints excluded: chain C residue  312 GLU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  305 PHE
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  483 LEU
Chi-restraints excluded: chain D residue  651 THR
Chi-restraints excluded: chain D residue  678 MET
Chi-restraints excluded: chain D residue  725 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 181 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 118 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 201 optimal weight:    2.9990
   chunk 167 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 ASN
** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  19300  Z= 0.235
  Angle     :  0.536   5.676  25744  Z= 0.277
  Chirality :  0.036   0.121   2708
  Planarity :  0.004   0.056   3012
  Dihedral  : 22.979 143.871   3880
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.09 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.18 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.41 (0.18), residues: 2068
  helix:  0.14 (0.15), residues: 1212
  sheet: -2.78 (0.50), residues: 76
  loop : -2.47 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 698 
 HIS   0.003   0.001   HIS A 290 
 PHE   0.024   0.002   PHE C 582 
 TYR   0.012   0.002   TYR B 511 
 ARG   0.005   0.001   ARG B 474 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 2.394 
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: A  201 LYS cc_start: 0.4504 (tptp) cc_final: 0.4067 (mmpt)
REVERT: A  235 ASP cc_start: 0.5358 (m-30) cc_final: 0.4990 (m-30)
REVERT: A  364 ARG cc_start: 0.6296 (ppt-90) cc_final: 0.5501 (ttt90)
REVERT: A  367 SER cc_start: 0.7664 (m) cc_final: 0.7445 (m)
REVERT: A  404 SER cc_start: 0.7376 (m) cc_final: 0.6927 (p)
REVERT: A  478 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6171 (mp0)
REVERT: A  503 MET cc_start: 0.5698 (mpt) cc_final: 0.5451 (mpm)
REVERT: A  725 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.5861 (mtmm)
REVERT: B  201 LYS cc_start: 0.4592 (tptp) cc_final: 0.4138 (mmpt)
REVERT: B  235 ASP cc_start: 0.5441 (m-30) cc_final: 0.5070 (m-30)
REVERT: B  364 ARG cc_start: 0.6312 (ppt-90) cc_final: 0.5552 (ttt90)
REVERT: B  367 SER cc_start: 0.7632 (m) cc_final: 0.7413 (m)
REVERT: B  404 SER cc_start: 0.7274 (m) cc_final: 0.6970 (p)
REVERT: B  725 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.5851 (mtmm)
REVERT: C  201 LYS cc_start: 0.4625 (tptp) cc_final: 0.4178 (mmpt)
REVERT: C  235 ASP cc_start: 0.5459 (m-30) cc_final: 0.5093 (m-30)
REVERT: C  364 ARG cc_start: 0.6355 (ppt-90) cc_final: 0.5590 (ttt90)
REVERT: C  367 SER cc_start: 0.7654 (m) cc_final: 0.7437 (m)
REVERT: C  404 SER cc_start: 0.7284 (m) cc_final: 0.6972 (p)
REVERT: C  725 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.5912 (mtmm)
REVERT: D  201 LYS cc_start: 0.4307 (tptp) cc_final: 0.3796 (mmpt)
REVERT: D  235 ASP cc_start: 0.5197 (m-30) cc_final: 0.4837 (m-30)
REVERT: D  364 ARG cc_start: 0.6034 (ppt-90) cc_final: 0.5217 (ttt90)
REVERT: D  367 SER cc_start: 0.7704 (m) cc_final: 0.7473 (m)
REVERT: D  404 SER cc_start: 0.7138 (m) cc_final: 0.6771 (p)
REVERT: D  503 MET cc_start: 0.5673 (mpt) cc_final: 0.5418 (mpm)
REVERT: D  725 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5735 (mtmm)
  outliers start: 40
  outliers final: 17
  residues processed: 229
  average time/residue: 2.6116
  time to fit residues: 680.8950
Evaluate side-chains
  208 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 187
  time to evaluate  : 2.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  500 ARG
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  725 LYS
Chi-restraints excluded: chain B residue  305 PHE
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  725 LYS
Chi-restraints excluded: chain C residue  305 PHE
Chi-restraints excluded: chain C residue  312 GLU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  305 PHE
Chi-restraints excluded: chain D residue  312 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  651 THR
Chi-restraints excluded: chain D residue  725 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 194 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 114 optimal weight:    9.9990
   chunk 146 optimal weight:    1.9990
   chunk 113 optimal weight:    8.9990
   chunk 169 optimal weight:    4.9990
   chunk 112 optimal weight:    9.9990
   chunk 200 optimal weight:    0.7980
   chunk 125 optimal weight:   10.0000
   chunk 122 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 ASN
** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  19300  Z= 0.227
  Angle     :  0.526   5.251  25744  Z= 0.272
  Chirality :  0.036   0.124   2708
  Planarity :  0.004   0.038   3012
  Dihedral  : 22.308 141.625   3880
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 19.45
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.24 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  9.40 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.13 (0.18), residues: 2068
  helix:  0.37 (0.15), residues: 1208
  sheet: -2.77 (0.50), residues: 76
  loop : -2.33 (0.21), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 698 
 HIS   0.003   0.001   HIS C 290 
 PHE   0.016   0.002   PHE D 248 
 TYR   0.011   0.001   TYR C 383 
 ARG   0.004   0.000   ARG A 474 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 200
  time to evaluate  : 2.522 
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: A  201 LYS cc_start: 0.4507 (tptp) cc_final: 0.4051 (mmpt)
REVERT: A  235 ASP cc_start: 0.5391 (m-30) cc_final: 0.4967 (m-30)
REVERT: A  364 ARG cc_start: 0.6360 (ppt-90) cc_final: 0.5583 (ttt90)
REVERT: A  367 SER cc_start: 0.7714 (m) cc_final: 0.7487 (m)
REVERT: A  404 SER cc_start: 0.7317 (m) cc_final: 0.6984 (p)
REVERT: A  503 MET cc_start: 0.5712 (mpt) cc_final: 0.5475 (mpm)
REVERT: A  725 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5835 (mtmm)
REVERT: B  201 LYS cc_start: 0.4592 (tptp) cc_final: 0.4125 (mmpt)
REVERT: B  235 ASP cc_start: 0.5435 (m-30) cc_final: 0.5036 (m-30)
REVERT: B  281 ARG cc_start: 0.5403 (mpt-90) cc_final: 0.4952 (mpp-170)
REVERT: B  364 ARG cc_start: 0.6369 (ppt-90) cc_final: 0.5587 (ttt90)
REVERT: B  367 SER cc_start: 0.7747 (m) cc_final: 0.7531 (m)
REVERT: B  404 SER cc_start: 0.7352 (m) cc_final: 0.6966 (p)
REVERT: B  725 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5858 (mtmm)
REVERT: C  201 LYS cc_start: 0.4658 (tptp) cc_final: 0.4191 (mmpt)
REVERT: C  235 ASP cc_start: 0.5446 (m-30) cc_final: 0.5079 (m-30)
REVERT: C  281 ARG cc_start: 0.5391 (mpt-90) cc_final: 0.4961 (mpp-170)
REVERT: C  364 ARG cc_start: 0.6367 (ppt-90) cc_final: 0.5609 (ttt90)
REVERT: C  367 SER cc_start: 0.7711 (m) cc_final: 0.7491 (m)
REVERT: C  404 SER cc_start: 0.7374 (m) cc_final: 0.7010 (p)
REVERT: C  725 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5860 (mtmm)
REVERT: D  235 ASP cc_start: 0.5258 (m-30) cc_final: 0.4860 (m-30)
REVERT: D  281 ARG cc_start: 0.5339 (mpt-90) cc_final: 0.4847 (mpp-170)
REVERT: D  364 ARG cc_start: 0.6073 (ppt-90) cc_final: 0.5273 (ttt90)
REVERT: D  367 SER cc_start: 0.7754 (m) cc_final: 0.7540 (m)
REVERT: D  404 SER cc_start: 0.7159 (m) cc_final: 0.6710 (p)
REVERT: D  503 MET cc_start: 0.5796 (mpt) cc_final: 0.5543 (mpm)
  outliers start: 44
  outliers final: 21
  residues processed: 229
  average time/residue: 2.7362
  time to fit residues: 714.4042
Evaluate side-chains
  214 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 2.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  328 GLU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  725 LYS
Chi-restraints excluded: chain B residue  305 PHE
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  328 GLU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  725 LYS
Chi-restraints excluded: chain C residue  305 PHE
Chi-restraints excluded: chain C residue  312 GLU
Chi-restraints excluded: chain C residue  328 GLU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  305 PHE
Chi-restraints excluded: chain D residue  312 GLU
Chi-restraints excluded: chain D residue  328 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  651 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 124 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 119 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 127 optimal weight:    0.6980
   chunk 136 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 157 optimal weight:   10.0000
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 ASN
** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 ASN
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  19300  Z= 0.252
  Angle     :  0.538   5.556  25744  Z= 0.278
  Chirality :  0.036   0.122   2708
  Planarity :  0.004   0.075   3012
  Dihedral  : 22.193 142.214   3880
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 20.82
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.38 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  :  9.67 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.02 (0.18), residues: 2068
  helix:  0.45 (0.15), residues: 1208
  sheet: -2.80 (0.50), residues: 76
  loop : -2.27 (0.21), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 698 
 HIS   0.004   0.001   HIS A 411 
 PHE   0.016   0.002   PHE C 582 
 TYR   0.012   0.002   TYR A 383 
 ARG   0.007   0.000   ARG B 744 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 197
  time to evaluate  : 2.683 
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: A  201 LYS cc_start: 0.4551 (tptp) cc_final: 0.4064 (mmpt)
REVERT: A  235 ASP cc_start: 0.5360 (m-30) cc_final: 0.5004 (m-30)
REVERT: A  281 ARG cc_start: 0.5402 (mpt-90) cc_final: 0.4953 (mpp-170)
REVERT: A  364 ARG cc_start: 0.6461 (ppt-90) cc_final: 0.5665 (ttt90)
REVERT: A  367 SER cc_start: 0.7865 (m) cc_final: 0.7656 (m)
REVERT: A  404 SER cc_start: 0.7407 (m) cc_final: 0.6990 (p)
REVERT: A  417 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7326 (tp30)
REVERT: A  494 GLN cc_start: 0.6130 (mt0) cc_final: 0.5739 (mm-40)
REVERT: A  503 MET cc_start: 0.5855 (mpt) cc_final: 0.5565 (mpm)
REVERT: A  725 LYS cc_start: 0.6372 (OUTLIER) cc_final: 0.5834 (mtmm)
REVERT: B  201 LYS cc_start: 0.4693 (tptp) cc_final: 0.4186 (mmpt)
REVERT: B  235 ASP cc_start: 0.5432 (m-30) cc_final: 0.5069 (m-30)
REVERT: B  281 ARG cc_start: 0.5409 (mpt-90) cc_final: 0.4965 (mpp-170)
REVERT: B  364 ARG cc_start: 0.6451 (ppt-90) cc_final: 0.5713 (ttt90)
REVERT: B  404 SER cc_start: 0.7521 (m) cc_final: 0.7038 (p)
REVERT: B  494 GLN cc_start: 0.6227 (mt0) cc_final: 0.5884 (mm-40)
REVERT: B  725 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.5910 (mtmm)
REVERT: C  201 LYS cc_start: 0.4731 (tptp) cc_final: 0.4229 (mmpt)
REVERT: C  235 ASP cc_start: 0.5435 (m-30) cc_final: 0.5066 (m-30)
REVERT: C  281 ARG cc_start: 0.5402 (mpt-90) cc_final: 0.4975 (mpp-170)
REVERT: C  364 ARG cc_start: 0.6413 (ppt-90) cc_final: 0.5681 (ttt90)
REVERT: C  367 SER cc_start: 0.7853 (m) cc_final: 0.7652 (m)
REVERT: C  404 SER cc_start: 0.7510 (m) cc_final: 0.7031 (p)
REVERT: C  417 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7330 (tp30)
REVERT: C  494 GLN cc_start: 0.6258 (mt0) cc_final: 0.5898 (mm-40)
REVERT: C  725 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5856 (mtmm)
REVERT: D  235 ASP cc_start: 0.5195 (m-30) cc_final: 0.4838 (m-30)
REVERT: D  281 ARG cc_start: 0.5367 (mpt-90) cc_final: 0.4904 (mpp-170)
REVERT: D  364 ARG cc_start: 0.6185 (ppt-90) cc_final: 0.5351 (ttt90)
REVERT: D  404 SER cc_start: 0.7323 (m) cc_final: 0.6803 (p)
REVERT: D  494 GLN cc_start: 0.6026 (mt0) cc_final: 0.5614 (mm-40)
REVERT: D  503 MET cc_start: 0.5840 (mpt) cc_final: 0.5555 (mpm)
  outliers start: 46
  outliers final: 17
  residues processed: 223
  average time/residue: 2.6718
  time to fit residues: 676.0739
Evaluate side-chains
  208 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 186
  time to evaluate  : 2.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  312 GLU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  678 MET
Chi-restraints excluded: chain A residue  725 LYS
Chi-restraints excluded: chain B residue  305 PHE
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  725 LYS
Chi-restraints excluded: chain C residue  305 PHE
Chi-restraints excluded: chain C residue  312 GLU
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  305 PHE
Chi-restraints excluded: chain D residue  312 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  651 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 182 optimal weight:    0.9980
   chunk 192 optimal weight:    0.9990
   chunk 175 optimal weight:    8.9990
   chunk 186 optimal weight:    0.1980
   chunk 112 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 146 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 168 optimal weight:   10.0000
   chunk 176 optimal weight:    5.9990
   chunk 122 optimal weight:    9.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 ASN
** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
moved from start:          0.4516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  19300  Z= 0.218
  Angle     :  0.516   5.558  25744  Z= 0.268
  Chirality :  0.035   0.125   2708
  Planarity :  0.003   0.039   3012
  Dihedral  : 21.776 140.607   3880
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 20.30
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.33 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.65 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.86 (0.18), residues: 2068
  helix:  0.59 (0.15), residues: 1220
  sheet: -2.84 (0.50), residues: 76
  loop : -2.24 (0.22), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 698 
 HIS   0.003   0.001   HIS C 290 
 PHE   0.013   0.002   PHE D 248 
 TYR   0.011   0.001   TYR B 383 
 ARG   0.001   0.000   ARG B 744 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 194
  time to evaluate  : 2.887 
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: A  201 LYS cc_start: 0.4627 (tptp) cc_final: 0.4128 (mmpt)
REVERT: A  235 ASP cc_start: 0.5358 (m-30) cc_final: 0.4997 (m-30)
REVERT: A  281 ARG cc_start: 0.5392 (mpt-90) cc_final: 0.4942 (mpp-170)
REVERT: A  364 ARG cc_start: 0.6472 (ppt-90) cc_final: 0.5659 (ttt90)
REVERT: A  367 SER cc_start: 0.7791 (m) cc_final: 0.7582 (m)
REVERT: A  404 SER cc_start: 0.7464 (m) cc_final: 0.6964 (p)
REVERT: A  466 MET cc_start: 0.6354 (mtp) cc_final: 0.6072 (mpp)
REVERT: A  494 GLN cc_start: 0.6107 (mt0) cc_final: 0.5721 (mm-40)
REVERT: A  503 MET cc_start: 0.5943 (mpt) cc_final: 0.5621 (mpm)
REVERT: A  725 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5840 (mtmm)
REVERT: B  201 LYS cc_start: 0.4693 (tptp) cc_final: 0.4167 (mmpt)
REVERT: B  235 ASP cc_start: 0.5446 (m-30) cc_final: 0.5059 (m-30)
REVERT: B  281 ARG cc_start: 0.5378 (mpt-90) cc_final: 0.4714 (mtm180)
REVERT: B  364 ARG cc_start: 0.6399 (ppt-90) cc_final: 0.5698 (ttt90)
REVERT: B  404 SER cc_start: 0.7416 (m) cc_final: 0.6997 (p)
REVERT: B  494 GLN cc_start: 0.6214 (mt0) cc_final: 0.5854 (mm-40)
REVERT: B  725 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5921 (mtmm)
REVERT: C  201 LYS cc_start: 0.4749 (tptp) cc_final: 0.4242 (mmpt)
REVERT: C  235 ASP cc_start: 0.5456 (m-30) cc_final: 0.5085 (m-30)
REVERT: C  281 ARG cc_start: 0.5366 (mpt-90) cc_final: 0.4723 (mtm180)
REVERT: C  364 ARG cc_start: 0.6420 (ppt-90) cc_final: 0.5674 (ttt90)
REVERT: C  367 SER cc_start: 0.7784 (m) cc_final: 0.7581 (m)
REVERT: C  404 SER cc_start: 0.7513 (m) cc_final: 0.7071 (p)
REVERT: C  417 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7329 (tp30)
REVERT: C  494 GLN cc_start: 0.6228 (mt0) cc_final: 0.5873 (mm-40)
REVERT: C  636 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7519 (tm)
REVERT: C  725 LYS cc_start: 0.6371 (OUTLIER) cc_final: 0.5841 (mtmm)
REVERT: D  235 ASP cc_start: 0.5220 (m-30) cc_final: 0.4851 (m-30)
REVERT: D  281 ARG cc_start: 0.5354 (mpt-90) cc_final: 0.4668 (mtm180)
REVERT: D  364 ARG cc_start: 0.6115 (ppt-90) cc_final: 0.5309 (ttt90)
REVERT: D  404 SER cc_start: 0.7203 (m) cc_final: 0.6719 (p)
REVERT: D  466 MET cc_start: 0.6363 (mtp) cc_final: 0.6030 (mpp)
REVERT: D  494 GLN cc_start: 0.5986 (mt0) cc_final: 0.5582 (mm-40)
REVERT: D  503 MET cc_start: 0.5875 (mpt) cc_final: 0.5636 (mpm)
REVERT: D  636 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7510 (tm)
  outliers start: 35
  outliers final: 17
  residues processed: 218
  average time/residue: 2.6575
  time to fit residues: 656.2892
Evaluate side-chains
  212 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 189
  time to evaluate  : 2.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  725 LYS
Chi-restraints excluded: chain B residue  305 PHE
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  725 LYS
Chi-restraints excluded: chain C residue  305 PHE
Chi-restraints excluded: chain C residue  312 GLU
Chi-restraints excluded: chain C residue  328 GLU
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  636 LEU
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  305 PHE
Chi-restraints excluded: chain D residue  312 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  553 LEU
Chi-restraints excluded: chain D residue  636 LEU
Chi-restraints excluded: chain D residue  651 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 197 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 137 optimal weight:    6.9990
   chunk 207 optimal weight:   10.0000
   chunk 190 optimal weight:    1.9990
   chunk 165 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 127 optimal weight:    4.9990
   chunk 101 optimal weight:   10.0000
   chunk 131 optimal weight:    9.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 ASN
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 ASN
** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 692 GLN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.4662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  19300  Z= 0.304
  Angle     :  0.561   5.790  25744  Z= 0.289
  Chirality :  0.037   0.119   2708
  Planarity :  0.004   0.071   3012
  Dihedral  : 21.981 143.402   3880
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 21.18
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.19 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.03 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.01 (0.18), residues: 2068
  helix:  0.47 (0.15), residues: 1212
  sheet: -2.81 (0.51), residues: 76
  loop : -2.29 (0.22), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 698 
 HIS   0.005   0.001   HIS A 411 
 PHE   0.016   0.002   PHE C 439 
 TYR   0.013   0.002   TYR B 383 
 ARG   0.006   0.001   ARG A 744 

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

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

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4136 Ramachandran restraints generated.
    2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 183
  time to evaluate  : 2.875 
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: A  201 LYS cc_start: 0.4650 (tptp) cc_final: 0.4126 (mmpt)
REVERT: A  235 ASP cc_start: 0.5340 (m-30) cc_final: 0.4932 (m-30)
REVERT: A  281 ARG cc_start: 0.5440 (mpt-90) cc_final: 0.4750 (mtm180)
REVERT: A  364 ARG cc_start: 0.6540 (ppt-90) cc_final: 0.5771 (ttt90)
REVERT: A  404 SER cc_start: 0.7470 (m) cc_final: 0.6992 (p)
REVERT: A  494 GLN cc_start: 0.6128 (mt0) cc_final: 0.5746 (mm-40)
REVERT: A  503 MET cc_start: 0.5900 (mpt) cc_final: 0.5652 (mpm)
REVERT: A  725 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5896 (mtmm)
REVERT: B  201 LYS cc_start: 0.4655 (tptp) cc_final: 0.4127 (mmtt)
REVERT: B  235 ASP cc_start: 0.5422 (m-30) cc_final: 0.5008 (m-30)
REVERT: B  281 ARG cc_start: 0.5374 (mpt-90) cc_final: 0.4721 (mtm180)
REVERT: B  364 ARG cc_start: 0.6500 (ppt-90) cc_final: 0.5816 (ttt90)
REVERT: B  404 SER cc_start: 0.7537 (m) cc_final: 0.7129 (p)
REVERT: B  494 GLN cc_start: 0.6235 (mt0) cc_final: 0.5877 (mm-40)
REVERT: B  725 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.5894 (mtmm)
REVERT: C  201 LYS cc_start: 0.4695 (tptp) cc_final: 0.4170 (mmtt)
REVERT: C  235 ASP cc_start: 0.5434 (m-30) cc_final: 0.5019 (m-30)
REVERT: C  281 ARG cc_start: 0.5388 (mpt-90) cc_final: 0.4739 (mtm180)
REVERT: C  364 ARG cc_start: 0.6550 (ppt-90) cc_final: 0.5858 (ttt90)
REVERT: C  404 SER cc_start: 0.7443 (m) cc_final: 0.7034 (p)
REVERT: C  417 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7360 (tp30)
REVERT: C  494 GLN cc_start: 0.6245 (mt0) cc_final: 0.5891 (mm-40)
REVERT: C  636 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7509 (tm)
REVERT: C  725 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5941 (mtmm)
REVERT: D  235 ASP cc_start: 0.5206 (m-30) cc_final: 0.4838 (m-30)
REVERT: D  281 ARG cc_start: 0.5359 (mpt-90) cc_final: 0.4707 (mtm180)
REVERT: D  364 ARG cc_start: 0.6237 (ppt-90) cc_final: 0.5445 (ttt90)
REVERT: D  404 SER cc_start: 0.7368 (m) cc_final: 0.6893 (p)
REVERT: D  494 GLN cc_start: 0.5981 (mt0) cc_final: 0.5585 (mm-40)
REVERT: D  503 MET cc_start: 0.5860 (mpt) cc_final: 0.5632 (mpm)
REVERT: D  636 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7497 (tm)
  outliers start: 38
  outliers final: 21
  residues processed: 208
  average time/residue: 2.6222
  time to fit residues: 619.2792
Evaluate side-chains
  205 residues out of total 1840 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 178
  time to evaluate  : 2.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  678 MET
Chi-restraints excluded: chain A residue  725 LYS
Chi-restraints excluded: chain B residue  305 PHE
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  486 VAL
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  725 LYS
Chi-restraints excluded: chain C residue  305 PHE
Chi-restraints excluded: chain C residue  312 GLU
Chi-restraints excluded: chain C residue  328 GLU
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  636 LEU
Chi-restraints excluded: chain C residue  651 THR
Chi-restraints excluded: chain C residue  725 LYS
Chi-restraints excluded: chain D residue  305 PHE
Chi-restraints excluded: chain D residue  312 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  486 VAL
Chi-restraints excluded: chain D residue  553 LEU
Chi-restraints excluded: chain D residue  636 LEU
Chi-restraints excluded: chain D residue  651 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 175 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 152 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 165 optimal weight:    9.9990
   chunk 69 optimal weight:    8.9990
   chunk 169 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 145 optimal weight:    0.5980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 GLN
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 692 GLN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.208113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.154491 restraints weight = 54198.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 1.85
r_work: 0.3664 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3523 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  19300  Z= 0.161
  Angle     :  0.490   6.032  25744  Z= 0.255
  Chirality :  0.034   0.127   2708
  Planarity :  0.003   0.033   3012
  Dihedral  : 21.121 135.739   3880
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 20.17
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.43 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.01 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -0.58 (0.18), residues: 2068
  helix:  0.83 (0.15), residues: 1216
  sheet: -2.81 (0.51), residues: 76
  loop : -2.14 (0.22), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 698 
 HIS   0.003   0.001   HIS C 290 
 PHE   0.012   0.001   PHE D 248 
 TYR   0.009   0.001   TYR A 383 
 ARG   0.002   0.000   ARG A 557 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12622.37 seconds
wall clock time: 221 minutes 29.31 seconds (13289.31 seconds total)