Starting phenix.real_space_refine
on Wed Mar  4 20:15:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kdp_22828/03_2026/7kdp_22828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kdp_22828/03_2026/7kdp_22828.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kdp_22828/03_2026/7kdp_22828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kdp_22828/03_2026/7kdp_22828.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kdp_22828/03_2026/7kdp_22828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kdp_22828/03_2026/7kdp_22828.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      84      5.16       5
     C   10065      2.51       5
     N    2616      2.21       5
     O    3060      1.98       5
     F      18      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15844
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 638, 5107
          Classifications: {'peptide': 638}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 617}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 5107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 638, 5107
          Classifications: {'peptide': 638}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 617}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 5107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 638, 5107
          Classifications: {'peptide': 638}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 617}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 175
          Unusual residues: {' CA': 1, 'NAG': 10, 'WCY': 1}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "B"
      Number of atoms: 174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 174
          Unusual residues: {'NAG': 10, 'WCY': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "C"
      Number of atoms: 174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 174
          Unusual residues: {'NAG': 10, 'WCY': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
  Time building chain proxies: 3.79, per 1000 atoms: 0.24
  Number of scatterers: 15844
  At special positions: 0
  Unit cell: (126.592, 125.216, 156.864, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      84     16.00
     F      18      9.00
     O    3060      8.00
     N    2616      7.00
     C   10065      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  94 " - pdb=" SG  CYS A 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 111 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 185 " - pdb=" SG  CYS A 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 391 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 574 " - pdb=" SG  CYS A 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 111 " - pdb=" SG  CYS B 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 344 " - pdb=" SG  CYS B 391 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 574 " - pdb=" SG  CYS B 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 111 " - pdb=" SG  CYS C 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 185 " - pdb=" SG  CYS C 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 344 " - pdb=" SG  CYS C 391 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 574 " - pdb=" SG  CYS C 611 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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
  Links applied
    NAG-ASN
      " NAG A1001 " - " ASN A 208 "
      " NAG A1002 " - " ASN A 281 "
      " NAG A1003 " - " ASN A 286 "
      " NAG A1004 " - " ASN A 302 "
      " NAG A1005 " - " ASN A 341 "
      " NAG A1006 " - " ASN A 383 "
      " NAG A1007 " - " ASN A 405 "
      " NAG A1008 " - " ASN A 417 "
      " NAG A1009 " - " ASN A 555 "
      " NAG A1010 " - " ASN A 586 "
      " NAG B1102 " - " ASN B 208 "
      " NAG B1103 " - " ASN B 281 "
      " NAG B1104 " - " ASN B 286 "
      " NAG B1105 " - " ASN B 302 "
      " NAG B1106 " - " ASN B 341 "
      " NAG B1107 " - " ASN B 383 "
      " NAG B1108 " - " ASN B 405 "
      " NAG B1109 " - " ASN B 417 "
      " NAG B1110 " - " ASN B 555 "
      " NAG B1111 " - " ASN B 586 "
      " NAG C1102 " - " ASN C 208 "
      " NAG C1103 " - " ASN C 281 "
      " NAG C1104 " - " ASN C 286 "
      " NAG C1105 " - " ASN C 302 "
      " NAG C1106 " - " ASN C 341 "
      " NAG C1107 " - " ASN C 383 "
      " NAG C1108 " - " ASN C 405 "
      " NAG C1109 " - " ASN C 417 "
      " NAG C1110 " - " ASN C 555 "
      " NAG C1111 " - " ASN C 586 "
  Time building additional restraints: 1.37
  Conformation dependent library (CDL) restraints added in 621.8 milliseconds
  

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3642

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 27 sheets defined
      27.1% alpha, 19.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 172 through 183
    Processing helix  chain 'A' and resid 391 through 408
      removed outlier: 4.736A  pdb=" N   GLU A 395 " --> pdb=" O   CYS A 391 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ILE A 397 " --> pdb=" O   ARG A 393 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASN A 398 " --> pdb=" O   ASP A 394 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   LYS A 399 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   LEU A 400 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 521
      removed outlier: 4.725A  pdb=" N   VAL A 508 " --> pdb=" O   GLU A 504 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   ASP A 509 " --> pdb=" O   ALA A 505 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLN A 510 " --> pdb=" O   TRP A 506 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ARG A 511 " --> pdb=" O   CYS A 507 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLU A 519 " --> pdb=" O   GLU A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 534
    Processing helix  chain 'A' and resid 646 through 649
      removed outlier: 3.908A  pdb=" N   ILE A 649 " --> pdb=" O   ASP A 646 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 646 through 649'
    Processing helix  chain 'A' and resid 660 through 668
      removed outlier: 3.782A  pdb=" N   LEU A 664 " --> pdb=" O   ASP A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 686
    Processing helix  chain 'A' and resid 689 through 703
      removed outlier: 3.580A  pdb=" N   LYS A 695 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP A 703 " --> pdb=" O   ASP A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 711
      No H-bonds generated for 'chain 'A' and resid 709 through 711'
    Processing helix  chain 'A' and resid 712 through 722
      removed outlier: 4.101A  pdb=" N   MET A 716 " --> pdb=" O   LEU A 712 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER A 717 " --> pdb=" O   ASP A 713 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ALA A 722 " --> pdb=" O   GLY A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 750
      removed outlier: 4.104A  pdb=" N   ALA A 729 " --> pdb=" O   ALA A 725 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLY A 743 " --> pdb=" O   SER A 739 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASN A 750 " --> pdb=" O   THR A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 769
      removed outlier: 3.774A  pdb=" N   TYR A 769 " --> pdb=" O   VAL A 765 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 183
    Processing helix  chain 'B' and resid 391 through 408
      removed outlier: 4.735A  pdb=" N   GLU B 395 " --> pdb=" O   CYS B 391 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ILE B 397 " --> pdb=" O   ARG B 393 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASN B 398 " --> pdb=" O   ASP B 394 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   LYS B 399 " --> pdb=" O   GLU B 395 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   LEU B 400 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 521
      removed outlier: 4.725A  pdb=" N   VAL B 508 " --> pdb=" O   GLU B 504 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   ASP B 509 " --> pdb=" O   ALA B 505 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLN B 510 " --> pdb=" O   TRP B 506 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ARG B 511 " --> pdb=" O   CYS B 507 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLU B 519 " --> pdb=" O   GLU B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 534
    Processing helix  chain 'B' and resid 646 through 649
      removed outlier: 3.908A  pdb=" N   ILE B 649 " --> pdb=" O   ASP B 646 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 646 through 649'
    Processing helix  chain 'B' and resid 660 through 668
      removed outlier: 3.781A  pdb=" N   LEU B 664 " --> pdb=" O   ASP B 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 681 through 686
    Processing helix  chain 'B' and resid 689 through 703
      removed outlier: 3.579A  pdb=" N   LYS B 695 " --> pdb=" O   LYS B 691 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP B 703 " --> pdb=" O   ASP B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 711
      No H-bonds generated for 'chain 'B' and resid 709 through 711'
    Processing helix  chain 'B' and resid 712 through 722
      removed outlier: 4.101A  pdb=" N   MET B 716 " --> pdb=" O   LEU B 712 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER B 717 " --> pdb=" O   ASP B 713 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ALA B 722 " --> pdb=" O   GLY B 718 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 725 through 750
      removed outlier: 4.104A  pdb=" N   ALA B 729 " --> pdb=" O   ALA B 725 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLY B 743 " --> pdb=" O   SER B 739 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASN B 750 " --> pdb=" O   THR B 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 769
      removed outlier: 3.774A  pdb=" N   TYR B 769 " --> pdb=" O   VAL B 765 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 183
    Processing helix  chain 'C' and resid 391 through 408
      removed outlier: 4.735A  pdb=" N   GLU C 395 " --> pdb=" O   CYS C 391 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ILE C 397 " --> pdb=" O   ARG C 393 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASN C 398 " --> pdb=" O   ASP C 394 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   LYS C 399 " --> pdb=" O   GLU C 395 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   LEU C 400 " --> pdb=" O   ALA C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 484 through 521
      removed outlier: 4.726A  pdb=" N   VAL C 508 " --> pdb=" O   GLU C 504 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   ASP C 509 " --> pdb=" O   ALA C 505 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLN C 510 " --> pdb=" O   TRP C 506 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ARG C 511 " --> pdb=" O   CYS C 507 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLU C 519 " --> pdb=" O   GLU C 515 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 524 through 534
    Processing helix  chain 'C' and resid 646 through 649
      removed outlier: 3.908A  pdb=" N   ILE C 649 " --> pdb=" O   ASP C 646 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 646 through 649'
    Processing helix  chain 'C' and resid 660 through 668
      removed outlier: 3.782A  pdb=" N   LEU C 664 " --> pdb=" O   ASP C 660 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 681 through 686
    Processing helix  chain 'C' and resid 689 through 703
      removed outlier: 3.579A  pdb=" N   LYS C 695 " --> pdb=" O   LYS C 691 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP C 703 " --> pdb=" O   ASP C 699 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 709 through 711
      No H-bonds generated for 'chain 'C' and resid 709 through 711'
    Processing helix  chain 'C' and resid 712 through 722
      removed outlier: 4.101A  pdb=" N   MET C 716 " --> pdb=" O   LEU C 712 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER C 717 " --> pdb=" O   ASP C 713 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ALA C 722 " --> pdb=" O   GLY C 718 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 725 through 750
      removed outlier: 4.104A  pdb=" N   ALA C 729 " --> pdb=" O   ALA C 725 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLY C 743 " --> pdb=" O   SER C 739 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASN C 750 " --> pdb=" O   THR C 746 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 750 through 769
      removed outlier: 3.774A  pdb=" N   TYR C 769 " --> pdb=" O   VAL C 765 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 541
      removed outlier: 3.881A  pdb=" N   SER B 643 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 351
      removed outlier: 4.860A  pdb=" N   GLY A 433 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ASN A 417 " --> pdb=" O   GLY A 433 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   LYS A 435 " --> pdb=" O   TYR A 415 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   TYR A 415 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137
      removed outlier: 3.624A  pdb=" N   ALA A 267 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A 274 " --> pdb=" O   PHE A 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 169
      removed outlier: 5.053A  pdb=" N   LEU A 161 " --> pdb=" O   TYR A 153 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TYR A 153 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLY A 163 " --> pdb=" O   ARG A 151 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 151 " --> pdb=" O   GLY A 163 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 249 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 246
      removed outlier: 6.667A  pdb=" N   LEU A 316 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL A 306 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   THR A 318 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   THR A 304 " --> pdb=" O   THR A 318 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   ARG A 320 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 186
    Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 561
      removed outlier: 3.664A  pdb=" N   LYS A 560 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 575
    Processing sheet with id=AA9, first strand: chain 'A' and resid 616 through 620
      removed outlier: 3.589A  pdb=" N   ARG A 635 " --> pdb=" O   GLU A 627 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 643 through 644
      removed outlier: 6.863A  pdb=" N   SER A 643 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 538 through 541
      removed outlier: 3.878A  pdb=" N   SER C 643 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 351
      removed outlier: 4.859A  pdb=" N   GLY B 433 " --> pdb=" O   ASN B 417 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ASN B 417 " --> pdb=" O   GLY B 433 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   LYS B 435 " --> pdb=" O   TYR B 415 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   TYR B 415 " --> pdb=" O   LYS B 435 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 136 through 137
      removed outlier: 3.623A  pdb=" N   ALA B 267 " --> pdb=" O   ARG B 258 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL B 274 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 159 through 169
      removed outlier: 5.053A  pdb=" N   LEU B 161 " --> pdb=" O   TYR B 153 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TYR B 153 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY B 163 " --> pdb=" O   ARG B 151 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG B 151 " --> pdb=" O   GLY B 163 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   VAL B 146 " --> pdb=" O   ASN B 249 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 243 through 246
      removed outlier: 6.667A  pdb=" N   LEU B 316 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL B 306 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   THR B 318 " --> pdb=" O   THR B 304 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   THR B 304 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   ARG B 320 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 184 through 186
    Processing sheet with id=AB8, first strand: chain 'B' and resid 560 through 561
      removed outlier: 3.664A  pdb=" N   LYS B 560 " --> pdb=" O   ILE B 581 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 573 through 575
    Processing sheet with id=AC1, first strand: chain 'B' and resid 616 through 620
      removed outlier: 3.589A  pdb=" N   ARG B 635 " --> pdb=" O   GLU B 627 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 350 through 351
      removed outlier: 4.860A  pdb=" N   GLY C 433 " --> pdb=" O   ASN C 417 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ASN C 417 " --> pdb=" O   GLY C 433 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   LYS C 435 " --> pdb=" O   TYR C 415 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   TYR C 415 " --> pdb=" O   LYS C 435 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 137
      removed outlier: 3.624A  pdb=" N   ALA C 267 " --> pdb=" O   ARG C 258 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL C 274 " --> pdb=" O   PHE C 266 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 159 through 169
      removed outlier: 5.054A  pdb=" N   LEU C 161 " --> pdb=" O   TYR C 153 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   TYR C 153 " --> pdb=" O   LEU C 161 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLY C 163 " --> pdb=" O   ARG C 151 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG C 151 " --> pdb=" O   GLY C 163 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   VAL C 146 " --> pdb=" O   ASN C 249 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 243 through 246
      removed outlier: 6.668A  pdb=" N   LEU C 316 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL C 306 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   THR C 318 " --> pdb=" O   THR C 304 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   THR C 304 " --> pdb=" O   THR C 318 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   ARG C 320 " --> pdb=" O   ASN C 302 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 184 through 186
    Processing sheet with id=AC7, first strand: chain 'C' and resid 560 through 561
      removed outlier: 3.664A  pdb=" N   LYS C 560 " --> pdb=" O   ILE C 581 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 573 through 575
    Processing sheet with id=AC9, first strand: chain 'C' and resid 616 through 620
      removed outlier: 3.589A  pdb=" N   ARG C 635 " --> pdb=" O   GLU C 627 " (cutoff:3.500A)

    506 hydrogen bonds defined for protein.
    1410 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.65

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5038
        1.34 -     1.46: 3803
        1.46 -     1.58: 7215
        1.58 -     1.70: 3
        1.70 -     1.82: 129
  Bond restraints: 16188
  Sorted by residual:
  bond pdb=" C   ASP B 703 "
       pdb=" N   PRO B 704 "
    ideal  model  delta    sigma   weight residual
    1.334  1.414 -0.081 2.34e-02 1.83e+03 1.18e+01
  bond pdb=" C   ASP A 703 "
       pdb=" N   PRO A 704 "
    ideal  model  delta    sigma   weight residual
    1.334  1.414 -0.080 2.34e-02 1.83e+03 1.16e+01
  bond pdb=" C   ASP C 703 "
       pdb=" N   PRO C 704 "
    ideal  model  delta    sigma   weight residual
    1.334  1.414 -0.080 2.34e-02 1.83e+03 1.16e+01
  bond pdb=" C1  NAG A1003 "
       pdb=" O5  NAG A1003 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.05e+00
  bond pdb=" C1  NAG B1104 "
       pdb=" O5  NAG B1104 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.02e+00
  ... (remaining 16183 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 21241
        1.85 -     3.70: 618
        3.70 -     5.55: 86
        5.55 -     7.41: 24
        7.41 -     9.26: 6
  Bond angle restraints: 21975
  Sorted by residual:
  angle pdb=" C   VAL B 192 "
        pdb=" N   ILE B 193 "
        pdb=" CA  ILE B 193 "
      ideal   model   delta    sigma   weight residual
     122.93  119.13    3.80 1.21e+00 6.83e-01 9.87e+00
  angle pdb=" C   VAL C 192 "
        pdb=" N   ILE C 193 "
        pdb=" CA  ILE C 193 "
      ideal   model   delta    sigma   weight residual
     122.93  119.14    3.79 1.21e+00 6.83e-01 9.82e+00
  angle pdb=" C   VAL A 192 "
        pdb=" N   ILE A 193 "
        pdb=" CA  ILE A 193 "
      ideal   model   delta    sigma   weight residual
     122.93  119.15    3.78 1.21e+00 6.83e-01 9.77e+00
  angle pdb=" CA  LEU C 616 "
        pdb=" CB  LEU C 616 "
        pdb=" CG  LEU C 616 "
      ideal   model   delta    sigma   weight residual
     116.30  125.56   -9.26 3.50e+00 8.16e-02 7.00e+00
  angle pdb=" CA  LEU A 616 "
        pdb=" CB  LEU A 616 "
        pdb=" CG  LEU A 616 "
      ideal   model   delta    sigma   weight residual
     116.30  125.55   -9.25 3.50e+00 8.16e-02 6.99e+00
  ... (remaining 21970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 8968
       17.36 -    34.71: 844
       34.71 -    52.07: 151
       52.07 -    69.43: 42
       69.43 -    86.79: 15
  Dihedral angle restraints: 10020
    sinusoidal: 4356
      harmonic: 5664
  Sorted by residual:
  dihedral pdb=" CB  CYS C 574 "
           pdb=" SG  CYS C 574 "
           pdb=" SG  CYS C 611 "
           pdb=" CB  CYS C 611 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.84  -61.84     1      1.00e+01 1.00e-02 5.07e+01
  dihedral pdb=" CB  CYS B 574 "
           pdb=" SG  CYS B 574 "
           pdb=" SG  CYS B 611 "
           pdb=" CB  CYS B 611 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.83  -61.83     1      1.00e+01 1.00e-02 5.07e+01
  dihedral pdb=" CB  CYS A 574 "
           pdb=" SG  CYS A 574 "
           pdb=" SG  CYS A 611 "
           pdb=" CB  CYS A 611 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.82  -61.82     1      1.00e+01 1.00e-02 5.07e+01
  ... (remaining 10017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 2243
       0.076 -    0.152: 268
       0.152 -    0.228: 12
       0.228 -    0.303: 3
       0.303 -    0.379: 3
  Chirality restraints: 2529
  Sorted by residual:
  chirality pdb=" C1  NAG C1103 "
            pdb=" ND2 ASN C 281 "
            pdb=" C2  NAG C1103 "
            pdb=" O5  NAG C1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.60e+00
  chirality pdb=" C1  NAG B1103 "
            pdb=" ND2 ASN B 281 "
            pdb=" C2  NAG B1103 "
            pdb=" O5  NAG B1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.58e+00
  chirality pdb=" C1  NAG A1002 "
            pdb=" ND2 ASN A 281 "
            pdb=" C2  NAG A1002 "
            pdb=" O5  NAG A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.56e+00
  ... (remaining 2526 not shown)

  Planarity restraints: 2790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 703 "    0.065 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO B 704 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO B 704 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO B 704 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 703 "    0.065 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO C 704 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO C 704 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO C 704 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 703 "    0.065 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO A 704 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO A 704 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 704 "    0.057 5.00e-02 4.00e+02
  ... (remaining 2787 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 1018
        2.73 -     3.27: 16187
        3.27 -     3.81: 23705
        3.81 -     4.36: 27174
        4.36 -     4.90: 47222
  Nonbonded interactions: 115306
  Sorted by model distance:
  nonbonded pdb=" O   TYR C 263 "
            pdb=" OG  SER C 277 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   TYR B 263 "
            pdb=" OG  SER B 277 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   TYR A 263 "
            pdb=" OG  SER A 277 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER A 385 "
            pdb=" O6  NAG A1006 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER C 385 "
            pdb=" O6  NAG C1107 "
     model   vdw
     2.206 3.040
  ... (remaining 115301 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 86 through 769 or resid 1002 through 1010))
  selection = (chain 'B' and (resid 86 through 769 or resid 1102 through 1110))
  selection = (chain 'C' and (resid 86 through 769 or resid 1102 through 1110))
}

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:             1.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.090
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
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      :  0.005   0.081  16233  Z= 0.212
  Angle     :  0.770   9.257  22095  Z= 0.401
  Chirality :  0.050   0.379   2529
  Planarity :  0.005   0.103   2760
  Dihedral  : 14.096  86.785   6333
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.83 %
    Favored  : 86.17 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.59 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.89 (0.18), residues: 1902
  helix:  1.05 (0.25), residues: 450
  sheet: -1.81 (0.24), residues: 423
  loop : -3.54 (0.15), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 357 
 TYR   0.015   0.001   TYR B 189 
 PHE   0.020   0.002   PHE C 678 
 TRP   0.023   0.002   TRP B 233 
 HIS   0.003   0.001   HIS C 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (16188)
  covalent geometry    : angle       0.75167 (21975)
  SS BOND              : bond        0.00246 (   15)
  SS BOND              : angle       1.98038 (   30)
  hydrogen bonds       : bond        0.16507 (  506)
  hydrogen bonds       : angle       7.10498 ( 1410)
  link_NAG-ASN         : bond        0.00564 (   30)
  link_NAG-ASN         : angle       2.49397 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 223
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  551 CYS cc_start: 0.6281 (m) cc_final: 0.5880 (m)
REVERT: A  686 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: B  364 TYR cc_start: 0.6053 (m-80) cc_final: 0.5608 (m-80)
REVERT: B  686 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: C  214 MET cc_start: 0.7684 (ptm) cc_final: 0.7473 (ptm)
REVERT: C  364 TYR cc_start: 0.6432 (m-80) cc_final: 0.6052 (m-80)
REVERT: C  483 GLN cc_start: 0.4347 (tp-100) cc_final: 0.3945 (mp10)
REVERT: C  551 CYS cc_start: 0.6419 (m) cc_final: 0.6040 (m)
REVERT: C  636 MET cc_start: 0.8569 (tpp) cc_final: 0.8353 (tpp)
REVERT: C  686 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8205 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 223
  average time/residue: 0.1315
  time to fit residues: 43.4793
Evaluate side-chains
  177 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 175
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  700 LYS
Chi-restraints excluded: chain C residue  700 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0770
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    8.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.9142

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

Flipped N/Q/H residues before XYZ refinement:
A 365 HIS
B 212 GLN
B 313 ASN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 623 ASN
C 313 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.151666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.122987 restraints weight = 27221.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126279 restraints weight = 15348.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.126636 restraints weight = 10330.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.127251 restraints weight = 9357.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.127259 restraints weight = 8185.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  16233  Z= 0.159
  Angle     :  0.687   9.848  22095  Z= 0.358
  Chirality :  0.049   0.354   2529
  Planarity :  0.004   0.068   2760
  Dihedral  :  7.659  58.459   2789
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.99 %
    Favored  : 87.01 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.06 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.18), residues: 1902
  helix:  1.29 (0.24), residues: 453
  sheet: -1.51 (0.25), residues: 411
  loop : -3.43 (0.16), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 357 
 TYR   0.016   0.001   TYR B 189 
 PHE   0.034   0.002   PHE B 678 
 TRP   0.026   0.002   TRP C 431 
 HIS   0.003   0.001   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (16188)
  covalent geometry    : angle       0.67050 (21975)
  SS BOND              : bond        0.00322 (   15)
  SS BOND              : angle       1.56531 (   30)
  hydrogen bonds       : bond        0.05137 (  506)
  hydrogen bonds       : angle       5.44390 ( 1410)
  link_NAG-ASN         : bond        0.00535 (   30)
  link_NAG-ASN         : angle       2.26678 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 194
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A  551 CYS cc_start: 0.6490 (m) cc_final: 0.6269 (m)
REVERT: A  686 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7960 (tm-30)
REVERT: A  752 PHE cc_start: 0.8164 (m-10) cc_final: 0.7875 (m-10)
REVERT: B  114 MET cc_start: 0.4800 (mtt) cc_final: 0.3107 (mtt)
REVERT: B  364 TYR cc_start: 0.5871 (m-80) cc_final: 0.5576 (m-80)
REVERT: B  623 ASN cc_start: 0.7823 (p0) cc_final: 0.7507 (p0)
REVERT: B  646 ASP cc_start: 0.8621 (t0) cc_final: 0.8353 (t0)
REVERT: B  686 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8181 (tm-30)
REVERT: B  700 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8797 (tmtt)
REVERT: C  364 TYR cc_start: 0.6383 (m-80) cc_final: 0.6080 (m-80)
REVERT: C  636 MET cc_start: 0.8585 (tpp) cc_final: 0.8361 (tpp)
REVERT: C  686 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8141 (tm-30)
  outliers start: 23
  outliers final: 14
  residues processed: 204
  average time/residue: 0.1201
  time to fit residues: 37.2379
Evaluate side-chains
  187 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  502 ILE
Chi-restraints excluded: chain B residue  744 VAL
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  700 LYS
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain C residue  744 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 159 optimal weight:    1.9990
   chunk 149 optimal weight:    3.9990
   chunk 52 optimal weight:    0.1980
   chunk 74 optimal weight:    0.0170
   chunk 139 optimal weight:    0.9990
   chunk 148 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 123 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   overall best weight:    0.8422

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
A 313 ASN
A 365 HIS
A 606 HIS
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 212 GLN
C 365 HIS
C 606 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.143389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.116088 restraints weight = 27742.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118225 restraints weight = 16173.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.119559 restraints weight = 10592.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.119745 restraints weight = 9171.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.119942 restraints weight = 8603.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  16233  Z= 0.148
  Angle     :  0.649   9.061  22095  Z= 0.339
  Chirality :  0.048   0.352   2529
  Planarity :  0.004   0.045   2760
  Dihedral  :  7.211  59.346   2785
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.62 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.15 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.18), residues: 1902
  helix:  1.37 (0.25), residues: 450
  sheet: -1.38 (0.26), residues: 411
  loop : -3.38 (0.16), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 357 
 TYR   0.013   0.001   TYR B 189 
 PHE   0.033   0.002   PHE B 678 
 TRP   0.038   0.002   TRP A 431 
 HIS   0.003   0.001   HIS B 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (16188)
  covalent geometry    : angle       0.63400 (21975)
  SS BOND              : bond        0.00305 (   15)
  SS BOND              : angle       1.35651 (   30)
  hydrogen bonds       : bond        0.04822 (  506)
  hydrogen bonds       : angle       5.22263 ( 1410)
  link_NAG-ASN         : bond        0.00498 (   30)
  link_NAG-ASN         : angle       2.17377 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 TRP cc_start: 0.6905 (p-90) cc_final: 0.6554 (p-90)
REVERT: A  551 CYS cc_start: 0.6544 (m) cc_final: 0.6323 (m)
REVERT: A  686 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: A  696 TYR cc_start: 0.7718 (m-10) cc_final: 0.7412 (m-10)
REVERT: A  752 PHE cc_start: 0.8159 (m-10) cc_final: 0.7861 (m-10)
REVERT: B  364 TYR cc_start: 0.6051 (m-80) cc_final: 0.5806 (m-80)
REVERT: B  370 LYS cc_start: 0.7384 (tppt) cc_final: 0.6991 (ttpt)
REVERT: B  371 MET cc_start: 0.7101 (tpt) cc_final: 0.6664 (tpt)
REVERT: B  506 TRP cc_start: 0.6097 (t-100) cc_final: 0.5888 (t-100)
REVERT: B  623 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7407 (p0)
REVERT: B  646 ASP cc_start: 0.8622 (t0) cc_final: 0.8209 (t0)
REVERT: B  686 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8169 (tm-30)
REVERT: C  364 TYR cc_start: 0.6215 (m-80) cc_final: 0.5756 (m-80)
REVERT: C  616 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8353 (tt)
REVERT: C  623 ASN cc_start: 0.8222 (p0) cc_final: 0.7979 (p0)
REVERT: C  636 MET cc_start: 0.8687 (tpp) cc_final: 0.8437 (tpp)
REVERT: C  686 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8141 (tm-30)
  outliers start: 28
  outliers final: 17
  residues processed: 211
  average time/residue: 0.1251
  time to fit residues: 40.1928
Evaluate side-chains
  195 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 176
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  502 ILE
Chi-restraints excluded: chain B residue  565 MET
Chi-restraints excluded: chain B residue  623 ASN
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  420 VAL
Chi-restraints excluded: chain C residue  616 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 145 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 160 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 183 optimal weight:    0.0970
   chunk 18 optimal weight:    0.5980
   chunk 96 optimal weight:    8.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    1.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 365 HIS
** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 178 HIS
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 606 HIS
** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 HIS
C 365 HIS
C 669 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.139601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.113150 restraints weight = 27542.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.114717 restraints weight = 18014.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.115744 restraints weight = 12782.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116205 restraints weight = 10687.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116232 restraints weight = 10094.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  16233  Z= 0.241
  Angle     :  0.737  10.045  22095  Z= 0.388
  Chirality :  0.051   0.374   2529
  Planarity :  0.004   0.039   2760
  Dihedral  :  7.747  59.134   2781
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.93 %
    Favored  : 85.07 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.87 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.18), residues: 1902
  helix:  1.11 (0.25), residues: 456
  sheet: -1.42 (0.26), residues: 417
  loop : -3.48 (0.15), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 357 
 TYR   0.013   0.001   TYR C 189 
 PHE   0.038   0.002   PHE B 678 
 TRP   0.048   0.003   TRP B 431 
 HIS   0.005   0.001   HIS B 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 (16188)
  covalent geometry    : angle       0.72187 (21975)
  SS BOND              : bond        0.00352 (   15)
  SS BOND              : angle       1.82762 (   30)
  hydrogen bonds       : bond        0.05730 (  506)
  hydrogen bonds       : angle       5.46948 ( 1410)
  link_NAG-ASN         : bond        0.00540 (   30)
  link_NAG-ASN         : angle       2.25648 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 181
  time to evaluate  : 0.610 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7082 (ptt) cc_final: 0.6850 (ptp)
REVERT: A  371 MET cc_start: 0.6168 (tpt) cc_final: 0.5875 (tpt)
REVERT: A  431 TRP cc_start: 0.7130 (p-90) cc_final: 0.6822 (p-90)
REVERT: A  551 CYS cc_start: 0.6106 (m) cc_final: 0.5714 (m)
REVERT: A  686 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8221 (tm-30)
REVERT: A  696 TYR cc_start: 0.7971 (m-10) cc_final: 0.7608 (m-10)
REVERT: A  752 PHE cc_start: 0.8257 (m-10) cc_final: 0.8007 (m-10)
REVERT: B  371 MET cc_start: 0.7436 (tpt) cc_final: 0.6982 (tpt)
REVERT: B  648 MET cc_start: 0.6999 (tpp) cc_final: 0.6322 (tpp)
REVERT: B  686 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: C  350 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7355 (tm-30)
REVERT: C  623 ASN cc_start: 0.8304 (p0) cc_final: 0.8061 (p0)
REVERT: C  636 MET cc_start: 0.8646 (tpp) cc_final: 0.8413 (tpp)
  outliers start: 56
  outliers final: 42
  residues processed: 221
  average time/residue: 0.1148
  time to fit residues: 39.5005
Evaluate side-chains
  204 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 162
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  679 ASP
Chi-restraints excluded: chain B residue  701 VAL
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  744 VAL
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  342 VAL
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  420 VAL
Chi-restraints excluded: chain C residue  502 ILE
Chi-restraints excluded: chain C residue  669 GLN
Chi-restraints excluded: chain C residue  679 ASP
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain C residue  744 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 184 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 188 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 365 HIS
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 669 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.144519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114206 restraints weight = 27541.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.117278 restraints weight = 15644.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.119153 restraints weight = 10919.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.120354 restraints weight = 8684.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.121069 restraints weight = 7493.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16233  Z= 0.155
  Angle     :  0.680   9.385  22095  Z= 0.353
  Chirality :  0.048   0.352   2529
  Planarity :  0.004   0.042   2760
  Dihedral  :  7.173  58.549   2781
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 13.09 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.88 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.18), residues: 1902
  helix:  1.27 (0.25), residues: 453
  sheet: -1.47 (0.25), residues: 435
  loop : -3.39 (0.16), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 357 
 TYR   0.010   0.001   TYR C 189 
 PHE   0.022   0.002   PHE A 266 
 TRP   0.040   0.002   TRP C 431 
 HIS   0.003   0.001   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (16188)
  covalent geometry    : angle       0.66127 (21975)
  SS BOND              : bond        0.00313 (   15)
  SS BOND              : angle       2.40850 (   30)
  hydrogen bonds       : bond        0.04859 (  506)
  hydrogen bonds       : angle       5.19179 ( 1410)
  link_NAG-ASN         : bond        0.00507 (   30)
  link_NAG-ASN         : angle       2.15876 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 183
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A  371 MET cc_start: 0.6080 (tpt) cc_final: 0.5781 (tpt)
REVERT: A  551 CYS cc_start: 0.6570 (m) cc_final: 0.6344 (m)
REVERT: A  686 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: A  696 TYR cc_start: 0.7853 (m-10) cc_final: 0.7550 (m-10)
REVERT: A  752 PHE cc_start: 0.8191 (m-10) cc_final: 0.7902 (m-10)
REVERT: B  371 MET cc_start: 0.6987 (tpt) cc_final: 0.6523 (tpt)
REVERT: B  623 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7593 (p0)
REVERT: B  684 MET cc_start: 0.7855 (tpp) cc_final: 0.7372 (tpp)
REVERT: C  364 TYR cc_start: 0.6044 (m-80) cc_final: 0.5768 (m-80)
REVERT: C  371 MET cc_start: 0.6356 (tpt) cc_final: 0.5969 (tpt)
REVERT: C  623 ASN cc_start: 0.8337 (p0) cc_final: 0.8078 (p0)
REVERT: C  636 MET cc_start: 0.8540 (tpp) cc_final: 0.8287 (tpp)
REVERT: C  683 ILE cc_start: 0.7716 (mm) cc_final: 0.7496 (mm)
REVERT: C  686 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8165 (tm-30)
  outliers start: 58
  outliers final: 44
  residues processed: 225
  average time/residue: 0.1147
  time to fit residues: 39.8232
Evaluate side-chains
  214 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 169
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  636 MET
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  502 ILE
Chi-restraints excluded: chain B residue  623 ASN
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  679 ASP
Chi-restraints excluded: chain B residue  701 VAL
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  744 VAL
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  342 VAL
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  420 VAL
Chi-restraints excluded: chain C residue  669 GLN
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain C residue  744 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 143 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0570
   chunk 158 optimal weight:    0.0670
   chunk 14 optimal weight:    0.1980
   chunk 32 optimal weight:    0.0000
   chunk 38 optimal weight:    0.8980
   chunk 170 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.2440

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 HIS
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 313 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.147411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.120322 restraints weight = 27195.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.122924 restraints weight = 14973.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.123741 restraints weight = 11047.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.125717 restraints weight = 9224.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.125695 restraints weight = 7870.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  16233  Z= 0.115
  Angle     :  0.637  10.604  22095  Z= 0.327
  Chirality :  0.047   0.422   2529
  Planarity :  0.003   0.042   2760
  Dihedral  :  6.261  59.827   2781
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.36 %
    Favored  : 88.64 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.65 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.19), residues: 1902
  helix:  1.18 (0.25), residues: 468
  sheet: -1.29 (0.25), residues: 435
  loop : -3.30 (0.16), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 357 
 TYR   0.011   0.001   TYR B 189 
 PHE   0.020   0.001   PHE B 687 
 TRP   0.039   0.002   TRP A 431 
 HIS   0.003   0.001   HIS C 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (16188)
  covalent geometry    : angle       0.62248 (21975)
  SS BOND              : bond        0.00342 (   15)
  SS BOND              : angle       1.49606 (   30)
  hydrogen bonds       : bond        0.03978 (  506)
  hydrogen bonds       : angle       4.84263 ( 1410)
  link_NAG-ASN         : bond        0.00477 (   30)
  link_NAG-ASN         : angle       2.05396 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 194
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
REVERT: A  371 MET cc_start: 0.6296 (tpt) cc_final: 0.6031 (tpt)
REVERT: A  427 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7328 (pp)
REVERT: A  431 TRP cc_start: 0.6644 (p-90) cc_final: 0.6346 (p-90)
REVERT: A  684 MET cc_start: 0.7245 (tpp) cc_final: 0.6443 (tpp)
REVERT: A  696 TYR cc_start: 0.7552 (m-10) cc_final: 0.7265 (m-10)
REVERT: A  752 PHE cc_start: 0.8034 (m-10) cc_final: 0.7804 (m-10)
REVERT: B  114 MET cc_start: 0.4791 (mtt) cc_final: 0.4494 (mtt)
REVERT: B  371 MET cc_start: 0.6338 (tpt) cc_final: 0.5888 (tpt)
REVERT: B  623 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7298 (p0)
REVERT: B  646 ASP cc_start: 0.8667 (t0) cc_final: 0.8175 (t0)
REVERT: C  350 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7565 (tm-30)
REVERT: C  357 ARG cc_start: 0.5877 (ttm110) cc_final: 0.5488 (mtm-85)
REVERT: C  602 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8639 (pp)
REVERT: C  636 MET cc_start: 0.8530 (tpp) cc_final: 0.8295 (tpp)
REVERT: C  639 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7884 (mt)
REVERT: C  696 TYR cc_start: 0.7567 (m-10) cc_final: 0.7220 (m-10)
REVERT: C  716 MET cc_start: 0.8740 (mmm) cc_final: 0.8090 (tpt)
  outliers start: 52
  outliers final: 29
  residues processed: 229
  average time/residue: 0.1116
  time to fit residues: 39.4664
Evaluate side-chains
  209 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  636 MET
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  502 ILE
Chi-restraints excluded: chain B residue  623 ASN
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  701 VAL
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  313 ASN
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  602 LEU
Chi-restraints excluded: chain C residue  639 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 121 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 119 optimal weight:    0.8980
   chunk 118 optimal weight:    2.9990
   chunk 182 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 153 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN
C 313 ASN
C 501 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.144721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.116184 restraints weight = 27442.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.117907 restraints weight = 19603.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.118836 restraints weight = 12456.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119328 restraints weight = 10898.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.119664 restraints weight = 10279.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  16233  Z= 0.171
  Angle     :  0.690   9.306  22095  Z= 0.359
  Chirality :  0.049   0.377   2529
  Planarity :  0.004   0.050   2760
  Dihedral  :  6.659  59.671   2781
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.30 %
    Favored  : 86.70 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 19.30 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.18), residues: 1902
  helix:  1.41 (0.25), residues: 456
  sheet: -1.27 (0.25), residues: 435
  loop : -3.33 (0.16), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 357 
 TYR   0.024   0.001   TYR A 289 
 PHE   0.024   0.002   PHE B 266 
 TRP   0.060   0.002   TRP B 431 
 HIS   0.006   0.001   HIS C 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (16188)
  covalent geometry    : angle       0.67581 (21975)
  SS BOND              : bond        0.00268 (   15)
  SS BOND              : angle       1.68546 (   30)
  hydrogen bonds       : bond        0.04790 (  506)
  hydrogen bonds       : angle       5.10315 ( 1410)
  link_NAG-ASN         : bond        0.00501 (   30)
  link_NAG-ASN         : angle       2.08308 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 177
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 MET cc_start: 0.6948 (ptt) cc_final: 0.6525 (ptp)
REVERT: A  371 MET cc_start: 0.6423 (tpt) cc_final: 0.6174 (tpt)
REVERT: A  696 TYR cc_start: 0.7745 (m-10) cc_final: 0.7389 (m-10)
REVERT: A  752 PHE cc_start: 0.8182 (m-10) cc_final: 0.7931 (m-10)
REVERT: B  354 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7452 (mmm-85)
REVERT: B  623 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7410 (p0)
REVERT: B  646 ASP cc_start: 0.8744 (t0) cc_final: 0.8298 (t0)
REVERT: B  648 MET cc_start: 0.6910 (tpp) cc_final: 0.6156 (mpp)
REVERT: C  350 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7439 (tm-30)
REVERT: C  357 ARG cc_start: 0.6267 (ttm110) cc_final: 0.5866 (mtm180)
REVERT: C  636 MET cc_start: 0.8579 (tpp) cc_final: 0.8314 (tpp)
REVERT: C  686 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: C  716 MET cc_start: 0.8593 (mmm) cc_final: 0.7972 (tpt)
  outliers start: 62
  outliers final: 49
  residues processed: 218
  average time/residue: 0.1134
  time to fit residues: 37.9197
Evaluate side-chains
  213 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 163
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  636 MET
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  502 ILE
Chi-restraints excluded: chain B residue  565 MET
Chi-restraints excluded: chain B residue  623 ASN
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  639 LEU
Chi-restraints excluded: chain B residue  667 TYR
Chi-restraints excluded: chain B residue  679 ASP
Chi-restraints excluded: chain B residue  701 VAL
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  342 VAL
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  420 VAL
Chi-restraints excluded: chain C residue  687 PHE
Chi-restraints excluded: chain C residue  702 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 175 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 151 optimal weight:    0.0060
   chunk 186 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 156 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 HIS
B 510 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.144282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114844 restraints weight = 27351.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.117915 restraints weight = 15182.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119821 restraints weight = 10415.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.121026 restraints weight = 8162.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.121668 restraints weight = 6986.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16233  Z= 0.152
  Angle     :  0.686  10.437  22095  Z= 0.353
  Chirality :  0.048   0.425   2529
  Planarity :  0.004   0.048   2760
  Dihedral  :  6.587  56.260   2781
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 12.15 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.66 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.19), residues: 1902
  helix:  1.20 (0.25), residues: 471
  sheet: -1.24 (0.25), residues: 435
  loop : -3.29 (0.16), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 357 
 TYR   0.024   0.001   TYR A 289 
 PHE   0.034   0.002   PHE A 678 
 TRP   0.066   0.003   TRP A 431 
 HIS   0.006   0.001   HIS C 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (16188)
  covalent geometry    : angle       0.67186 (21975)
  SS BOND              : bond        0.00325 (   15)
  SS BOND              : angle       1.59146 (   30)
  hydrogen bonds       : bond        0.04555 (  506)
  hydrogen bonds       : angle       5.04121 ( 1410)
  link_NAG-ASN         : bond        0.00508 (   30)
  link_NAG-ASN         : angle       2.09622 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 169
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
REVERT: A  371 MET cc_start: 0.6343 (tpt) cc_final: 0.6132 (tpt)
REVERT: A  696 TYR cc_start: 0.7777 (m-10) cc_final: 0.7446 (m-10)
REVERT: A  752 PHE cc_start: 0.8175 (m-10) cc_final: 0.7941 (m-10)
REVERT: B  354 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7423 (mmm160)
REVERT: B  623 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7414 (p0)
REVERT: B  646 ASP cc_start: 0.8682 (t0) cc_final: 0.8221 (t0)
REVERT: B  716 MET cc_start: 0.8457 (tpp) cc_final: 0.7971 (tpp)
REVERT: C  636 MET cc_start: 0.8562 (tpp) cc_final: 0.8331 (tpp)
REVERT: C  696 TYR cc_start: 0.7842 (m-10) cc_final: 0.7494 (m-10)
REVERT: C  716 MET cc_start: 0.8452 (mmm) cc_final: 0.7891 (tpt)
  outliers start: 56
  outliers final: 48
  residues processed: 206
  average time/residue: 0.1184
  time to fit residues: 37.1382
Evaluate side-chains
  210 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 161
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  636 MET
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  502 ILE
Chi-restraints excluded: chain B residue  565 MET
Chi-restraints excluded: chain B residue  623 ASN
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  667 TYR
Chi-restraints excluded: chain B residue  679 ASP
Chi-restraints excluded: chain B residue  701 VAL
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  768 ILE
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  342 VAL
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  420 VAL
Chi-restraints excluded: chain C residue  639 LEU
Chi-restraints excluded: chain C residue  687 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 174 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 67 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 135 optimal weight:    1.9990
   chunk 150 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 132 optimal weight:    0.9980
   chunk 127 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0670
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.143308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.114514 restraints weight = 27030.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117614 restraints weight = 14901.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.119514 restraints weight = 10169.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.120690 restraints weight = 7962.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.121343 restraints weight = 6828.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  16233  Z= 0.137
  Angle     :  0.681  11.118  22095  Z= 0.349
  Chirality :  0.048   0.412   2529
  Planarity :  0.004   0.060   2760
  Dihedral  :  6.341  53.136   2781
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 11.78 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.89 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.19), residues: 1902
  helix:  1.31 (0.25), residues: 468
  sheet: -1.19 (0.25), residues: 435
  loop : -3.17 (0.16), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 357 
 TYR   0.023   0.001   TYR A 289 
 PHE   0.034   0.001   PHE B 678 
 TRP   0.054   0.003   TRP A 431 
 HIS   0.005   0.001   HIS B 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (16188)
  covalent geometry    : angle       0.66258 (21975)
  SS BOND              : bond        0.00561 (   15)
  SS BOND              : angle       2.70744 (   30)
  hydrogen bonds       : bond        0.04306 (  506)
  hydrogen bonds       : angle       4.97172 ( 1410)
  link_NAG-ASN         : bond        0.00514 (   30)
  link_NAG-ASN         : angle       2.04811 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 170
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  371 MET cc_start: 0.6486 (tpt) cc_final: 0.6281 (tpt)
REVERT: A  696 TYR cc_start: 0.7720 (m-10) cc_final: 0.7419 (m-10)
REVERT: A  752 PHE cc_start: 0.8136 (m-10) cc_final: 0.7895 (m-10)
REVERT: B  114 MET cc_start: 0.4194 (mtt) cc_final: 0.3745 (mtt)
REVERT: B  504 GLU cc_start: 0.7732 (tp30) cc_final: 0.6994 (tt0)
REVERT: B  623 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7343 (p0)
REVERT: B  646 ASP cc_start: 0.8651 (t0) cc_final: 0.8197 (t0)
REVERT: C  295 ASP cc_start: 0.6464 (t0) cc_final: 0.6226 (t70)
REVERT: C  609 GLU cc_start: 0.7706 (pt0) cc_final: 0.7323 (pt0)
REVERT: C  636 MET cc_start: 0.8548 (tpp) cc_final: 0.8308 (tpp)
REVERT: C  716 MET cc_start: 0.8398 (mmm) cc_final: 0.7691 (tpt)
  outliers start: 54
  outliers final: 51
  residues processed: 207
  average time/residue: 0.1153
  time to fit residues: 36.7234
Evaluate side-chains
  220 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 168
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  636 MET
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  667 TYR
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  565 MET
Chi-restraints excluded: chain B residue  623 ASN
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  639 LEU
Chi-restraints excluded: chain B residue  667 TYR
Chi-restraints excluded: chain B residue  679 ASP
Chi-restraints excluded: chain B residue  701 VAL
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  768 ILE
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  342 VAL
Chi-restraints excluded: chain C residue  371 MET
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  420 VAL
Chi-restraints excluded: chain C residue  639 LEU
Chi-restraints excluded: chain C residue  702 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 144 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 181 optimal weight:    0.2980
   chunk 60 optimal weight:    0.6980
   chunk 89 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 165 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.144206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.115850 restraints weight = 27295.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118915 restraints weight = 14939.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.120174 restraints weight = 9823.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.120284 restraints weight = 8381.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.120371 restraints weight = 8125.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16233  Z= 0.157
  Angle     :  0.695   9.991  22095  Z= 0.359
  Chirality :  0.048   0.416   2529
  Planarity :  0.004   0.053   2760
  Dihedral  :  6.474  53.099   2781
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 12.25 %
    Favored  : 87.70 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.42 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.19), residues: 1902
  helix:  1.23 (0.25), residues: 471
  sheet: -1.18 (0.25), residues: 444
  loop : -3.19 (0.16), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 357 
 TYR   0.023   0.001   TYR A 289 
 PHE   0.033   0.002   PHE B 678 
 TRP   0.051   0.003   TRP A 431 
 HIS   0.003   0.001   HIS B 606 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (16188)
  covalent geometry    : angle       0.67808 (21975)
  SS BOND              : bond        0.00389 (   15)
  SS BOND              : angle       2.57616 (   30)
  hydrogen bonds       : bond        0.04593 (  506)
  hydrogen bonds       : angle       5.03902 ( 1410)
  link_NAG-ASN         : bond        0.00514 (   30)
  link_NAG-ASN         : angle       2.04128 (   90)

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

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

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3804 Ramachandran restraints generated.
    1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 173
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
REVERT: A  696 TYR cc_start: 0.7782 (m-10) cc_final: 0.7488 (m-10)
REVERT: A  752 PHE cc_start: 0.8163 (m-10) cc_final: 0.7922 (m-10)
REVERT: A  769 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5072 (t80)
REVERT: B  114 MET cc_start: 0.3801 (mtt) cc_final: 0.3274 (mtt)
REVERT: B  354 ARG cc_start: 0.7680 (mmm160) cc_final: 0.7419 (mmm-85)
REVERT: B  504 GLU cc_start: 0.7615 (tp30) cc_final: 0.6918 (tt0)
REVERT: B  623 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7381 (p0)
REVERT: B  646 ASP cc_start: 0.8739 (t0) cc_final: 0.8276 (t0)
REVERT: B  692 GLN cc_start: 0.7547 (tp40) cc_final: 0.7270 (tp-100)
REVERT: C  371 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5708 (mmm)
REVERT: C  609 GLU cc_start: 0.7749 (pt0) cc_final: 0.7433 (pt0)
REVERT: C  636 MET cc_start: 0.8578 (tpp) cc_final: 0.8335 (tpp)
REVERT: C  696 TYR cc_start: 0.7799 (m-10) cc_final: 0.7462 (m-10)
REVERT: C  716 MET cc_start: 0.8441 (mmm) cc_final: 0.7698 (tpt)
  outliers start: 59
  outliers final: 54
  residues processed: 212
  average time/residue: 0.1141
  time to fit residues: 37.1889
Evaluate side-chains
  228 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 171
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  636 MET
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  667 TYR
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  769 TYR
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 THR
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  565 MET
Chi-restraints excluded: chain B residue  623 ASN
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  639 LEU
Chi-restraints excluded: chain B residue  667 TYR
Chi-restraints excluded: chain B residue  679 ASP
Chi-restraints excluded: chain B residue  701 VAL
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  768 ILE
Chi-restraints excluded: chain C residue   96 MET
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  342 VAL
Chi-restraints excluded: chain C residue  371 MET
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  420 VAL
Chi-restraints excluded: chain C residue  639 LEU
Chi-restraints excluded: chain C residue  687 PHE
Chi-restraints excluded: chain C residue  702 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 150 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 129 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 136 optimal weight:    0.8980
   chunk 146 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN
** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.141872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112007 restraints weight = 27231.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.115067 restraints weight = 15456.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116822 restraints weight = 10700.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.118124 restraints weight = 8543.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.118857 restraints weight = 7323.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  16233  Z= 0.201
  Angle     :  0.735  10.950  22095  Z= 0.381
  Chirality :  0.050   0.411   2529
  Planarity :  0.004   0.054   2760
  Dihedral  :  7.052  53.344   2781
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 13.62 %
    Favored  : 86.33 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.01 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.19), residues: 1902
  helix:  1.14 (0.25), residues: 471
  sheet: -1.25 (0.25), residues: 435
  loop : -3.28 (0.16), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 357 
 TYR   0.024   0.001   TYR A 289 
 PHE   0.036   0.002   PHE B 678 
 TRP   0.055   0.003   TRP A 431 
 HIS   0.004   0.001   HIS C 606 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (16188)
  covalent geometry    : angle       0.71937 (21975)
  SS BOND              : bond        0.00354 (   15)
  SS BOND              : angle       2.37681 (   30)
  hydrogen bonds       : bond        0.05168 (  506)
  hydrogen bonds       : angle       5.23773 ( 1410)
  link_NAG-ASN         : bond        0.00514 (   30)
  link_NAG-ASN         : angle       2.07161 (   90)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2373.83 seconds
wall clock time: 41 minutes 56.16 seconds (2516.16 seconds total)