Starting phenix.real_space_refine
on Fri Jul  3 20:39:03 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7kdp_22828/07_2026/7kdp_22828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kdp_22828/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kdp_22828/07_2026/7kdp_22828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kdp_22828/07_2026/7kdp_22828.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7kdp_22828/07_2026/7kdp_22828.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7kdp_22828/07_2026/7kdp_22828.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kdp_22828/07_2026/7kdp_22828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kdp_22828/07_2026/7kdp_22828.map"
  }
  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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 chiralities: 10
  Time building chain proxies: 2.86, per 1000 atoms: 0.18
  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: 1.14
  Conformation dependent library (CDL) restraints added in 685.2 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: 0.41
  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: 2.07

  Time building geometry restraints manager: 1.52 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: 8404
       17.36 -    34.71: 790
       34.71 -    52.07: 127
       52.07 -    69.43: 36
       69.43 -    86.79: 15
  Dihedral angle restraints: 9372
    sinusoidal: 3708
      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 9369 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:             1.320
  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:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.250
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
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  : 14.126  86.785   5685
  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/Z
  covalent geometry    : bond        0.00452 /  0.21 (16188)
  covalent geometry    : angle       0.75167 /  0.40 (21975)
  SS BOND              : bond        0.00246 /  0.16 (   15)
  SS BOND              : angle       1.98038 /  1.31 (   30)
  hydrogen bonds       : bond        0.16507 / 10.47 (  506)
  hydrogen bonds       : angle       7.10498 /  4.93 ( 1410)
  link_NAG-ASN         : bond        0.00564 /  0.29 (   30)
  link_NAG-ASN         : angle       2.49397 /  1.81 (   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  : 0.472 
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: 0.1072
  time to fit residues: 35.9423
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  : 0.550 
-------------------------------------------------------------------------------
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...
A 212 GLN
A 365 HIS
B 212 GLN
B 313 ASN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 623 ASN
C 212 GLN
C 313 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.147968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.121239 restraints weight = 26932.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.123923 restraints weight = 14931.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.124887 restraints weight = 10330.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.125320 restraints weight = 8584.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.125502 restraints weight = 8027.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1134

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   9.790  22095  Z= 0.358
  Chirality :  0.048   0.345   2529
  Planarity :  0.004   0.066   2760
  Dihedral  :  5.586  59.196   2141
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.93 %
    Favored  : 87.07 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.06 %
    Favored  : 89.52 %
  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:  1.28 (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   0.008   0.001   ARG C 357 
 TYR   0.015   0.001   TYR B 189 
 PHE   0.033   0.002   PHE B 678 
 TRP   0.025   0.002   TRP C 431 
 HIS   0.003   0.001   HIS B 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.16 (16188)
  covalent geometry    : angle       0.67152 /  0.35 (21975)
  SS BOND              : bond        0.00331 /  0.21 (   15)
  SS BOND              : angle       1.56111 /  1.06 (   30)
  hydrogen bonds       : bond        0.05315 /  3.59 (  506)
  hydrogen bonds       : angle       5.52613 /  3.87 ( 1410)
  link_NAG-ASN         : bond        0.00507 /  0.26 (   30)
  link_NAG-ASN         : angle       2.25751 /  1.71 (   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
  216 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 192
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  551 CYS cc_start: 0.6237 (m) cc_final: 0.5854 (m)
REVERT: A  686 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7957 (tm-30)
REVERT: A  752 PHE cc_start: 0.8162 (m-10) cc_final: 0.7806 (m-10)
REVERT: B  114 MET cc_start: 0.4718 (mtt) cc_final: 0.3109 (mtt)
REVERT: B  364 TYR cc_start: 0.5949 (m-80) cc_final: 0.5679 (m-80)
REVERT: B  623 ASN cc_start: 0.7871 (p0) cc_final: 0.7594 (p0)
REVERT: B  646 ASP cc_start: 0.8579 (t0) cc_final: 0.8323 (t0)
REVERT: B  686 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: C  364 TYR cc_start: 0.6450 (m-80) cc_final: 0.6173 (m-80)
REVERT: C  636 MET cc_start: 0.8609 (tpp) cc_final: 0.8304 (tpp)
REVERT: C  686 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8163 (tm-30)
  outliers start: 24
  outliers final: 15
  residues processed: 201
  average time/residue: 0.1023
  time to fit residues: 31.2791
Evaluate side-chains
  185 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 170
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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  700 LYS
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  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  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:    6.9990
   chunk 159 optimal weight:    0.9990
   chunk 149 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 139 optimal weight:    2.9990
   chunk 148 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 123 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 313 ASN
A 365 HIS
A 606 HIS
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 365 HIS
C 606 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.145530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.116369 restraints weight = 28126.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.119913 restraints weight = 15130.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.121003 restraints weight = 10338.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.122171 restraints weight = 8347.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.122204 restraints weight = 8056.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16233  Z= 0.152
  Angle     :  0.657   9.101  22095  Z= 0.342
  Chirality :  0.048   0.346   2529
  Planarity :  0.004   0.043   2760
  Dihedral  :  5.464  59.128   2141
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.72 %
    Favored  : 87.28 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.74 %
    Favored  : 83.48 %
  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: -2.53 (0.18), residues: 1902
  helix:  1.33 (0.25), residues: 450
  sheet: -1.40 (0.26), residues: 411
  loop : -3.39 (0.16), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 357 
 TYR   0.014   0.001   TYR B 189 
 PHE   0.033   0.002   PHE B 678 
 TRP   0.040   0.003   TRP C 431 
 HIS   0.003   0.001   HIS B 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.15 (16188)
  covalent geometry    : angle       0.64156 /  0.34 (21975)
  SS BOND              : bond        0.00297 /  0.19 (   15)
  SS BOND              : angle       1.38323 /  0.96 (   30)
  hydrogen bonds       : bond        0.04874 /  3.36 (  506)
  hydrogen bonds       : angle       5.21754 /  3.66 ( 1410)
  link_NAG-ASN         : bond        0.00499 /  0.25 (   30)
  link_NAG-ASN         : angle       2.18531 /  1.67 (   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
  230 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 200
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 MET cc_start: 0.6953 (ptt) cc_final: 0.6545 (ptp)
REVERT: A  431 TRP cc_start: 0.6854 (p-90) cc_final: 0.6509 (p-90)
REVERT: A  551 CYS cc_start: 0.6589 (m) cc_final: 0.6352 (m)
REVERT: A  686 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7872 (tm-30)
REVERT: A  752 PHE cc_start: 0.8166 (m-10) cc_final: 0.7873 (m-10)
REVERT: B  364 TYR cc_start: 0.5927 (m-80) cc_final: 0.5653 (m-80)
REVERT: B  370 LYS cc_start: 0.7304 (tppt) cc_final: 0.6904 (ttpt)
REVERT: B  371 MET cc_start: 0.7181 (tpt) cc_final: 0.6697 (tpt)
REVERT: B  506 TRP cc_start: 0.6085 (t-100) cc_final: 0.5848 (t-100)
REVERT: B  623 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7432 (p0)
REVERT: B  646 ASP cc_start: 0.8621 (t0) cc_final: 0.8210 (t0)
REVERT: B  686 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: C  114 MET cc_start: 0.2798 (mtt) cc_final: 0.2023 (mtt)
REVERT: C  123 GLU cc_start: 0.8189 (pp20) cc_final: 0.7986 (pp20)
REVERT: C  364 TYR cc_start: 0.6223 (m-80) cc_final: 0.5770 (m-80)
REVERT: C  371 MET cc_start: 0.6751 (tpt) cc_final: 0.6424 (tpt)
REVERT: C  616 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8366 (tt)
REVERT: C  623 ASN cc_start: 0.8224 (p0) cc_final: 0.8011 (p0)
REVERT: C  636 MET cc_start: 0.8688 (tpp) cc_final: 0.8438 (tpp)
REVERT: C  686 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8149 (tm-30)
  outliers start: 30
  outliers final: 21
  residues processed: 214
  average time/residue: 0.1070
  time to fit residues: 34.9258
Evaluate side-chains
  196 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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  696 TYR
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  679 ASP
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  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
Chi-restraints excluded: chain C residue  700 LYS
Chi-restraints excluded: chain C residue  744 VAL
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:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 160 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 183 optimal weight:    0.0570
   chunk 18 optimal weight:    0.4980
   chunk 96 optimal weight:   10.0000
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.8302

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 365 HIS
A 669 GLN
B 178 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 606 HIS
** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3872 r_free = 0.3872 target = 0.145744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116438 restraints weight = 27701.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.119833 restraints weight = 15372.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.120698 restraints weight = 10692.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.123246 restraints weight = 8721.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.123156 restraints weight = 7300.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16233  Z= 0.146
  Angle     :  0.655  10.406  22095  Z= 0.340
  Chirality :  0.048   0.370   2529
  Planarity :  0.004   0.041   2760
  Dihedral  :  5.281  58.006   2137
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.93 %
    Favored  : 87.07 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.80 %
    Favored  : 82.12 %
  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: -2.43 (0.18), residues: 1902
  helix:  1.39 (0.25), residues: 450
  sheet: -1.30 (0.26), residues: 417
  loop : -3.34 (0.16), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 357 
 TYR   0.011   0.001   TYR B 189 
 PHE   0.034   0.002   PHE B 678 
 TRP   0.044   0.002   TRP B 431 
 HIS   0.012   0.001   HIS B 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 (16188)
  covalent geometry    : angle       0.64098 /  0.34 (21975)
  SS BOND              : bond        0.00293 /  0.19 (   15)
  SS BOND              : angle       1.31586 /  0.91 (   30)
  hydrogen bonds       : bond        0.04690 /  3.25 (  506)
  hydrogen bonds       : angle       5.10140 /  3.57 ( 1410)
  link_NAG-ASN         : bond        0.00485 /  0.25 (   30)
  link_NAG-ASN         : angle       2.11644 /  1.62 (   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
  244 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 192
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
REVERT: A  371 MET cc_start: 0.6033 (tpt) cc_final: 0.5737 (tpt)
REVERT: A  431 TRP cc_start: 0.6915 (p-90) cc_final: 0.6611 (p-90)
REVERT: A  551 CYS cc_start: 0.6511 (m) cc_final: 0.6275 (m)
REVERT: A  686 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: A  704 PRO cc_start: 0.8821 (Cg_endo) cc_final: 0.8580 (Cg_exo)
REVERT: A  752 PHE cc_start: 0.8159 (m-10) cc_final: 0.7860 (m-10)
REVERT: B  364 TYR cc_start: 0.5925 (m-80) cc_final: 0.5688 (m-80)
REVERT: B  371 MET cc_start: 0.7308 (tpt) cc_final: 0.6739 (tpt)
REVERT: B  506 TRP cc_start: 0.6083 (t-100) cc_final: 0.5874 (t-100)
REVERT: B  646 ASP cc_start: 0.8660 (t0) cc_final: 0.8198 (t0)
REVERT: B  684 MET cc_start: 0.7749 (tpp) cc_final: 0.7429 (tpp)
REVERT: B  686 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8240 (tm-30)
REVERT: C  123 GLU cc_start: 0.8229 (pp20) cc_final: 0.7822 (pp20)
REVERT: C  350 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7360 (tm-30)
REVERT: C  364 TYR cc_start: 0.6112 (m-80) cc_final: 0.5664 (m-80)
REVERT: C  371 MET cc_start: 0.6733 (tpt) cc_final: 0.6420 (tpt)
REVERT: C  616 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8311 (tt)
REVERT: C  623 ASN cc_start: 0.8219 (p0) cc_final: 0.7933 (p0)
REVERT: C  636 MET cc_start: 0.8614 (tpp) cc_final: 0.8323 (tpp)
REVERT: C  686 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8195 (tm-30)
  outliers start: 52
  outliers final: 34
  residues processed: 225
  average time/residue: 0.1006
  time to fit residues: 35.1023
Evaluate side-chains
  206 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 171
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
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  636 MET
Chi-restraints excluded: chain A residue  702 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  338 ASP
Chi-restraints excluded: chain B residue  342 VAL
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  636 MET
Chi-restraints excluded: chain B residue  679 ASP
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  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  616 LEU
Chi-restraints excluded: chain C residue  669 GLN
Chi-restraints excluded: chain C residue  679 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 184 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 188 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 365 HIS
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.143198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.116645 restraints weight = 27129.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118704 restraints weight = 15406.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119377 restraints weight = 11677.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.119894 restraints weight = 9698.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.119957 restraints weight = 8675.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  16233  Z= 0.156
  Angle     :  0.671   8.935  22095  Z= 0.347
  Chirality :  0.048   0.407   2529
  Planarity :  0.004   0.039   2760
  Dihedral  :  5.073  24.513   2133
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.25 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 16.16 %
    Favored  : 79.87 %
  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: -2.39 (0.18), residues: 1902
  helix:  1.43 (0.25), residues: 450
  sheet: -1.22 (0.26), residues: 417
  loop : -3.34 (0.16), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 357 
 TYR   0.012   0.001   TYR A 289 
 PHE   0.039   0.002   PHE A 678 
 TRP   0.036   0.002   TRP C 431 
 HIS   0.012   0.001   HIS A 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 (16188)
  covalent geometry    : angle       0.65553 /  0.34 (21975)
  SS BOND              : bond        0.00206 /  0.13 (   15)
  SS BOND              : angle       1.96839 /  1.35 (   30)
  hydrogen bonds       : bond        0.04752 /  3.30 (  506)
  hydrogen bonds       : angle       5.10362 /  3.57 ( 1410)
  link_NAG-ASN         : bond        0.00505 /  0.26 (   30)
  link_NAG-ASN         : angle       2.10460 /  1.61 (   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
  250 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 183
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 TRP cc_start: 0.7023 (p-90) cc_final: 0.6717 (p-90)
REVERT: A  684 MET cc_start: 0.7387 (tpp) cc_final: 0.7091 (tpp)
REVERT: A  686 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: A  752 PHE cc_start: 0.8155 (m-10) cc_final: 0.7847 (m-10)
REVERT: B  364 TYR cc_start: 0.5988 (m-80) cc_final: 0.5739 (m-80)
REVERT: B  371 MET cc_start: 0.7268 (tpt) cc_final: 0.6786 (tpt)
REVERT: B  506 TRP cc_start: 0.6118 (t-100) cc_final: 0.5888 (t-100)
REVERT: B  623 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7446 (p0)
REVERT: B  646 ASP cc_start: 0.8699 (t0) cc_final: 0.8232 (t0)
REVERT: B  686 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: C  114 MET cc_start: 0.3546 (mtt) cc_final: 0.2432 (mtt)
REVERT: C  123 GLU cc_start: 0.8192 (pp20) cc_final: 0.7772 (pp20)
REVERT: C  350 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7390 (tm-30)
REVERT: C  364 TYR cc_start: 0.6304 (m-80) cc_final: 0.5899 (m-80)
REVERT: C  371 MET cc_start: 0.6793 (tpt) cc_final: 0.6452 (tpt)
REVERT: C  616 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8320 (tt)
REVERT: C  623 ASN cc_start: 0.8186 (p0) cc_final: 0.7926 (p0)
REVERT: C  636 MET cc_start: 0.8562 (tpp) cc_final: 0.8299 (tpp)
REVERT: C  686 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8203 (tm-30)
  outliers start: 67
  outliers final: 44
  residues processed: 232
  average time/residue: 0.0945
  time to fit residues: 34.5905
Evaluate side-chains
  217 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 171
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  719 LEU
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  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  565 MET
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  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  372 THR
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  616 LEU
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:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 158 optimal weight:    8.9990
   chunk 14 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 170 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 365 HIS
** 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 = 0.3874 r_free = 0.3874 target = 0.145872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.115801 restraints weight = 27396.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118887 restraints weight = 15467.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.120774 restraints weight = 10711.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.121951 restraints weight = 8467.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.122590 restraints weight = 7293.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  16233  Z= 0.146
  Angle     :  0.661   9.580  22095  Z= 0.341
  Chirality :  0.047   0.340   2529
  Planarity :  0.004   0.042   2760
  Dihedral  :  5.012  24.441   2133
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.46 %
    Favored  : 87.54 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 17.53 %
    Favored  : 78.86 %
  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: -2.39 (0.18), residues: 1902
  helix:  1.45 (0.25), residues: 453
  sheet: -1.35 (0.25), residues: 444
  loop : -3.33 (0.16), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 357 
 TYR   0.012   0.001   TYR B 189 
 PHE   0.030   0.002   PHE A 678 
 TRP   0.040   0.002   TRP C 431 
 HIS   0.003   0.001   HIS A 606 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 (16188)
  covalent geometry    : angle       0.64656 /  0.34 (21975)
  SS BOND              : bond        0.00275 /  0.19 (   15)
  SS BOND              : angle       1.51974 /  1.06 (   30)
  hydrogen bonds       : bond        0.04597 /  3.20 (  506)
  hydrogen bonds       : angle       5.06056 /  3.54 ( 1410)
  link_NAG-ASN         : bond        0.00500 /  0.26 (   30)
  link_NAG-ASN         : angle       2.07429 /  1.59 (   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
  241 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 180
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
REVERT: A  371 MET cc_start: 0.6184 (tpt) cc_final: 0.5954 (tpt)
REVERT: A  686 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: A  716 MET cc_start: 0.8382 (tpp) cc_final: 0.8058 (tpp)
REVERT: A  752 PHE cc_start: 0.8169 (m-10) cc_final: 0.7866 (m-10)
REVERT: B  364 TYR cc_start: 0.5803 (m-80) cc_final: 0.5572 (m-80)
REVERT: B  371 MET cc_start: 0.7423 (tpt) cc_final: 0.7132 (tpt)
REVERT: B  623 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7444 (p0)
REVERT: B  646 ASP cc_start: 0.8711 (t0) cc_final: 0.8227 (t0)
REVERT: B  686 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: B  716 MET cc_start: 0.8352 (tpp) cc_final: 0.8082 (tpp)
REVERT: C  123 GLU cc_start: 0.8278 (pp20) cc_final: 0.7742 (pp20)
REVERT: C  350 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7519 (tm-30)
REVERT: C  357 ARG cc_start: 0.6300 (ttm110) cc_final: 0.5525 (mtm110)
REVERT: C  371 MET cc_start: 0.6763 (tpt) cc_final: 0.6456 (tpt)
REVERT: C  616 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8353 (tt)
REVERT: C  623 ASN cc_start: 0.8183 (p0) cc_final: 0.7968 (p0)
REVERT: C  636 MET cc_start: 0.8460 (tpp) cc_final: 0.8222 (tpp)
REVERT: C  668 SER cc_start: 0.9104 (t) cc_final: 0.8863 (p)
REVERT: C  686 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: C  716 MET cc_start: 0.8576 (mmm) cc_final: 0.7692 (tpt)
  outliers start: 61
  outliers final: 45
  residues processed: 223
  average time/residue: 0.1004
  time to fit residues: 35.0890
Evaluate side-chains
  217 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 170
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 VAL
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  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  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  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  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  372 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  420 VAL
Chi-restraints excluded: chain C residue  616 LEU
Chi-restraints excluded: chain C residue  669 GLN
Chi-restraints excluded: chain C residue  679 ASP
Chi-restraints excluded: chain C residue  702 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 121 optimal weight:    0.2980
   chunk 90 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 119 optimal weight:    0.8980
   chunk 118 optimal weight:    0.4980
   chunk 182 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 153 optimal weight:    7.9990
   chunk 75 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 365 HIS
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN
C 313 ASN
C 669 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.144918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.117144 restraints weight = 26974.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.120067 restraints weight = 15318.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.120969 restraints weight = 9692.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.122500 restraints weight = 8633.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.122552 restraints weight = 7985.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16233  Z= 0.128
  Angle     :  0.658  10.964  22095  Z= 0.337
  Chirality :  0.047   0.332   2529
  Planarity :  0.004   0.046   2760
  Dihedral  :  4.885  24.810   2133
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.62 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.00 %
    Favored  : 78.74 %
  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: -2.22 (0.19), residues: 1902
  helix:  1.61 (0.25), residues: 450
  sheet: -1.28 (0.25), residues: 444
  loop : -3.21 (0.16), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 357 
 TYR   0.033   0.001   TYR A 289 
 PHE   0.029   0.001   PHE A 678 
 TRP   0.040   0.002   TRP A 431 
 HIS   0.002   0.001   HIS C 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 (16188)
  covalent geometry    : angle       0.63995 /  0.33 (21975)
  SS BOND              : bond        0.00583 /  0.43 (   15)
  SS BOND              : angle       2.56738 /  1.73 (   30)
  hydrogen bonds       : bond        0.04327 /  3.03 (  506)
  hydrogen bonds       : angle       4.96040 /  3.47 ( 1410)
  link_NAG-ASN         : bond        0.00510 /  0.26 (   30)
  link_NAG-ASN         : angle       2.05046 /  1.57 (   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
  240 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 185
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
REVERT: A  686 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8037 (tm-30)
REVERT: A  716 MET cc_start: 0.8344 (tpp) cc_final: 0.8035 (tpp)
REVERT: A  752 PHE cc_start: 0.8130 (m-10) cc_final: 0.7823 (m-10)
REVERT: B  371 MET cc_start: 0.7333 (tpt) cc_final: 0.6879 (tpt)
REVERT: B  506 TRP cc_start: 0.6030 (t-100) cc_final: 0.5756 (t-100)
REVERT: B  510 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7851 (mm110)
REVERT: B  623 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7351 (p0)
REVERT: B  646 ASP cc_start: 0.8705 (t0) cc_final: 0.8221 (t0)
REVERT: B  686 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: C  123 GLU cc_start: 0.8279 (pp20) cc_final: 0.7752 (pp20)
REVERT: C  350 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: C  357 ARG cc_start: 0.5917 (ttm110) cc_final: 0.5407 (ttp80)
REVERT: C  371 MET cc_start: 0.6701 (tpt) cc_final: 0.6380 (tpt)
REVERT: C  616 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8315 (tt)
REVERT: C  636 MET cc_start: 0.8540 (tpp) cc_final: 0.8320 (tpp)
REVERT: C  686 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8112 (tm-30)
REVERT: C  716 MET cc_start: 0.8579 (mmm) cc_final: 0.7687 (tpt)
  outliers start: 55
  outliers final: 42
  residues processed: 225
  average time/residue: 0.1064
  time to fit residues: 37.2188
Evaluate side-chains
  210 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 166
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  667 TYR
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  313 ASN
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  616 LEU
Chi-restraints excluded: chain C residue  679 ASP
Chi-restraints excluded: chain C residue  717 SER
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:    0.9990
   chunk 151 optimal weight:    0.5980
   chunk 186 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 156 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 178 HIS
** B 501 GLN ** 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 = 0.3859 r_free = 0.3859 target = 0.143385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.116619 restraints weight = 27136.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.118087 restraints weight = 19464.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.118926 restraints weight = 12779.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.119573 restraints weight = 10924.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.119792 restraints weight = 10330.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  16233  Z= 0.157
  Angle     :  0.690  10.277  22095  Z= 0.354
  Chirality :  0.048   0.428   2529
  Planarity :  0.004   0.048   2760
  Dihedral  :  4.944  24.404   2133
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.67 %
    Favored  : 87.33 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.71 %
    Favored  : 78.09 %
  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:  1.57 (0.25), residues: 453
  sheet: -1.28 (0.25), residues: 444
  loop : -3.24 (0.16), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 357 
 TYR   0.029   0.001   TYR A 289 
 PHE   0.031   0.002   PHE A 678 
 TRP   0.067   0.002   TRP A 431 
 HIS   0.003   0.001   HIS B 606 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 (16188)
  covalent geometry    : angle       0.67227 /  0.35 (21975)
  SS BOND              : bond        0.00432 /  0.28 (   15)
  SS BOND              : angle       2.57105 /  1.66 (   30)
  hydrogen bonds       : bond        0.04619 /  3.20 (  506)
  hydrogen bonds       : angle       5.03784 /  3.53 ( 1410)
  link_NAG-ASN         : bond        0.00516 /  0.26 (   30)
  link_NAG-ASN         : angle       2.08689 /  1.59 (   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
  223 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 169
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 MET cc_start: 0.6899 (ptt) cc_final: 0.6521 (ptp)
REVERT: A  686 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8093 (tm-30)
REVERT: A  752 PHE cc_start: 0.8131 (m-10) cc_final: 0.7827 (m-10)
REVERT: A  769 TYR cc_start: 0.6189 (OUTLIER) cc_final: 0.5202 (t80)
REVERT: B  371 MET cc_start: 0.7361 (tpt) cc_final: 0.6962 (tpt)
REVERT: B  506 TRP cc_start: 0.6163 (t-100) cc_final: 0.5945 (t-100)
REVERT: B  623 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7360 (p0)
REVERT: B  646 ASP cc_start: 0.8727 (t0) cc_final: 0.8267 (t0)
REVERT: B  648 MET cc_start: 0.6882 (tpp) cc_final: 0.6132 (mpp)
REVERT: B  684 MET cc_start: 0.7684 (tpp) cc_final: 0.7448 (tpp)
REVERT: B  686 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: C  123 GLU cc_start: 0.8242 (pp20) cc_final: 0.7814 (pp20)
REVERT: C  357 ARG cc_start: 0.6330 (ttm110) cc_final: 0.6007 (mtm180)
REVERT: C  364 TYR cc_start: 0.6352 (m-80) cc_final: 0.6078 (m-80)
REVERT: C  371 MET cc_start: 0.6773 (tpt) cc_final: 0.6454 (tpt)
REVERT: C  616 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8348 (tt)
REVERT: C  636 MET cc_start: 0.8480 (tpp) cc_final: 0.8248 (tpp)
REVERT: C  686 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8118 (tm-30)
REVERT: C  696 TYR cc_start: 0.7739 (m-10) cc_final: 0.7377 (m-10)
REVERT: C  716 MET cc_start: 0.8607 (mmm) cc_final: 0.7833 (tpt)
  outliers start: 54
  outliers final: 46
  residues processed: 209
  average time/residue: 0.1049
  time to fit residues: 33.9621
Evaluate side-chains
  214 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 165
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
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  602 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 A residue  744 VAL
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  623 ASN
Chi-restraints excluded: chain B residue  636 MET
Chi-restraints excluded: chain B residue  667 TYR
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  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  616 LEU
Chi-restraints excluded: chain C residue  679 ASP
Chi-restraints excluded: chain C residue  717 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 174 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0670
   chunk 67 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   chunk 96 optimal weight:    8.9990
   chunk 135 optimal weight:    1.9990
   chunk 150 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 132 optimal weight:    0.6980
   chunk 127 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 365 HIS
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN
B 510 GLN
C 313 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.147113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.117628 restraints weight = 27295.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.120732 restraints weight = 15149.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.122683 restraints weight = 10369.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.123866 restraints weight = 8129.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.124671 restraints weight = 6954.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2509

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= 0.124
  Angle     :  0.670  10.652  22095  Z= 0.340
  Chirality :  0.047   0.442   2529
  Planarity :  0.004   0.051   2760
  Dihedral  :  4.772  24.857   2133
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.83 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.06 %
    Favored  : 78.03 %
  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: -2.06 (0.19), residues: 1902
  helix:  1.66 (0.25), residues: 447
  sheet: -1.18 (0.25), residues: 444
  loop : -3.05 (0.17), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 357 
 TYR   0.026   0.001   TYR A 289 
 PHE   0.025   0.001   PHE A 678 
 TRP   0.055   0.002   TRP A 431 
 HIS   0.004   0.001   HIS A 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 (16188)
  covalent geometry    : angle       0.65467 /  0.34 (21975)
  SS BOND              : bond        0.00319 /  0.20 (   15)
  SS BOND              : angle       2.07421 /  1.35 (   30)
  hydrogen bonds       : bond        0.04055 /  2.84 (  506)
  hydrogen bonds       : angle       4.87901 /  3.41 ( 1410)
  link_NAG-ASN         : bond        0.00513 /  0.26 (   30)
  link_NAG-ASN         : angle       2.01138 /  1.54 (   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
  228 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 179
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A  686 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7992 (tm-30)
REVERT: A  752 PHE cc_start: 0.8101 (m-10) cc_final: 0.7795 (m-10)
REVERT: A  769 TYR cc_start: 0.6237 (OUTLIER) cc_final: 0.5177 (t80)
REVERT: B  371 MET cc_start: 0.7185 (tpt) cc_final: 0.6879 (tpt)
REVERT: B  623 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.7263 (p0)
REVERT: B  646 ASP cc_start: 0.8639 (t0) cc_final: 0.8253 (t0)
REVERT: B  686 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: B  704 PRO cc_start: 0.8627 (Cg_endo) cc_final: 0.8361 (Cg_exo)
REVERT: C  123 GLU cc_start: 0.8329 (pp20) cc_final: 0.7731 (pp20)
REVERT: C  371 MET cc_start: 0.6672 (tpt) cc_final: 0.6376 (tpt)
REVERT: C  616 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8283 (tt)
REVERT: C  636 MET cc_start: 0.8489 (tpp) cc_final: 0.8252 (tpp)
REVERT: C  686 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: C  700 LYS cc_start: 0.8721 (tppt) cc_final: 0.8436 (tppt)
REVERT: C  716 MET cc_start: 0.8507 (mmm) cc_final: 0.7778 (tpt)
  outliers start: 49
  outliers final: 40
  residues processed: 212
  average time/residue: 0.1049
  time to fit residues: 34.1726
Evaluate side-chains
  209 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 166
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  667 TYR
Chi-restraints excluded: chain A residue  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  769 TYR
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  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  701 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  274 VAL
Chi-restraints excluded: chain C residue  338 ASP
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  616 LEU
Chi-restraints excluded: chain C residue  679 ASP
Chi-restraints excluded: chain C residue  717 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 144 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 181 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 125 optimal weight:    2.9990
   chunk 165 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 365 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.145028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.116868 restraints weight = 27271.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.119875 restraints weight = 14134.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.120998 restraints weight = 9680.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.121288 restraints weight = 8159.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.121430 restraints weight = 7646.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16233  Z= 0.152
  Angle     :  0.693  10.102  22095  Z= 0.355
  Chirality :  0.048   0.458   2529
  Planarity :  0.004   0.053   2760
  Dihedral  :  4.823  24.138   2133
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.72 %
    Favored  : 87.28 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.12 %
    Favored  : 78.21 %
  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: -2.13 (0.19), residues: 1902
  helix:  1.60 (0.25), residues: 453
  sheet: -1.17 (0.25), residues: 444
  loop : -3.14 (0.16), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG B 357 
 TYR   0.026   0.001   TYR A 289 
 PHE   0.026   0.002   PHE A 678 
 TRP   0.057   0.003   TRP B 431 
 HIS   0.004   0.001   HIS A 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 (16188)
  covalent geometry    : angle       0.67955 /  0.35 (21975)
  SS BOND              : bond        0.00268 /  0.18 (   15)
  SS BOND              : angle       1.93060 /  1.28 (   30)
  hydrogen bonds       : bond        0.04484 /  3.12 (  506)
  hydrogen bonds       : angle       4.97734 /  3.47 ( 1410)
  link_NAG-ASN         : bond        0.00517 /  0.26 (   30)
  link_NAG-ASN         : angle       2.01625 /  1.54 (   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
  213 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 168
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  504 GLU cc_start: 0.7430 (pt0) cc_final: 0.7223 (pt0)
REVERT: A  686 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: A  752 PHE cc_start: 0.8153 (m-10) cc_final: 0.7912 (m-10)
REVERT: A  769 TYR cc_start: 0.6194 (OUTLIER) cc_final: 0.5134 (t80)
REVERT: B  371 MET cc_start: 0.7237 (tpt) cc_final: 0.6998 (tpt)
REVERT: B  623 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7277 (p0)
REVERT: B  646 ASP cc_start: 0.8717 (t0) cc_final: 0.8277 (t0)
REVERT: B  648 MET cc_start: 0.6668 (tpp) cc_final: 0.5904 (mpp)
REVERT: B  705 LEU cc_start: 0.6813 (tp) cc_final: 0.6500 (tp)
REVERT: C  123 GLU cc_start: 0.8334 (pp20) cc_final: 0.7736 (pp20)
REVERT: C  295 ASP cc_start: 0.6540 (t0) cc_final: 0.6310 (t70)
REVERT: C  371 MET cc_start: 0.6720 (tpt) cc_final: 0.6447 (tpt)
REVERT: C  616 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8342 (tt)
REVERT: C  636 MET cc_start: 0.8555 (tpp) cc_final: 0.8309 (tpp)
REVERT: C  686 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: C  696 TYR cc_start: 0.7702 (m-10) cc_final: 0.7319 (m-10)
REVERT: C  700 LYS cc_start: 0.8745 (tppt) cc_final: 0.8485 (tppt)
REVERT: C  716 MET cc_start: 0.8585 (mmm) cc_final: 0.7815 (tpt)
  outliers start: 45
  outliers final: 41
  residues processed: 198
  average time/residue: 0.0987
  time to fit residues: 30.5523
Evaluate side-chains
  209 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 165
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  687 PHE
Chi-restraints excluded: chain A residue  702 VAL
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  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  687 PHE
Chi-restraints excluded: chain B residue  701 VAL
Chi-restraints excluded: chain B residue  702 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  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  616 LEU
Chi-restraints excluded: chain C residue  679 ASP
Chi-restraints excluded: chain C residue  717 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 150 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 129 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 103 optimal weight:    0.7980
   chunk 136 optimal weight:    0.6980
   chunk 146 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 365 HIS
** C 365 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 = 0.3868 r_free = 0.3868 target = 0.145902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.117545 restraints weight = 27135.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.120679 restraints weight = 14741.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.121488 restraints weight = 10032.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.121500 restraints weight = 8650.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.123002 restraints weight = 8161.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  16233  Z= 0.137
  Angle     :  0.680  10.227  22095  Z= 0.347
  Chirality :  0.048   0.454   2529
  Planarity :  0.004   0.092   2760
  Dihedral  :  4.786  24.682   2133
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.30 %
    Favored  : 87.70 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.12 %
    Favored  : 77.98 %
  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: -2.09 (0.19), residues: 1902
  helix:  1.60 (0.25), residues: 453
  sheet: -1.13 (0.25), residues: 444
  loop : -3.11 (0.16), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 357 
 TYR   0.025   0.001   TYR A 289 
 PHE   0.021   0.002   PHE A 678 
 TRP   0.050   0.003   TRP A 431 
 HIS   0.003   0.001   HIS A 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 (16188)
  covalent geometry    : angle       0.66673 /  0.34 (21975)
  SS BOND              : bond        0.00287 /  0.19 (   15)
  SS BOND              : angle       1.74300 /  1.16 (   30)
  hydrogen bonds       : bond        0.04261 /  2.98 (  506)
  hydrogen bonds       : angle       4.91741 /  3.43 ( 1410)
  link_NAG-ASN         : bond        0.00505 /  0.25 (   30)
  link_NAG-ASN         : angle       1.99905 /  1.53 (   90)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2086.05 seconds
wall clock time: 36 minutes 53.53 seconds (2213.53 seconds total)