Starting phenix.real_space_refine
on Fri Mar 22 05:21:58 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot2_20192/03_2024/6ot2_20192_neut_trim.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot2_20192/03_2024/6ot2_20192.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot2_20192/03_2024/6ot2_20192.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot2_20192/03_2024/6ot2_20192.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot2_20192/03_2024/6ot2_20192_neut_trim.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot2_20192/03_2024/6ot2_20192_neut_trim.pdb"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C   11344      2.51       5
     N    3000      2.21       5
     O    2932      1.98       5
     H   14975      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A ASP  315": "OD1" <-> "OD2"
    Residue "A PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "A PHE  654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ARG  693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B TYR  208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B ASP  315": "OD1" <-> "OD2"
    Residue "B PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "B PHE  654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ARG  693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D TYR  208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ARG  225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D ASP  315": "OD1" <-> "OD2"
    Residue "D PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ARG  567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "D PHE  654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ARG  693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C TYR  208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ARG  225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C ASP  315": "OD1" <-> "OD2"
    Residue "C PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR  390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ARG  567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
    Residue "C PHE  654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ARG  693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 32311
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 625, 8077
          Classifications: {'peptide': 625}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 11, 'TRANS': 613}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 765
          Unresolved non-hydrogen angles: 953
          Unresolved non-hydrogen dihedrals: 610
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2, 'UNK:plan-1': 14, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 42, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 468
    Chain: "B"
      Number of atoms: 8077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 625, 8077
          Classifications: {'peptide': 625}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 11, 'TRANS': 613}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 765
          Unresolved non-hydrogen angles: 953
          Unresolved non-hydrogen dihedrals: 610
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2, 'UNK:plan-1': 14, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 42, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 468
    Chain: "D"
      Number of atoms: 8080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 625, 8080
          Classifications: {'peptide': 625}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 11, 'TRANS': 613}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 765
          Unresolved non-hydrogen angles: 953
          Unresolved non-hydrogen dihedrals: 610
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2, 'UNK:plan-1': 14, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 42, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 468
    Chain: "C"
      Number of atoms: 8077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 625, 8077
          Classifications: {'peptide': 625}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 11, 'TRANS': 613}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 765
          Unresolved non-hydrogen angles: 953
          Unresolved non-hydrogen dihedrals: 610
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2, 'UNK:plan-1': 14, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 42, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 468
  Time building chain proxies: 14.72, per 1000 atoms: 0.46
  Number of scatterers: 32311
  At special positions: 0
  Unit cell: (140.98, 140.98, 121.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     O    2932      8.00
     N    3000      7.00
     C   11344      6.00
     H   14975      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 24.10
  Conformation dependent library (CDL) restraints added in 3.7 seconds
  

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4784

  Finding SS restraints...
    Secondary structure from input PDB file:
      116 helices and 4 sheets defined
      70.5% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 111 through 130
    Processing helix  chain 'A' and resid 132 through 149
    Processing helix  chain 'A' and resid 155 through 163
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 182 through 198
    Processing helix  chain 'A' and resid 199 through 205
    Processing helix  chain 'A' and resid 217 through 225
      removed outlier: 3.903A  pdb=" N   ILE A 221 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 239
      removed outlier: 3.518A  pdb=" N   GLY A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 239 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 272
    Processing helix  chain 'A' and resid 275 through 284
    Processing helix  chain 'A' and resid 298 through 305
    Processing helix  chain 'A' and resid 315 through 328
      removed outlier: 3.997A  pdb=" N   ARG A 319 " --> pdb=" O   ASP A 315 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ASP A 322 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 351
    Processing helix  chain 'A' and resid 354 through 362
    Processing helix  chain 'A' and resid 367 through 374
    Processing helix  chain 'A' and resid 402 through 409
    Processing helix  chain 'A' and resid 415 through 421
    Processing helix  chain 'A' and resid 422 through 461
      removed outlier: 5.637A  pdb=" N   LYS A 438 " --> pdb=" O   LYS A 434 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   HIS A 439 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   PHE A 442 " --> pdb=" O   LYS A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 507
      removed outlier: 3.622A  pdb=" N   PHE A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU A 491 " --> pdb=" O   ARG A 487 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ILE A 503 " --> pdb=" O   VAL A 499 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ALA A 504 " --> pdb=" O   LYS A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 542
      removed outlier: 3.555A  pdb=" N   PHE A 524 " --> pdb=" O   ALA A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 561
      removed outlier: 3.533A  pdb=" N   CYS A 550 " --> pdb=" O   GLU A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 568
      removed outlier: 3.850A  pdb=" N   ARG A 567 " --> pdb=" O   TYR A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 586
      removed outlier: 3.804A  pdb=" N   TYR A 575 " --> pdb=" O   SER A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 609
      removed outlier: 4.044A  pdb=" N   PHE A 590 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL A 593 " --> pdb=" O   LYS A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 638
    Processing helix  chain 'A' and resid 650 through 680
      removed outlier: 3.635A  pdb=" N   PHE A 654 " --> pdb=" O   TYR A 650 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET A 677 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLY A 678 " --> pdb=" O   ILE A 674 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLU A 679 " --> pdb=" O   ALA A 675 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A 680 " --> pdb=" O   LEU A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 707
    Processing helix  chain 'A' and resid 708 through 716
    Processing helix  chain 'A' and resid 738 through 750
      removed outlier: 3.716A  pdb=" N   ASN A 750 " --> pdb=" O   VAL A 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 130
    Processing helix  chain 'B' and resid 132 through 149
    Processing helix  chain 'B' and resid 155 through 163
    Processing helix  chain 'B' and resid 170 through 178
    Processing helix  chain 'B' and resid 182 through 198
    Processing helix  chain 'B' and resid 199 through 205
    Processing helix  chain 'B' and resid 217 through 225
      removed outlier: 3.903A  pdb=" N   ILE B 221 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 239
      removed outlier: 3.519A  pdb=" N   GLY B 238 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA B 239 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 272
    Processing helix  chain 'B' and resid 275 through 284
    Processing helix  chain 'B' and resid 298 through 305
    Processing helix  chain 'B' and resid 315 through 328
      removed outlier: 3.997A  pdb=" N   ARG B 319 " --> pdb=" O   ASP B 315 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ASP B 322 " --> pdb=" O   LYS B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 351
    Processing helix  chain 'B' and resid 354 through 362
    Processing helix  chain 'B' and resid 367 through 374
    Processing helix  chain 'B' and resid 402 through 409
    Processing helix  chain 'B' and resid 415 through 421
    Processing helix  chain 'B' and resid 422 through 461
      removed outlier: 5.637A  pdb=" N   LYS B 438 " --> pdb=" O   LYS B 434 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   HIS B 439 " --> pdb=" O   LYS B 435 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   PHE B 442 " --> pdb=" O   LYS B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 507
      removed outlier: 3.622A  pdb=" N   PHE B 489 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ILE B 503 " --> pdb=" O   VAL B 499 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ALA B 504 " --> pdb=" O   LYS B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 542
      removed outlier: 3.555A  pdb=" N   PHE B 524 " --> pdb=" O   ALA B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 561
      removed outlier: 3.533A  pdb=" N   CYS B 550 " --> pdb=" O   GLU B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 568
      removed outlier: 3.850A  pdb=" N   ARG B 567 " --> pdb=" O   TYR B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 586
      removed outlier: 3.805A  pdb=" N   TYR B 575 " --> pdb=" O   SER B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 609
      removed outlier: 4.045A  pdb=" N   PHE B 590 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   VAL B 593 " --> pdb=" O   LYS B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 638
    Processing helix  chain 'B' and resid 650 through 680
      removed outlier: 3.636A  pdb=" N   PHE B 654 " --> pdb=" O   TYR B 650 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET B 677 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLY B 678 " --> pdb=" O   ILE B 674 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLU B 679 " --> pdb=" O   ALA B 675 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR B 680 " --> pdb=" O   LEU B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 707
    Processing helix  chain 'B' and resid 708 through 716
    Processing helix  chain 'B' and resid 738 through 750
      removed outlier: 3.716A  pdb=" N   ASN B 750 " --> pdb=" O   VAL B 746 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 130
    Processing helix  chain 'D' and resid 132 through 149
    Processing helix  chain 'D' and resid 155 through 163
    Processing helix  chain 'D' and resid 170 through 178
    Processing helix  chain 'D' and resid 182 through 198
    Processing helix  chain 'D' and resid 199 through 205
    Processing helix  chain 'D' and resid 217 through 225
      removed outlier: 3.904A  pdb=" N   ILE D 221 " --> pdb=" O   THR D 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 239
      removed outlier: 3.518A  pdb=" N   GLY D 238 " --> pdb=" O   LEU D 234 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA D 239 " --> pdb=" O   ILE D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 272
    Processing helix  chain 'D' and resid 275 through 284
    Processing helix  chain 'D' and resid 298 through 305
    Processing helix  chain 'D' and resid 315 through 328
      removed outlier: 3.997A  pdb=" N   ARG D 319 " --> pdb=" O   ASP D 315 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ASP D 322 " --> pdb=" O   LYS D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 343 through 351
    Processing helix  chain 'D' and resid 354 through 362
    Processing helix  chain 'D' and resid 367 through 374
    Processing helix  chain 'D' and resid 402 through 409
    Processing helix  chain 'D' and resid 415 through 421
    Processing helix  chain 'D' and resid 422 through 461
      removed outlier: 5.638A  pdb=" N   LYS D 438 " --> pdb=" O   LYS D 434 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   HIS D 439 " --> pdb=" O   LYS D 435 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   PHE D 442 " --> pdb=" O   LYS D 438 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 481 through 507
      removed outlier: 3.622A  pdb=" N   PHE D 489 " --> pdb=" O   LEU D 485 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU D 491 " --> pdb=" O   ARG D 487 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ILE D 503 " --> pdb=" O   VAL D 499 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ALA D 504 " --> pdb=" O   LYS D 500 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 520 through 542
      removed outlier: 3.555A  pdb=" N   PHE D 524 " --> pdb=" O   ALA D 520 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 546 through 561
      removed outlier: 3.533A  pdb=" N   CYS D 550 " --> pdb=" O   GLU D 546 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 562 through 568
      removed outlier: 3.851A  pdb=" N   ARG D 567 " --> pdb=" O   TYR D 564 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 569 through 586
      removed outlier: 3.804A  pdb=" N   TYR D 575 " --> pdb=" O   SER D 571 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 586 through 609
      removed outlier: 4.045A  pdb=" N   PHE D 590 " --> pdb=" O   ASP D 586 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL D 593 " --> pdb=" O   LYS D 589 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 624 through 638
    Processing helix  chain 'D' and resid 650 through 680
      removed outlier: 3.636A  pdb=" N   PHE D 654 " --> pdb=" O   TYR D 650 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET D 677 " --> pdb=" O   LEU D 673 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLY D 678 " --> pdb=" O   ILE D 674 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLU D 679 " --> pdb=" O   ALA D 675 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR D 680 " --> pdb=" O   LEU D 676 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 683 through 707
    Processing helix  chain 'D' and resid 708 through 716
    Processing helix  chain 'D' and resid 738 through 750
      removed outlier: 3.716A  pdb=" N   ASN D 750 " --> pdb=" O   VAL D 746 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 130
    Processing helix  chain 'C' and resid 132 through 149
    Processing helix  chain 'C' and resid 155 through 163
    Processing helix  chain 'C' and resid 170 through 178
    Processing helix  chain 'C' and resid 182 through 198
    Processing helix  chain 'C' and resid 199 through 205
    Processing helix  chain 'C' and resid 217 through 225
      removed outlier: 3.903A  pdb=" N   ILE C 221 " --> pdb=" O   THR C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 239
      removed outlier: 3.519A  pdb=" N   GLY C 238 " --> pdb=" O   LEU C 234 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA C 239 " --> pdb=" O   ILE C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 272
    Processing helix  chain 'C' and resid 275 through 284
    Processing helix  chain 'C' and resid 298 through 305
    Processing helix  chain 'C' and resid 315 through 328
      removed outlier: 3.997A  pdb=" N   ARG C 319 " --> pdb=" O   ASP C 315 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ASP C 322 " --> pdb=" O   LYS C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 351
    Processing helix  chain 'C' and resid 354 through 362
    Processing helix  chain 'C' and resid 367 through 374
    Processing helix  chain 'C' and resid 402 through 409
    Processing helix  chain 'C' and resid 415 through 421
    Processing helix  chain 'C' and resid 422 through 461
      removed outlier: 5.638A  pdb=" N   LYS C 438 " --> pdb=" O   LYS C 434 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   HIS C 439 " --> pdb=" O   LYS C 435 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   PHE C 442 " --> pdb=" O   LYS C 438 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 481 through 507
      removed outlier: 3.622A  pdb=" N   PHE C 489 " --> pdb=" O   LEU C 485 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU C 491 " --> pdb=" O   ARG C 487 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ILE C 503 " --> pdb=" O   VAL C 499 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ALA C 504 " --> pdb=" O   LYS C 500 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 520 through 542
      removed outlier: 3.555A  pdb=" N   PHE C 524 " --> pdb=" O   ALA C 520 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 546 through 561
      removed outlier: 3.532A  pdb=" N   CYS C 550 " --> pdb=" O   GLU C 546 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 562 through 568
      removed outlier: 3.851A  pdb=" N   ARG C 567 " --> pdb=" O   TYR C 564 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 569 through 586
      removed outlier: 3.803A  pdb=" N   TYR C 575 " --> pdb=" O   SER C 571 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 586 through 609
      removed outlier: 4.045A  pdb=" N   PHE C 590 " --> pdb=" O   ASP C 586 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   VAL C 593 " --> pdb=" O   LYS C 589 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 624 through 638
    Processing helix  chain 'C' and resid 650 through 680
      removed outlier: 3.636A  pdb=" N   PHE C 654 " --> pdb=" O   TYR C 650 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET C 677 " --> pdb=" O   LEU C 673 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLY C 678 " --> pdb=" O   ILE C 674 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLU C 679 " --> pdb=" O   ALA C 675 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR C 680 " --> pdb=" O   LEU C 676 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 683 through 707
    Processing helix  chain 'C' and resid 708 through 716
    Processing helix  chain 'C' and resid 738 through 750
      removed outlier: 3.716A  pdb=" N   ASN C 750 " --> pdb=" O   VAL C 746 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382
      removed outlier: 3.622A  pdb=" N   SER A 387 " --> pdb=" O   ASP A 379 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   ALA A 381 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   VAL A 385 " --> pdb=" O   ALA A 381 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382
      removed outlier: 3.622A  pdb=" N   SER B 387 " --> pdb=" O   ASP B 379 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   ALA B 381 " --> pdb=" O   VAL B 385 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   VAL B 385 " --> pdb=" O   ALA B 381 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 377 through 382
      removed outlier: 3.622A  pdb=" N   SER D 387 " --> pdb=" O   ASP D 379 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   ALA D 381 " --> pdb=" O   VAL D 385 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   VAL D 385 " --> pdb=" O   ALA D 381 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 377 through 382
      removed outlier: 3.622A  pdb=" N   SER C 387 " --> pdb=" O   ASP C 379 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   ALA C 381 " --> pdb=" O   VAL C 385 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   VAL C 385 " --> pdb=" O   ALA C 381 " (cutoff:3.500A)

    1212 hydrogen bonds defined for protein.
    3576 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: 11.68

  Time building geometry restraints manager: 25.33 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 14967
        1.02 -     1.22: 12
        1.22 -     1.41: 7431
        1.41 -     1.61: 10157
        1.61 -     1.81: 100
  Bond restraints: 32667
  Sorted by residual:
  bond pdb=" ND2 ASN B 415 "
       pdb="HD21 ASN B 415 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" ND2 ASN B 415 "
       pdb="HD22 ASN B 415 "
    ideal  model  delta    sigma   weight residual
    0.860  0.980 -0.120 2.00e-02 2.50e+03 3.61e+01
  bond pdb=" ND2 ASN D 415 "
       pdb="HD21 ASN D 415 "
    ideal  model  delta    sigma   weight residual
    0.860  0.980 -0.120 2.00e-02 2.50e+03 3.61e+01
  bond pdb=" ND2 ASN C 415 "
       pdb="HD21 ASN C 415 "
    ideal  model  delta    sigma   weight residual
    0.860  0.980 -0.120 2.00e-02 2.50e+03 3.60e+01
  bond pdb=" ND2 ASN C 415 "
       pdb="HD22 ASN C 415 "
    ideal  model  delta    sigma   weight residual
    0.860  0.980 -0.120 2.00e-02 2.50e+03 3.59e+01
  ... (remaining 32662 not shown)

  Histogram of bond angle deviations from ideal:
       98.48 -   105.59: 259
      105.59 -   112.70: 35465
      112.70 -   119.81: 9059
      119.81 -   126.92: 13321
      126.92 -   134.03: 218
  Bond angle restraints: 58322
  Sorted by residual:
  angle pdb=" C   GLU B 308 "
        pdb=" N   ASP B 309 "
        pdb=" CA  ASP B 309 "
      ideal   model   delta    sigma   weight residual
     121.86  130.82   -8.96 1.65e+00 3.67e-01 2.95e+01
  angle pdb=" C   GLU D 308 "
        pdb=" N   ASP D 309 "
        pdb=" CA  ASP D 309 "
      ideal   model   delta    sigma   weight residual
     121.86  130.81   -8.95 1.65e+00 3.67e-01 2.94e+01
  angle pdb=" C   GLU C 308 "
        pdb=" N   ASP C 309 "
        pdb=" CA  ASP C 309 "
      ideal   model   delta    sigma   weight residual
     121.86  130.80   -8.94 1.65e+00 3.67e-01 2.93e+01
  angle pdb=" C   GLU A 308 "
        pdb=" N   ASP A 309 "
        pdb=" CA  ASP A 309 "
      ideal   model   delta    sigma   weight residual
     121.86  130.79   -8.93 1.65e+00 3.67e-01 2.93e+01
  angle pdb=" C   ARG B 319 "
        pdb=" N   MET B 320 "
        pdb=" CA  MET B 320 "
      ideal   model   delta    sigma   weight residual
     120.28  126.39   -6.11 1.34e+00 5.57e-01 2.08e+01
  ... (remaining 58317 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.81: 14590
       15.81 -    31.61: 967
       31.61 -    47.42: 196
       47.42 -    63.23: 120
       63.23 -    79.03: 8
  Dihedral angle restraints: 15881
    sinusoidal: 7205
      harmonic: 8676
  Sorted by residual:
  dihedral pdb=" CA  UNK D   4 "
           pdb=" C   UNK D   4 "
           pdb=" N   UNK D   5 "
           pdb=" CA  UNK D   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.22  -27.78     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  UNK B   4 "
           pdb=" C   UNK B   4 "
           pdb=" N   UNK B   5 "
           pdb=" CA  UNK B   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.23  -27.77     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  UNK A   4 "
           pdb=" C   UNK A   4 "
           pdb=" N   UNK A   5 "
           pdb=" CA  UNK A   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.24  -27.76     0      5.00e+00 4.00e-02 3.08e+01
  ... (remaining 15878 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1725
       0.031 -    0.062: 752
       0.062 -    0.093: 365
       0.093 -    0.124: 118
       0.124 -    0.155: 44
  Chirality restraints: 3004
  Sorted by residual:
  chirality pdb=" CA  GLU A 308 "
            pdb=" N   GLU A 308 "
            pdb=" C   GLU A 308 "
            pdb=" CB  GLU A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.04e-01
  chirality pdb=" CA  GLU C 308 "
            pdb=" N   GLU C 308 "
            pdb=" C   GLU C 308 "
            pdb=" CB  GLU C 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.94e-01
  chirality pdb=" CA  GLU B 308 "
            pdb=" N   GLU B 308 "
            pdb=" C   GLU B 308 "
            pdb=" CB  GLU B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 3001 not shown)

  Planarity restraints: 5408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 319 "    0.015 2.00e-02 2.50e+03   2.98e-02 8.88e+00
        pdb=" N   MET B 320 "   -0.051 2.00e-02 2.50e+03
        pdb=" CA  MET B 320 "    0.014 2.00e-02 2.50e+03
        pdb=" H   MET B 320 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 319 "    0.015 2.00e-02 2.50e+03   2.98e-02 8.86e+00
        pdb=" N   MET C 320 "   -0.051 2.00e-02 2.50e+03
        pdb=" CA  MET C 320 "    0.014 2.00e-02 2.50e+03
        pdb=" H   MET C 320 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 319 "    0.015 2.00e-02 2.50e+03   2.97e-02 8.85e+00
        pdb=" N   MET D 320 "   -0.051 2.00e-02 2.50e+03
        pdb=" CA  MET D 320 "    0.014 2.00e-02 2.50e+03
        pdb=" H   MET D 320 "    0.022 2.00e-02 2.50e+03
  ... (remaining 5405 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 637
        2.14 -     2.76: 57834
        2.76 -     3.37: 83456
        3.37 -     3.99: 100986
        3.99 -     4.60: 161131
  Nonbonded interactions: 404044
  Sorted by model distance:
  nonbonded pdb=" HG3 LYS A 743 "
            pdb=" HE2 PHE B 316 "
     model   vdw
     1.528 2.270
  nonbonded pdb=" HG3 LYS B 743 "
            pdb=" HE2 PHE C 316 "
     model   vdw
     1.531 2.270
  nonbonded pdb=" HE2 PHE A 316 "
            pdb=" HG3 LYS D 743 "
     model   vdw
     1.534 2.270
  nonbonded pdb=" HE2 PHE D 316 "
            pdb=" HG3 LYS C 743 "
     model   vdw
     1.535 2.270
  nonbonded pdb=" O   LEU D 563 "
            pdb=" HG1 THR D 566 "
     model   vdw
     1.661 1.850
  ... (remaining 404039 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = (chain 'D' and (resid 1 through 168 or (resid 169 and (name N or name CA or name \ 
 C or name O or name CB or name H or name HA )) or resid 170 through 750))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             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:             0.560
  Extract box with map and model:          5.560
  Check model and map are aligned:         0.500
  Set scattering table:                    0.310
  Process input model:                     96.980
  Find NCS groups from input model:        1.690
  Set up NCS constraints:                  0.160
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.020
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  109.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.075  17692  Z= 0.621
  Angle     :  0.873   8.962  24240  Z= 0.519
  Chirality :  0.046   0.155   3004
  Planarity :  0.005   0.045   3024
  Dihedral  :  8.411  43.917   5404
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.15), residues: 2412
  helix: -0.89 (0.11), residues: 1668
  sheet: -2.72 (0.55), residues: 68
  loop : -2.62 (0.21), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP D 493 
 HIS   0.006   0.002   HIS D 160 
 PHE   0.030   0.003   PHE A 526 
 TYR   0.022   0.003   TYR C 460 
 ARG   0.014   0.002   ARG C 375 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  337 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 2.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  691 ILE cc_start: 0.9378 (mt) cc_final: 0.9178 (tp)
REVERT: B  691 ILE cc_start: 0.9369 (mt) cc_final: 0.9167 (tp)
REVERT: D  691 ILE cc_start: 0.9368 (mt) cc_final: 0.9164 (tp)
REVERT: C  691 ILE cc_start: 0.9368 (mt) cc_final: 0.9165 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.5702
  time to fit residues: 286.5141
Evaluate side-chains
  218 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 2.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 209 optimal weight:    4.9990
   chunk 187 optimal weight:   30.0000
   chunk 104 optimal weight:    0.7980
   chunk 64 optimal weight:   20.0000
   chunk 126 optimal weight:   20.0000
   chunk 100 optimal weight:    6.9990
   chunk 194 optimal weight:    0.3980
   chunk 75 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 144 optimal weight:    0.6980
   chunk 225 optimal weight:   10.0000
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 671 ASN
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 671 ASN
** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 671 ASN
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  17692  Z= 0.183
  Angle     :  0.507   5.045  24240  Z= 0.282
  Chirality :  0.034   0.130   3004
  Planarity :  0.003   0.037   3024
  Dihedral  :  4.264  22.320   2640
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.12 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.17), residues: 2412
  helix:  0.80 (0.12), residues: 1676
  sheet: -2.12 (0.57), residues: 64
  loop : -2.48 (0.21), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 559 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.017   0.001   PHE D 654 
 TYR   0.015   0.002   TYR D 359 
 ARG   0.002   0.000   ARG D 693 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  300 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 296
  time to evaluate  : 2.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  691 ILE cc_start: 0.9362 (mt) cc_final: 0.9133 (tp)
REVERT: B  691 ILE cc_start: 0.9363 (mt) cc_final: 0.9130 (tp)
REVERT: D  691 ILE cc_start: 0.9361 (mt) cc_final: 0.9130 (tp)
REVERT: C  691 ILE cc_start: 0.9365 (mt) cc_final: 0.9131 (tp)
  outliers start: 4
  outliers final: 4
  residues processed: 300
  average time/residue: 0.4452
  time to fit residues: 222.9167
Evaluate side-chains
  216 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 212
  time to evaluate  : 2.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 125 optimal weight:   40.0000
   chunk 69 optimal weight:    7.9990
   chunk 187 optimal weight:   40.0000
   chunk 153 optimal weight:    2.9990
   chunk 62 optimal weight:   20.0000
   chunk 225 optimal weight:    9.9990
   chunk 243 optimal weight:    3.9990
   chunk 200 optimal weight:   10.0000
   chunk 223 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 180 optimal weight:    7.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055  17692  Z= 0.524
  Angle     :  0.730   7.040  24240  Z= 0.410
  Chirality :  0.039   0.130   3004
  Planarity :  0.005   0.040   3024
  Dihedral  :  4.790  26.676   2640
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.16 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.17), residues: 2412
  helix:  0.32 (0.12), residues: 1672
  sheet: -1.37 (0.66), residues: 56
  loop : -2.42 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 559 
 HIS   0.007   0.002   HIS D 284 
 PHE   0.023   0.003   PHE A 259 
 TYR   0.025   0.003   TYR A 208 
 ARG   0.006   0.001   ARG A 375 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  238 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 2.547 
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  653 LEU cc_start: 0.9108 (tp) cc_final: 0.8831 (mm)
REVERT: A  691 ILE cc_start: 0.9361 (mt) cc_final: 0.9140 (tp)
REVERT: B  653 LEU cc_start: 0.9113 (tp) cc_final: 0.8843 (mm)
REVERT: B  691 ILE cc_start: 0.9360 (mt) cc_final: 0.9135 (tp)
REVERT: B  701 LEU cc_start: 0.9293 (tp) cc_final: 0.8955 (tt)
REVERT: D  691 ILE cc_start: 0.9364 (mt) cc_final: 0.9143 (tp)
REVERT: C  653 LEU cc_start: 0.9112 (tp) cc_final: 0.8844 (mm)
REVERT: C  691 ILE cc_start: 0.9358 (mt) cc_final: 0.9137 (tp)
REVERT: C  701 LEU cc_start: 0.9297 (tp) cc_final: 0.8959 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.4729
  time to fit residues: 189.6123
Evaluate side-chains
  196 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 2.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 222 optimal weight:   10.0000
   chunk 169 optimal weight:    9.9990
   chunk 117 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 151 optimal weight:    0.9990
   chunk 226 optimal weight:    1.9990
   chunk 239 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 214 optimal weight:    3.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 301 HIS
A 671 ASN
B 301 HIS
B 671 ASN
** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 HIS
D 671 ASN
C 301 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  17692  Z= 0.211
  Angle     :  0.483   4.654  24240  Z= 0.272
  Chirality :  0.034   0.132   3004
  Planarity :  0.003   0.031   3024
  Dihedral  :  4.068  22.735   2640
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.17), residues: 2412
  helix:  1.27 (0.13), residues: 1672
  sheet: -1.03 (0.70), residues: 56
  loop : -2.19 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 559 
 HIS   0.002   0.001   HIS C 160 
 PHE   0.012   0.001   PHE C 654 
 TYR   0.015   0.002   TYR D 451 
 ARG   0.003   0.000   ARG A 363 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  271 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 2.517 
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  691 ILE cc_start: 0.9307 (mt) cc_final: 0.9084 (tp)
REVERT: B  691 ILE cc_start: 0.9304 (mt) cc_final: 0.9082 (tp)
REVERT: B  701 LEU cc_start: 0.9240 (tp) cc_final: 0.9028 (tt)
REVERT: D  691 ILE cc_start: 0.9306 (mt) cc_final: 0.9086 (tp)
REVERT: C  672 MET cc_start: 0.9040 (tmm) cc_final: 0.8818 (tmm)
REVERT: C  691 ILE cc_start: 0.9303 (mt) cc_final: 0.9084 (tp)
REVERT: C  701 LEU cc_start: 0.9244 (tp) cc_final: 0.9033 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.4210
  time to fit residues: 190.9364
Evaluate side-chains
  232 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 2.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 199 optimal weight:    2.9990
   chunk 136 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 178 optimal weight:    5.9990
   chunk 98 optimal weight:   10.0000
   chunk 204 optimal weight:    6.9990
   chunk 165 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 122 optimal weight:    0.5980
   chunk 215 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
B 671 ASN
D 671 ASN
C 671 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  17692  Z= 0.167
  Angle     :  0.455   4.734  24240  Z= 0.254
  Chirality :  0.033   0.130   3004
  Planarity :  0.003   0.030   3024
  Dihedral  :  3.781  27.632   2640
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.18), residues: 2412
  helix:  1.72 (0.13), residues: 1704
  sheet: -0.81 (0.72), residues: 56
  loop : -2.12 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 559 
 HIS   0.002   0.000   HIS D 160 
 PHE   0.012   0.001   PHE C 654 
 TYR   0.010   0.001   TYR A 390 
 ARG   0.005   0.000   ARG B 295 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  273 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 2.486 
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  672 MET cc_start: 0.9094 (tmm) cc_final: 0.8873 (tmm)
REVERT: B  672 MET cc_start: 0.9085 (tmm) cc_final: 0.8870 (tmm)
REVERT: B  701 LEU cc_start: 0.9240 (tp) cc_final: 0.9025 (tt)
REVERT: D  672 MET cc_start: 0.9083 (tmm) cc_final: 0.8864 (tmm)
REVERT: C  672 MET cc_start: 0.9080 (tmm) cc_final: 0.8878 (tmm)
REVERT: C  701 LEU cc_start: 0.9245 (tp) cc_final: 0.9031 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.4261
  time to fit residues: 194.4047
Evaluate side-chains
  231 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 2.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 215 optimal weight:    0.2980
   chunk 47 optimal weight:    4.9990
   chunk 140 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 239 optimal weight:    4.9990
   chunk 199 optimal weight:    6.9990
   chunk 111 optimal weight:    0.0010
   chunk 19 optimal weight:   10.0000
   chunk 79 optimal weight:    0.8980
   chunk 125 optimal weight:   40.0000
   overall best weight:    1.6390

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
B 671 ASN
D 671 ASN
C 671 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  17692  Z= 0.154
  Angle     :  0.432   4.612  24240  Z= 0.242
  Chirality :  0.033   0.127   3004
  Planarity :  0.002   0.031   3024
  Dihedral  :  3.580  24.412   2640
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.18), residues: 2412
  helix:  1.98 (0.13), residues: 1704
  sheet: -1.03 (0.63), residues: 64
  loop : -2.04 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 559 
 HIS   0.003   0.000   HIS A 439 
 PHE   0.009   0.001   PHE D 259 
 TYR   0.010   0.001   TYR A 390 
 ARG   0.002   0.000   ARG B 295 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  264 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 2.545 
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  692 TRP cc_start: 0.8375 (t60) cc_final: 0.7956 (t60)
REVERT: B  692 TRP cc_start: 0.8373 (t60) cc_final: 0.7956 (t60)
REVERT: B  701 LEU cc_start: 0.9249 (tp) cc_final: 0.8909 (tt)
REVERT: D  692 TRP cc_start: 0.8361 (t60) cc_final: 0.7946 (t60)
REVERT: C  692 TRP cc_start: 0.8374 (t60) cc_final: 0.7956 (t60)
REVERT: C  701 LEU cc_start: 0.9253 (tp) cc_final: 0.8913 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.4289
  time to fit residues: 191.2006
Evaluate side-chains
  227 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 2.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 231 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 136 optimal weight:    4.9990
   chunk 175 optimal weight:    7.9990
   chunk 135 optimal weight:    0.9980
   chunk 201 optimal weight:    0.9980
   chunk 133 optimal weight:    9.9990
   chunk 239 optimal weight:    4.9990
   chunk 149 optimal weight:    1.9990
   chunk 145 optimal weight:    4.9990
   chunk 110 optimal weight:    0.1980
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
B 671 ASN
D 671 ASN
C 671 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  17692  Z= 0.164
  Angle     :  0.436   4.701  24240  Z= 0.243
  Chirality :  0.033   0.126   3004
  Planarity :  0.002   0.027   3024
  Dihedral  :  3.464  23.417   2640
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.18), residues: 2412
  helix:  2.14 (0.13), residues: 1708
  sheet: -1.06 (0.61), residues: 64
  loop : -2.04 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 559 
 HIS   0.002   0.001   HIS B 439 
 PHE   0.011   0.001   PHE A 436 
 TYR   0.017   0.001   TYR A 213 
 ARG   0.002   0.000   ARG B 375 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  276 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 2.291 
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  653 LEU cc_start: 0.8898 (tp) cc_final: 0.8658 (mm)
REVERT: A  692 TRP cc_start: 0.8385 (t60) cc_final: 0.7988 (t60)
REVERT: A  701 LEU cc_start: 0.9357 (tp) cc_final: 0.9151 (tt)
REVERT: B  653 LEU cc_start: 0.8895 (tp) cc_final: 0.8650 (mm)
REVERT: B  692 TRP cc_start: 0.8397 (t60) cc_final: 0.7978 (t60)
REVERT: B  701 LEU cc_start: 0.9264 (tp) cc_final: 0.8928 (tt)
REVERT: D  653 LEU cc_start: 0.8901 (tp) cc_final: 0.8649 (mm)
REVERT: D  672 MET cc_start: 0.8853 (tmm) cc_final: 0.8630 (tmm)
REVERT: D  692 TRP cc_start: 0.8391 (t60) cc_final: 0.7975 (t60)
REVERT: C  653 LEU cc_start: 0.8892 (tp) cc_final: 0.8653 (mm)
REVERT: C  692 TRP cc_start: 0.8398 (t60) cc_final: 0.7983 (t60)
REVERT: C  701 LEU cc_start: 0.9267 (tp) cc_final: 0.8933 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.4817
  time to fit residues: 222.5170
Evaluate side-chains
  230 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 2.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 147 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 142 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 151 optimal weight:    6.9990
   chunk 162 optimal weight:   10.0000
   chunk 118 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 187 optimal weight:   40.0000
   chunk 217 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 671 ASN
** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  17692  Z= 0.386
  Angle     :  0.594   4.794  24240  Z= 0.332
  Chirality :  0.036   0.122   3004
  Planarity :  0.004   0.031   3024
  Dihedral  :  3.992  23.520   2640
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.17), residues: 2412
  helix:  1.48 (0.12), residues: 1692
  sheet: -1.27 (0.65), residues: 56
  loop : -2.26 (0.23), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 739 
 HIS   0.005   0.001   HIS A 439 
 PHE   0.016   0.002   PHE A 259 
 TYR   0.021   0.002   TYR A 208 
 ARG   0.005   0.001   ARG A 375 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  242 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 2.866 
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  653 LEU cc_start: 0.9088 (tp) cc_final: 0.8754 (mm)
REVERT: B  653 LEU cc_start: 0.9079 (tp) cc_final: 0.8758 (mm)
REVERT: B  701 LEU cc_start: 0.9319 (tp) cc_final: 0.9010 (tt)
REVERT: D  653 LEU cc_start: 0.9086 (tp) cc_final: 0.8761 (mm)
REVERT: C  653 LEU cc_start: 0.9086 (tp) cc_final: 0.8763 (mm)
REVERT: C  701 LEU cc_start: 0.9319 (tp) cc_final: 0.9014 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.4416
  time to fit residues: 178.9504
Evaluate side-chains
  218 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 2.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 228 optimal weight:    3.9990
   chunk 208 optimal weight:    1.9990
   chunk 222 optimal weight:   10.0000
   chunk 134 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 174 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 201 optimal weight:    0.4980
   chunk 210 optimal weight:    0.5980
   chunk 221 optimal weight:    0.8980
   chunk 146 optimal weight:    4.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
B 671 ASN
D 671 ASN
C 671 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  17692  Z= 0.145
  Angle     :  0.452   5.269  24240  Z= 0.250
  Chirality :  0.033   0.125   3004
  Planarity :  0.002   0.026   3024
  Dihedral  :  3.598  28.350   2640
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.18), residues: 2412
  helix:  2.16 (0.13), residues: 1684
  sheet: -1.18 (0.61), residues: 64
  loop : -2.00 (0.24), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 559 
 HIS   0.002   0.000   HIS D 745 
 PHE   0.023   0.001   PHE A 447 
 TYR   0.011   0.001   TYR C 260 
 ARG   0.002   0.000   ARG D 375 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  281 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 2.430 
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  653 LEU cc_start: 0.8982 (tp) cc_final: 0.8684 (mm)
REVERT: B  653 LEU cc_start: 0.8959 (tp) cc_final: 0.8689 (mm)
REVERT: B  701 LEU cc_start: 0.9261 (tp) cc_final: 0.8920 (tt)
REVERT: D  653 LEU cc_start: 0.8975 (tp) cc_final: 0.8687 (mm)
REVERT: C  653 LEU cc_start: 0.8964 (tp) cc_final: 0.8692 (mm)
REVERT: C  701 LEU cc_start: 0.9264 (tp) cc_final: 0.8925 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.4324
  time to fit residues: 203.3941
Evaluate side-chains
  240 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 2.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 235 optimal weight:    3.9990
   chunk 143 optimal weight:    0.9980
   chunk 111 optimal weight:   10.0000
   chunk 163 optimal weight:   10.0000
   chunk 247 optimal weight:    2.9990
   chunk 227 optimal weight:   10.0000
   chunk 196 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 151 optimal weight:    6.9990
   chunk 120 optimal weight:    7.9990
   chunk 156 optimal weight:    4.9990
   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 671 ASN
B 671 ASN
D 671 ASN
C 671 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.4994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  17692  Z= 0.213
  Angle     :  0.479   5.271  24240  Z= 0.265
  Chirality :  0.033   0.124   3004
  Planarity :  0.003   0.025   3024
  Dihedral  :  3.632  28.807   2640
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.18), residues: 2412
  helix:  2.14 (0.13), residues: 1688
  sheet: -1.16 (0.61), residues: 64
  loop : -1.96 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 710 
 HIS   0.003   0.001   HIS A 439 
 PHE   0.011   0.001   PHE A 436 
 TYR   0.011   0.002   TYR B 359 
 ARG   0.004   0.000   ARG C 371 

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

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

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4824 Ramachandran restraints generated.
    2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Residue LYS  115 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue LEU  119 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  121 is missing expected H atoms. Skipping.
Residue ILE  123 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue SER  128 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue VAL  136 is missing expected H atoms. Skipping.
Residue LEU  138 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue LEU  142 is missing expected H atoms. Skipping.
Residue LEU  145 is missing expected H atoms. Skipping.
Residue MET  159 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue THR  163 is missing expected H atoms. Skipping.
Residue SER  165 is missing expected H atoms. Skipping.
Residue THR  167 is missing expected H atoms. Skipping.
Residue ALA  169 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue ILE  179 is missing expected H atoms. Skipping.
Residue THR  183 is missing expected H atoms. Skipping.
Residue LYS  184 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue ILE  199 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue LEU  234 is missing expected H atoms. Skipping.
Residue ILE  235 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue TYR  254 is missing expected H atoms. Skipping.
Residue LYS  311 is missing expected H atoms. Skipping.
Residue MET  320 is missing expected H atoms. Skipping.
Residue MET  323 is missing expected H atoms. Skipping.
Residue LEU  326 is missing expected H atoms. Skipping.
Residue THR  335 is missing expected H atoms. Skipping.
Residue LYS  366 is missing expected H atoms. Skipping.
Residue LYS  368 is missing expected H atoms. Skipping.
Residue SER  372 is missing expected H atoms. Skipping.
Residue LEU  373 is missing expected H atoms. Skipping.
Residue SER  374 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue LYS  438 is missing expected H atoms. Skipping.
Residue LEU  482 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue LEU  485 is missing expected H atoms. Skipping.
Residue MET  488 is missing expected H atoms. Skipping.
Residue LEU  491 is missing expected H atoms. Skipping.
Residue ILE  492 is missing expected H atoms. Skipping.
Residue MET  495 is missing expected H atoms. Skipping.
Residue SER  498 is missing expected H atoms. Skipping.
Residue VAL  499 is missing expected H atoms. Skipping.
Residue LYS  500 is missing expected H atoms. Skipping.
Residue ILE  503 is missing expected H atoms. Skipping.
Residue ILE  505 is missing expected H atoms. Skipping.
Residue LEU  507 is missing expected H atoms. Skipping.
Residue LEU  508 is missing expected H atoms. Skipping.
Residue SER  518 is missing expected H atoms. Skipping.
Residue ILE  534 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  537 is missing expected H atoms. Skipping.
Residue LEU  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LYS  545 is missing expected H atoms. Skipping.
Residue MET  572 is missing expected H atoms. Skipping.
Residue MET  574 is missing expected H atoms. Skipping.
Residue VAL  577 is missing expected H atoms. Skipping.
Residue MET  578 is missing expected H atoms. Skipping.
Residue ILE  579 is missing expected H atoms. Skipping.
Residue ILE  583 is missing expected H atoms. Skipping.
Residue LEU  584 is missing expected H atoms. Skipping.
Residue ILE  609 is missing expected H atoms. Skipping.
Residue LYS  611 is missing expected H atoms. Skipping.
Residue LYS  614 is missing expected H atoms. Skipping.
Residue LYS  617 is missing expected H atoms. Skipping.
Residue SER  624 is missing expected H atoms. Skipping.
Residue SER  648 is missing expected H atoms. Skipping.
Residue LYS  649 is missing expected H atoms. Skipping.
Residue VAL  681 is missing expected H atoms. Skipping.
Residue VAL  684 is missing expected H atoms. Skipping.
Residue SER  685 is missing expected H atoms. Skipping.
Residue ILE  700 is missing expected H atoms. Skipping.
Residue LYS  705 is missing expected H atoms. Skipping.
Residue MET  706 is missing expected H atoms. Skipping.
Residue LEU  711 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue LYS  738 is missing expected H atoms. Skipping.
Residue LEU  749 is missing expected H atoms. Skipping.
Evaluate side-chains
  261 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 2.500 
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  653 LEU cc_start: 0.9026 (tp) cc_final: 0.8709 (mm)
REVERT: B  653 LEU cc_start: 0.9022 (tp) cc_final: 0.8714 (mm)
REVERT: B  701 LEU cc_start: 0.9278 (tp) cc_final: 0.8948 (tt)
REVERT: D  653 LEU cc_start: 0.9031 (tp) cc_final: 0.8706 (mm)
REVERT: C  653 LEU cc_start: 0.9020 (tp) cc_final: 0.8714 (mm)
REVERT: C  701 LEU cc_start: 0.9285 (tp) cc_final: 0.8952 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.4438
  time to fit residues: 191.6368
Evaluate side-chains
  234 residues out of total 2160 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 2.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 209 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 181 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 197 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9990
   chunk 202 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 173 optimal weight:    0.0670
   overall best weight:    1.3922

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
B 671 ASN
D 671 ASN
C 671 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.106208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.090468 restraints weight = 143848.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.094250 restraints weight = 62418.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.096583 restraints weight = 34831.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.5067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  17692  Z= 0.137
  Angle     :  0.434   5.488  24240  Z= 0.238
  Chirality :  0.033   0.124   3004
  Planarity :  0.002   0.025   3024
  Dihedral  :  3.414  28.211   2640
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.18), residues: 2412
  helix:  2.36 (0.13), residues: 1716
  sheet: -1.04 (0.62), residues: 64
  loop : -1.97 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 559 
 HIS   0.001   0.000   HIS B 439 
 PHE   0.009   0.001   PHE B 259 
 TYR   0.010   0.001   TYR B 451 
 ARG   0.002   0.000   ARG D 375 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5290.93 seconds
wall clock time: 94 minutes 20.91 seconds (5660.91 seconds total)