Starting phenix.real_space_refine
on Tue Nov 18 07:04:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ceb_7463/11_2025/6ceb_7463_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ceb_7463/11_2025/6ceb_7463.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ceb_7463/11_2025/6ceb_7463.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ceb_7463/11_2025/6ceb_7463.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ceb_7463/11_2025/6ceb_7463_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ceb_7463/11_2025/6ceb_7463_neut.cif"
  }
  resolution = 4.7
  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=   0.003 sd=   0.054
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: 4
    Type Number    sf(0)   Gaussians
     S      96      5.16       5
     C    7417      2.51       5
     N    1969      2.21       5
     O    2240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11722
  Number of models: 1
  Model: ""
    Number of chains: 20
    Chain: "A"
      Number of atoms: 5500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 682, 5500
          Classifications: {'peptide': 682}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 645}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 4540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 562, 4540
          Classifications: {'peptide': 562}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 535}
          Chain breaks: 4
    Chain: "M"
      Number of atoms: 243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 243
          Classifications: {'peptide': 30}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 27}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "K"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 163
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
    Chain: "L"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 240
          Classifications: {'peptide': 30}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 28}
    Chain: "N"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 163
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
    Chain: "O"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 240
          Classifications: {'peptide': 30}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 28}
    Chain: "P"
      Number of atoms: 243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 243
          Classifications: {'peptide': 30}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 27}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 24
          Unusual residues: {'FUC': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "I"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "J"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "Q"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "R"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 24
          Unusual residues: {'FUC': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.98, per 1000 atoms: 0.25
  Number of scatterers: 11722
  At special positions: 0
  Unit cell: (91.3, 149.6, 154, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      96     16.00
     O    2240      8.00
     N    1969      7.00
     C    7417      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=31, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 169 " - pdb=" SG  CYS A 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 253 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 435 " - pdb=" SG  CYS A 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 786 " - pdb=" SG  CYS A 795 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   8 " - pdb=" SG  CYS B  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 192 " - pdb=" SG  CYS B 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 196 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 216 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 228 " - pdb=" SG  CYS B 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 253 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 259 " - pdb=" SG  CYS B 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 266 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 288 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 312 " - pdb=" SG  CYS B 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 435 " - pdb=" SG  CYS B 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K   6 " - pdb=" SG  CYS K  11 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N   6 " - pdb=" SG  CYS N  11 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
      " NAG Q   1 " - " NAG Q   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
      " NAG E   1 " - " FUC E   3 "
      " NAG G   1 " - " FUC G   2 "
      " NAG H   1 " - " FUC H   3 "
      " NAG J   1 " - " FUC J   3 "
      " NAG R   1 " - " FUC R   2 "
    NAG-ASN
      " NAG A1014 " - " ASN A  16 "
      " NAG B1014 " - " ASN B  16 "
      " NAG C   1 " - " ASN A  25 "
      " NAG D   1 " - " ASN A 111 "
      " NAG E   1 " - " ASN A 255 "
      " NAG F   1 " - " ASN A 397 "
      " NAG G   1 " - " ASN A 418 "
      " NAG H   1 " - " ASN B  25 "
      " NAG I   1 " - " ASN B 111 "
      " NAG J   1 " - " ASN B 255 "
      " NAG Q   1 " - " ASN B 397 "
      " NAG R   1 " - " ASN B 418 "
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 573.3 milliseconds
  

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2656

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 29 sheets defined
      17.6% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 24
      removed outlier: 3.648A  pdb=" N   HIS A  21 " --> pdb=" O   THR A  18 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLU A  24 " --> pdb=" O   HIS A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 48
      removed outlier: 3.628A  pdb=" N   ARG A  47 " --> pdb=" O   PRO A  43 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ASP A  48 " --> pdb=" O   GLU A  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 43 through 48'
    Processing helix  chain 'A' and resid 139 through 143
      removed outlier: 3.592A  pdb=" N   ASP A 142 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN A 143 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 139 through 143'
    Processing helix  chain 'A' and resid 150 through 152
      No H-bonds generated for 'chain 'A' and resid 150 through 152'
    Processing helix  chain 'A' and resid 221 through 224
    Processing helix  chain 'A' and resid 255 through 264
      removed outlier: 3.847A  pdb=" N   CYS A 259 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   HIS A 263 " --> pdb=" O   CYS A 259 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   HIS A 264 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 328
    Processing helix  chain 'A' and resid 329 through 331
      No H-bonds generated for 'chain 'A' and resid 329 through 331'
    Processing helix  chain 'A' and resid 350 through 356
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.834A  pdb=" N   ILE A 439 " --> pdb=" O   CYS A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.815A  pdb=" N   GLN A 452 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 638 through 644
      removed outlier: 3.569A  pdb=" N   PHE A 642 " --> pdb=" O   SER A 639 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLU A 643 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A 644 " --> pdb=" O   LEU A 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 24
      removed outlier: 3.741A  pdb=" N   HIS B  21 " --> pdb=" O   THR B  18 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLU B  24 " --> pdb=" O   HIS B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 48
      removed outlier: 4.017A  pdb=" N   ARG B  47 " --> pdb=" O   PRO B  43 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ASP B  48 " --> pdb=" O   GLU B  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 43 through 48'
    Processing helix  chain 'B' and resid 139 through 143
      removed outlier: 3.639A  pdb=" N   ASN B 143 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 264
      removed outlier: 3.759A  pdb=" N   CYS B 259 " --> pdb=" O   ASN B 255 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   HIS B 263 " --> pdb=" O   CYS B 259 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   HIS B 264 " --> pdb=" O   GLN B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 328
    Processing helix  chain 'B' and resid 329 through 331
      No H-bonds generated for 'chain 'B' and resid 329 through 331'
    Processing helix  chain 'B' and resid 350 through 357
      removed outlier: 3.738A  pdb=" N   ASN B 357 " --> pdb=" O   GLU B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 447
      removed outlier: 3.834A  pdb=" N   ILE B 439 " --> pdb=" O   CYS B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 452
      removed outlier: 3.528A  pdb=" N   ARG B 451 " --> pdb=" O   THR B 448 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLN B 452 " --> pdb=" O   LYS B 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 448 through 452'
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'M' and resid 692 through 715
      removed outlier: 3.539A  pdb=" N   LEU M 696 " --> pdb=" O   ILE M 692 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU M 709 " --> pdb=" O   PHE M 705 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   VAL M 715 " --> pdb=" O   ASN M 711 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 7
    Processing helix  chain 'K' and resid 12 through 18
      removed outlier: 3.792A  pdb=" N   ASN K  18 " --> pdb=" O   TYR K  14 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 7 through 20
    Processing helix  chain 'N' and resid 2 through 7
    Processing helix  chain 'N' and resid 12 through 18
      removed outlier: 3.792A  pdb=" N   ASN N  18 " --> pdb=" O   TYR N  14 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 7 through 20
    Processing helix  chain 'P' and resid 692 through 715
      removed outlier: 3.538A  pdb=" N   LEU P 696 " --> pdb=" O   ILE P 692 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU P 709 " --> pdb=" O   PHE P 705 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   VAL P 715 " --> pdb=" O   ASN P 711 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14
      removed outlier: 6.647A  pdb=" N   VAL A  66 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   LEU A  61 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   PHE A  96 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   LEU A  63 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU A  93 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   GLU A 120 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ILE A  95 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ASN A 122 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   VAL A 146 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ILE A 119 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ASN A 148 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   LYS A 121 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173
    Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216
      removed outlier: 4.765A  pdb=" N   LEU A 213 " --> pdb=" O   CYS A 228 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   CYS A 228 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ASN A 215 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 232
      removed outlier: 3.607A  pdb=" N   PHE A 231 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 254
      removed outlier: 3.514A  pdb=" N   ARG A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   HIS A 247 " --> pdb=" O   CYS A 284 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 293
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321
      removed outlier: 3.686A  pdb=" N   LEU A 314 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   SER A 339 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   GLU A 316 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
      removed outlier: 10.129A  pdb=" N   ILE A 341 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
      removed outlier: 9.462A  pdb=" N   GLU A 318 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364
    Processing sheet with id=AB1, first strand: chain 'A' and resid 402 through 403
      removed outlier: 6.452A  pdb=" N   ALA A 402 " --> pdb=" O   HIS A 429 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 472
      removed outlier: 6.395A  pdb=" N   GLU A 471 " --> pdb=" O   LYS A 582 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 475 through 480
      removed outlier: 3.811A  pdb=" N   LEU A 487 " --> pdb=" O   TRP A 551 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   TRP A 551 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 532 through 534
    Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 604
    Processing sheet with id=AB6, first strand: chain 'A' and resid 759 through 762
    Processing sheet with id=AB7, first strand: chain 'B' and resid 13 through 14
      removed outlier: 6.731A  pdb=" N   LEU B  33 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   PHE B  64 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE B  35 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   VAL B  66 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   LEU B  37 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LEU B  61 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 8.099A  pdb=" N   PHE B  96 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LEU B  63 " --> pdb=" O   PHE B  96 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU B  93 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   GLU B 120 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ILE B  95 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ASN B 122 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ASN B 148 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29
    Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173
    Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 216
      removed outlier: 4.576A  pdb=" N   LEU B 213 " --> pdb=" O   CYS B 228 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   CYS B 228 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   ASN B 215 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 231 through 233
      removed outlier: 3.539A  pdb=" N   PHE B 231 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.525A  pdb=" N   ARG B 252 " --> pdb=" O   PHE B 248 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   HIS B 247 " --> pdb=" O   CYS B 284 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 292 through 293
    Processing sheet with id=AC5, first strand: chain 'B' and resid 318 through 321
    Processing sheet with id=AC6, first strand: chain 'B' and resid 335 through 336
      removed outlier: 3.760A  pdb=" N   ILE B 336 " --> pdb=" O   GLU B 363 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'B' and resid 387 through 388
    Processing sheet with id=AC8, first strand: chain 'B' and resid 402 through 403
      removed outlier: 6.622A  pdb=" N   ALA B 402 " --> pdb=" O   HIS B 429 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC8
    Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 472
      removed outlier: 6.301A  pdb=" N   GLU B 471 " --> pdb=" O   LYS B 582 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC9
    Processing sheet with id=AD1, first strand: chain 'B' and resid 475 through 480
    Processing sheet with id=AD2, first strand: chain 'B' and resid 532 through 534

    230 hydrogen bonds defined for protein.
    591 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: 2.26

  Time building geometry restraints manager: 1.28 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: 3729
        1.34 -     1.46: 2850
        1.46 -     1.58: 5292
        1.58 -     1.70: 0
        1.70 -     1.83: 115
  Bond restraints: 11986
  Sorted by residual:
  bond pdb=" C5  FUC G   2 "
       pdb=" O5  FUC G   2 "
    ideal  model  delta    sigma   weight residual
    1.423  1.471 -0.048 2.00e-02 2.50e+03 5.72e+00
  bond pdb=" C5  FUC R   2 "
       pdb=" O5  FUC R   2 "
    ideal  model  delta    sigma   weight residual
    1.423  1.468 -0.045 2.00e-02 2.50e+03 5.07e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.560 -0.041 2.00e-02 2.50e+03 4.23e+00
  bond pdb=" C1  BMA I   3 "
       pdb=" C2  BMA I   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.558 -0.039 2.00e-02 2.50e+03 3.90e+00
  bond pdb=" CA  ASN B 405 "
       pdb=" CB  ASN B 405 "
    ideal  model  delta    sigma   weight residual
    1.527  1.493  0.034 1.75e-02 3.27e+03 3.77e+00
  ... (remaining 11981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 15383
        2.07 -     4.14: 705
        4.14 -     6.21: 120
        6.21 -     8.28: 23
        8.28 -    10.35: 3
  Bond angle restraints: 16234
  Sorted by residual:
  angle pdb=" C   HIS B   1 "
        pdb=" N   LEU B   2 "
        pdb=" CA  LEU B   2 "
      ideal   model   delta    sigma   weight residual
     121.54  131.89  -10.35 1.91e+00 2.74e-01 2.94e+01
  angle pdb=" C   HIS A   1 "
        pdb=" N   LEU A   2 "
        pdb=" CA  LEU A   2 "
      ideal   model   delta    sigma   weight residual
     121.54  131.14   -9.60 1.91e+00 2.74e-01 2.53e+01
  angle pdb=" CA  ASP A 591 "
        pdb=" C   ASP A 591 "
        pdb=" O   ASP A 591 "
      ideal   model   delta    sigma   weight residual
     117.94  120.79   -2.85 5.80e-01 2.97e+00 2.41e+01
  angle pdb=" C   ASP A 591 "
        pdb=" CA  ASP A 591 "
        pdb=" CB  ASP A 591 "
      ideal   model   delta    sigma   weight residual
     117.07  110.09    6.98 1.44e+00 4.82e-01 2.35e+01
  angle pdb=" N   GLY B  10 "
        pdb=" CA  GLY B  10 "
        pdb=" C   GLY B  10 "
      ideal   model   delta    sigma   weight residual
     110.97  118.48   -7.51 1.56e+00 4.11e-01 2.32e+01
  ... (remaining 16229 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.75: 7385
       21.75 -    43.51: 211
       43.51 -    65.26: 18
       65.26 -    87.02: 21
       87.02 -   108.77: 8
  Dihedral angle restraints: 7643
    sinusoidal: 3538
      harmonic: 4105
  Sorted by residual:
  dihedral pdb=" CA  CYS B 468 "
           pdb=" C   CYS B 468 "
           pdb=" N   GLU B 469 "
           pdb=" CA  GLU B 469 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -133.50  -46.50     0      5.00e+00 4.00e-02 8.65e+01
  dihedral pdb=" CA  CYS A 468 "
           pdb=" C   CYS A 468 "
           pdb=" N   GLU A 469 "
           pdb=" CA  GLU A 469 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.96  -44.04     0      5.00e+00 4.00e-02 7.76e+01
  dihedral pdb=" CA  VAL P 715 "
           pdb=" C   VAL P 715 "
           pdb=" N   PRO P 716 "
           pdb=" CA  PRO P 716 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.45   41.55     0      5.00e+00 4.00e-02 6.90e+01
  ... (remaining 7640 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1652
       0.090 -    0.181: 191
       0.181 -    0.271: 11
       0.271 -    0.362: 4
       0.362 -    0.452: 4
  Chirality restraints: 1862
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN A 418 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.95   -0.45 2.00e-01 2.50e+01 5.11e+00
  chirality pdb=" C1  NAG R   1 "
            pdb=" ND2 ASN B 418 "
            pdb=" C2  NAG R   1 "
            pdb=" O5  NAG R   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.43e+00
  chirality pdb=" C1  NAG Q   1 "
            pdb=" ND2 ASN B 397 "
            pdb=" C2  NAG Q   1 "
            pdb=" O5  NAG Q   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.99   -0.41 2.00e-01 2.50e+01 4.30e+00
  ... (remaining 1859 not shown)

  Planarity restraints: 2062
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL M 715 "    0.064 5.00e-02 4.00e+02   9.77e-02 1.53e+01
        pdb=" N   PRO M 716 "   -0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO M 716 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO M 716 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL P 715 "   -0.064 5.00e-02 4.00e+02   9.75e-02 1.52e+01
        pdb=" N   PRO P 716 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO P 716 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO P 716 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL P 715 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.91e+00
        pdb=" C   VAL P 715 "    0.045 2.00e-02 2.50e+03
        pdb=" O   VAL P 715 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PRO P 716 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2059 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     2.01: 1
        2.01 -     2.73: 871
        2.73 -     3.46: 16598
        3.46 -     4.18: 28856
        4.18 -     4.90: 47535
  Nonbonded interactions: 93861
  Sorted by model distance:
  nonbonded pdb=" N   THR A 560 "
            pdb=" OG1 THR A 590 "
     model   vdw
     1.288 3.120
  nonbonded pdb=" N   TRP A 559 "
            pdb=" O   ASP A 591 "
     model   vdw
     2.146 3.120
  nonbonded pdb=" CA  THR A 560 "
            pdb=" OG1 THR A 590 "
     model   vdw
     2.249 3.470
  nonbonded pdb=" O   THR A 593 "
            pdb=" ND2 ASN A 787 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   SER A 323 "
            pdb=" OG  SER A 326 "
     model   vdw
     2.288 3.040
  ... (remaining 93856 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 'C' and resid 1 through 2)
  selection = (chain 'D' and resid 1 through 2)
  selection = (chain 'E' and resid 1 through 2)
  selection = (chain 'H' and resid 1 through 2)
  selection = (chain 'I' and resid 1 through 2)
  selection = (chain 'J' and resid 1 through 2)
}
ncs_group {
  reference = (chain 'F' and resid 1)
  selection = (chain 'G' and resid 1)
  selection = (chain 'Q' and resid 1)
  selection = (chain 'R' and resid 1)
}
ncs_group {
  reference = chain 'K'
  selection = chain 'N'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'P'
}

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:             2.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.600
  Find NCS groups from input model:        0.130
  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:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  12045  Z= 0.301
  Angle     :  1.055  12.507  16380  Z= 0.551
  Chirality :  0.060   0.452   1862
  Planarity :  0.007   0.098   2050
  Dihedral  : 11.439 108.769   4894
  Min Nonbonded Distance : 1.288

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 11.81 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.41 %
    Twisted General : 0.68 %

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: -3.39 (0.20), residues: 1372
  helix: -2.41 (0.29), residues: 180
  sheet: -0.68 (0.35), residues: 200
  loop : -2.78 (0.18), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 181 
 TYR   0.026   0.003   TYR N  19 
 PHE   0.040   0.004   PHE P 714 
 TRP   0.025   0.003   TRP B 251 
 HIS   0.014   0.003   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 (11986)
  covalent geometry    : angle       1.02002 (16234)
  SS BOND              : bond        0.00431 (   31)
  SS BOND              : angle       1.28113 (   62)
  hydrogen bonds       : bond        0.17943 (  230)
  hydrogen bonds       : angle       9.38196 (  591)
  link_BETA1-4         : bond        0.00605 (   10)
  link_BETA1-4         : angle       3.55580 (   30)
  link_BETA1-6         : bond        0.00511 (    6)
  link_BETA1-6         : angle       2.18023 (   18)
  link_NAG-ASN         : bond        0.00460 (   12)
  link_NAG-ASN         : angle       4.65761 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 LEU cc_start: 0.9790 (tt) cc_final: 0.9560 (mt)
REVERT: A  101 LEU cc_start: 0.9692 (tp) cc_final: 0.9385 (mt)
REVERT: A  110 MET cc_start: 0.9009 (mmt) cc_final: 0.8644 (mmm)
REVERT: A  120 GLU cc_start: 0.9675 (tt0) cc_final: 0.8604 (mt-10)
REVERT: A  137 LEU cc_start: 0.9415 (mp) cc_final: 0.9098 (tp)
REVERT: A  294 MET cc_start: 0.8938 (ppp) cc_final: 0.8595 (ppp)
REVERT: A  350 LEU cc_start: 0.9507 (mt) cc_final: 0.9131 (mm)
REVERT: A  353 GLU cc_start: 0.9678 (mt-10) cc_final: 0.9443 (mp0)
REVERT: A  442 MET cc_start: 0.9785 (ttt) cc_final: 0.9557 (tmm)
REVERT: B  101 LEU cc_start: 0.9869 (tp) cc_final: 0.9656 (mt)
REVERT: B  110 MET cc_start: 0.9688 (mmt) cc_final: 0.9237 (mmm)
REVERT: B  120 GLU cc_start: 0.9642 (tt0) cc_final: 0.8981 (mt-10)
REVERT: B  294 MET cc_start: 0.9548 (ppp) cc_final: 0.8887 (ppp)
REVERT: B  376 LEU cc_start: 0.9512 (mt) cc_final: 0.8991 (tt)
REVERT: B  442 MET cc_start: 0.9779 (ttt) cc_final: 0.9434 (tmm)
REVERT: B  487 LEU cc_start: 0.9855 (mt) cc_final: 0.9565 (mm)
REVERT: B  551 TRP cc_start: 0.9378 (t-100) cc_final: 0.8091 (t-100)
REVERT: M  706 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8874 (mm-30)
REVERT: L   26 TYR cc_start: 0.8399 (t80) cc_final: 0.7847 (t80)
REVERT: O    3 ASN cc_start: 0.9625 (t160) cc_final: 0.9344 (m-40)
REVERT: O   26 TYR cc_start: 0.8996 (t80) cc_final: 0.8637 (t80)
REVERT: P  707 ASP cc_start: 0.9517 (t70) cc_final: 0.9293 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1356
  time to fit residues: 32.3383
Evaluate side-chains
  94 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 100 HIS
A 187 HIS
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 328 GLN
A 410 GLN
A 417 HIS
A 594 ASN
B  78 ASN
B 100 HIS
B 108 ASN
B 144 HIS
B 187 HIS
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 410 GLN
** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  18 ASN
L   4 GLN
O  10 HIS
P 711 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.033539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2502 r_free = 0.2502 target = 0.022305 restraints weight = 124389.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.023024 restraints weight = 86914.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.023554 restraints weight = 67278.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.023989 restraints weight = 55840.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.024322 restraints weight = 48213.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12045  Z= 0.241
  Angle     :  0.826   9.981  16380  Z= 0.404
  Chirality :  0.048   0.245   1862
  Planarity :  0.006   0.097   2050
  Dihedral  : 10.178  68.013   2130
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.81 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.11 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.45 %

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 (0.21), residues: 1372
  helix: -1.92 (0.30), residues: 199
  sheet: -0.78 (0.35), residues: 207
  loop : -2.35 (0.20), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 498 
 TYR   0.030   0.002   TYR K  19 
 PHE   0.018   0.002   PHE A 497 
 TRP   0.016   0.002   TRP A 414 
 HIS   0.007   0.002   HIS A   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (11986)
  covalent geometry    : angle       0.80081 (16234)
  SS BOND              : bond        0.00322 (   31)
  SS BOND              : angle       1.01751 (   62)
  hydrogen bonds       : bond        0.05060 (  230)
  hydrogen bonds       : angle       7.79404 (  591)
  link_BETA1-4         : bond        0.00353 (   10)
  link_BETA1-4         : angle       2.80940 (   30)
  link_BETA1-6         : bond        0.00546 (    6)
  link_BETA1-6         : angle       1.66192 (   18)
  link_NAG-ASN         : bond        0.00602 (   12)
  link_NAG-ASN         : angle       3.43515 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.9708 (tp) cc_final: 0.9499 (tp)
REVERT: A  101 LEU cc_start: 0.9747 (tp) cc_final: 0.9416 (mt)
REVERT: A  109 LEU cc_start: 0.9742 (tp) cc_final: 0.9535 (tp)
REVERT: A  110 MET cc_start: 0.8997 (mmt) cc_final: 0.8468 (mmm)
REVERT: A  120 GLU cc_start: 0.9659 (tt0) cc_final: 0.8645 (mt-10)
REVERT: A  137 LEU cc_start: 0.9482 (mp) cc_final: 0.9126 (tp)
REVERT: A  294 MET cc_start: 0.8768 (ppp) cc_final: 0.8409 (ppp)
REVERT: A  350 LEU cc_start: 0.9597 (mt) cc_final: 0.9203 (pp)
REVERT: A  353 GLU cc_start: 0.9710 (mt-10) cc_final: 0.9496 (pm20)
REVERT: A  504 MET cc_start: 0.9670 (mmp) cc_final: 0.9271 (mmm)
REVERT: A  553 MET cc_start: 0.9607 (tpt) cc_final: 0.9381 (tpp)
REVERT: B  101 LEU cc_start: 0.9833 (tp) cc_final: 0.9624 (mt)
REVERT: B  108 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8764 (m110)
REVERT: B  110 MET cc_start: 0.9492 (mmt) cc_final: 0.9202 (mmm)
REVERT: B  120 GLU cc_start: 0.9641 (tt0) cc_final: 0.9085 (mt-10)
REVERT: B  294 MET cc_start: 0.9566 (ppp) cc_final: 0.9064 (ppp)
REVERT: B  376 LEU cc_start: 0.9485 (mt) cc_final: 0.8946 (tt)
REVERT: B  442 MET cc_start: 0.9784 (ttt) cc_final: 0.9427 (tmm)
REVERT: B  455 ASN cc_start: 0.9322 (m110) cc_final: 0.9007 (m110)
REVERT: B  487 LEU cc_start: 0.9876 (mt) cc_final: 0.9602 (mm)
REVERT: B  551 TRP cc_start: 0.9135 (t-100) cc_final: 0.8564 (t-100)
REVERT: B  553 MET cc_start: 0.9751 (mmm) cc_final: 0.9511 (mmm)
REVERT: B  559 TRP cc_start: 0.8278 (m-10) cc_final: 0.8063 (m-10)
REVERT: M  706 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9080 (mp0)
REVERT: M  710 HIS cc_start: 0.9717 (m90) cc_final: 0.9308 (m90)
REVERT: O    6 LEU cc_start: 0.8901 (mt) cc_final: 0.8694 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1131
  time to fit residues: 18.3014
Evaluate side-chains
  94 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 111 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 126 optimal weight:    0.0980
   chunk 23 optimal weight:    0.7980
   chunk 26 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
A   1 HIS
** A  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 784 GLN
** B   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 ASN
B 108 ASN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 GLN
** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   4 GLN
P 710 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.033491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2493 r_free = 0.2493 target = 0.022140 restraints weight = 125064.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.022919 restraints weight = 87260.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.023482 restraints weight = 67026.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.023932 restraints weight = 55229.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.024272 restraints weight = 47459.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12045  Z= 0.169
  Angle     :  0.723   9.284  16380  Z= 0.354
  Chirality :  0.047   0.255   1862
  Planarity :  0.005   0.063   2050
  Dihedral  :  8.683  59.586   2130
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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: -2.67 (0.22), residues: 1372
  helix: -1.49 (0.33), residues: 201
  sheet: -0.96 (0.35), residues: 204
  loop : -2.17 (0.20), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 577 
 TYR   0.021   0.002   TYR K  19 
 PHE   0.019   0.002   PHE P 714 
 TRP   0.013   0.001   TRP A 551 
 HIS   0.007   0.001   HIS A   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (11986)
  covalent geometry    : angle       0.69705 (16234)
  SS BOND              : bond        0.00245 (   31)
  SS BOND              : angle       1.11006 (   62)
  hydrogen bonds       : bond        0.04014 (  230)
  hydrogen bonds       : angle       7.19867 (  591)
  link_BETA1-4         : bond        0.00386 (   10)
  link_BETA1-4         : angle       2.64774 (   30)
  link_BETA1-6         : bond        0.00394 (    6)
  link_BETA1-6         : angle       1.43812 (   18)
  link_NAG-ASN         : bond        0.00449 (   12)
  link_NAG-ASN         : angle       3.10359 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.9707 (tp) cc_final: 0.9373 (mt)
REVERT: A  110 MET cc_start: 0.9048 (mmt) cc_final: 0.8498 (mmm)
REVERT: A  120 GLU cc_start: 0.9627 (tt0) cc_final: 0.8705 (mt-10)
REVERT: A  137 LEU cc_start: 0.9451 (mp) cc_final: 0.9115 (tp)
REVERT: A  294 MET cc_start: 0.8822 (ppp) cc_final: 0.8459 (ppp)
REVERT: A  504 MET cc_start: 0.9646 (mmp) cc_final: 0.9249 (mmm)
REVERT: A  553 MET cc_start: 0.9607 (tpt) cc_final: 0.9363 (tpp)
REVERT: B  101 LEU cc_start: 0.9842 (tp) cc_final: 0.9633 (mt)
REVERT: B  110 MET cc_start: 0.9492 (mmt) cc_final: 0.9179 (mmm)
REVERT: B  120 GLU cc_start: 0.9660 (tt0) cc_final: 0.9099 (mt-10)
REVERT: B  294 MET cc_start: 0.9516 (ppp) cc_final: 0.8994 (ppp)
REVERT: B  376 LEU cc_start: 0.9497 (mt) cc_final: 0.8979 (tt)
REVERT: B  442 MET cc_start: 0.9799 (ttt) cc_final: 0.9429 (tmm)
REVERT: B  455 ASN cc_start: 0.9398 (m110) cc_final: 0.9098 (m110)
REVERT: B  487 LEU cc_start: 0.9860 (mt) cc_final: 0.9569 (mm)
REVERT: B  559 TRP cc_start: 0.8318 (m-10) cc_final: 0.8094 (m-10)
REVERT: M  706 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9169 (mt-10)
REVERT: M  708 TYR cc_start: 0.9647 (t80) cc_final: 0.9343 (t80)
REVERT: M  710 HIS cc_start: 0.9640 (m90) cc_final: 0.9268 (m90)
REVERT: O    6 LEU cc_start: 0.8971 (mt) cc_final: 0.8719 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1225
  time to fit residues: 18.5210
Evaluate side-chains
  91 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 123 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 61 optimal weight:   20.0000
   chunk 17 optimal weight:    3.9990
   chunk 56 optimal weight:   20.0000
   chunk 24 optimal weight:    0.7980
   chunk 43 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0670
   chunk 114 optimal weight:    4.9990
   overall best weight:    3.1724

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   4 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 = 0.2889 r_free = 0.2889 target = 0.032448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2476 r_free = 0.2476 target = 0.021529 restraints weight = 128226.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2510 r_free = 0.2510 target = 0.022268 restraints weight = 90020.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2537 r_free = 0.2537 target = 0.022851 restraints weight = 69479.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.023259 restraints weight = 57495.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.023564 restraints weight = 49685.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12045  Z= 0.191
  Angle     :  0.740  10.097  16380  Z= 0.358
  Chirality :  0.046   0.245   1862
  Planarity :  0.005   0.078   2050
  Dihedral  :  8.401  59.192   2130
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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: -2.52 (0.22), residues: 1372
  helix: -1.46 (0.33), residues: 195
  sheet: -0.95 (0.35), residues: 204
  loop : -2.01 (0.20), residues: 973

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  47 
 TYR   0.023   0.002   TYR K  19 
 PHE   0.014   0.002   PHE P 714 
 TRP   0.013   0.002   TRP A 551 
 HIS   0.006   0.001   HIS B   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (11986)
  covalent geometry    : angle       0.71423 (16234)
  SS BOND              : bond        0.00303 (   31)
  SS BOND              : angle       0.88023 (   62)
  hydrogen bonds       : bond        0.03919 (  230)
  hydrogen bonds       : angle       7.15409 (  591)
  link_BETA1-4         : bond        0.00320 (   10)
  link_BETA1-4         : angle       2.55908 (   30)
  link_BETA1-6         : bond        0.00304 (    6)
  link_BETA1-6         : angle       1.44165 (   18)
  link_NAG-ASN         : bond        0.00616 (   12)
  link_NAG-ASN         : angle       3.37143 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8652 (mmp) cc_final: 0.7998 (mmm)
REVERT: A  101 LEU cc_start: 0.9683 (tp) cc_final: 0.9252 (mt)
REVERT: A  120 GLU cc_start: 0.9584 (tt0) cc_final: 0.8745 (mt-10)
REVERT: A  137 LEU cc_start: 0.9464 (mp) cc_final: 0.9117 (tp)
REVERT: A  294 MET cc_start: 0.8696 (ppp) cc_final: 0.8311 (ppp)
REVERT: A  434 LEU cc_start: 0.9212 (mt) cc_final: 0.8876 (mt)
REVERT: A  504 MET cc_start: 0.9632 (mmp) cc_final: 0.9151 (mmp)
REVERT: A  553 MET cc_start: 0.9577 (tpt) cc_final: 0.9276 (tpp)
REVERT: B   98 MET cc_start: 0.8713 (mmm) cc_final: 0.8501 (mmm)
REVERT: B  101 LEU cc_start: 0.9833 (tp) cc_final: 0.9623 (mt)
REVERT: B  120 GLU cc_start: 0.9652 (tt0) cc_final: 0.9143 (mt-10)
REVERT: B  294 MET cc_start: 0.9521 (ppp) cc_final: 0.8942 (ppp)
REVERT: B  376 LEU cc_start: 0.9518 (mt) cc_final: 0.9003 (tt)
REVERT: B  442 MET cc_start: 0.9781 (ttt) cc_final: 0.9416 (tmm)
REVERT: B  455 ASN cc_start: 0.9415 (m110) cc_final: 0.9076 (m110)
REVERT: B  487 LEU cc_start: 0.9845 (mt) cc_final: 0.9560 (mm)
REVERT: B  551 TRP cc_start: 0.9327 (t-100) cc_final: 0.8754 (t-100)
REVERT: B  559 TRP cc_start: 0.8327 (m-10) cc_final: 0.8107 (m-10)
REVERT: M  703 LYS cc_start: 0.9718 (tptm) cc_final: 0.9360 (tptm)
REVERT: M  708 TYR cc_start: 0.9628 (t80) cc_final: 0.9287 (t80)
REVERT: M  710 HIS cc_start: 0.9686 (m90) cc_final: 0.9292 (m90)
REVERT: L   15 LEU cc_start: 0.9788 (mm) cc_final: 0.9535 (pp)
REVERT: O    6 LEU cc_start: 0.8978 (mt) cc_final: 0.8715 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1063
  time to fit residues: 15.8557
Evaluate side-chains
  84 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   chunk 101 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   chunk 121 optimal weight:    9.9990
   chunk 73 optimal weight:    8.9990
   chunk 119 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   overall best weight:    5.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 ASN
A 589 GLN
A 627 HIS
B  78 ASN
** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 108 ASN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.030953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2431 r_free = 0.2431 target = 0.020557 restraints weight = 136580.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2463 r_free = 0.2463 target = 0.021237 restraints weight = 96086.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2485 r_free = 0.2485 target = 0.021715 restraints weight = 74718.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2503 r_free = 0.2503 target = 0.022116 restraints weight = 62334.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2515 r_free = 0.2515 target = 0.022392 restraints weight = 53990.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.2504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  12045  Z= 0.328
  Angle     :  0.923  10.152  16380  Z= 0.445
  Chirality :  0.049   0.238   1862
  Planarity :  0.006   0.062   2050
  Dihedral  :  8.499  59.429   2130
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 26.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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: -2.69 (0.22), residues: 1372
  helix: -1.86 (0.31), residues: 195
  sheet: -1.04 (0.33), residues: 223
  loop : -2.09 (0.20), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  42 
 TYR   0.026   0.003   TYR K  19 
 PHE   0.019   0.003   PHE L  25 
 TRP   0.019   0.003   TRP B 493 
 HIS   0.011   0.002   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00672 (11986)
  covalent geometry    : angle       0.90008 (16234)
  SS BOND              : bond        0.00390 (   31)
  SS BOND              : angle       1.17946 (   62)
  hydrogen bonds       : bond        0.04546 (  230)
  hydrogen bonds       : angle       7.79115 (  591)
  link_BETA1-4         : bond        0.00340 (   10)
  link_BETA1-4         : angle       2.70004 (   30)
  link_BETA1-6         : bond        0.00339 (    6)
  link_BETA1-6         : angle       1.70376 (   18)
  link_NAG-ASN         : bond        0.00632 (   12)
  link_NAG-ASN         : angle       3.49777 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8635 (mmp) cc_final: 0.8052 (mmm)
REVERT: A  101 LEU cc_start: 0.9619 (tp) cc_final: 0.9311 (mt)
REVERT: A  109 LEU cc_start: 0.9742 (tp) cc_final: 0.9507 (tp)
REVERT: A  110 MET cc_start: 0.9083 (mmt) cc_final: 0.8517 (mmm)
REVERT: A  120 GLU cc_start: 0.9624 (tt0) cc_final: 0.8930 (mt-10)
REVERT: A  137 LEU cc_start: 0.9502 (mp) cc_final: 0.9108 (tt)
REVERT: A  294 MET cc_start: 0.8597 (ppp) cc_final: 0.8127 (ppp)
REVERT: A  434 LEU cc_start: 0.9234 (mt) cc_final: 0.8901 (mt)
REVERT: A  504 MET cc_start: 0.9493 (mmp) cc_final: 0.9055 (mmp)
REVERT: A  553 MET cc_start: 0.9652 (tpt) cc_final: 0.9383 (tpp)
REVERT: B   98 MET cc_start: 0.8755 (mmm) cc_final: 0.8097 (mmm)
REVERT: B  101 LEU cc_start: 0.9855 (tp) cc_final: 0.9529 (mp)
REVERT: B  110 MET cc_start: 0.9378 (mmt) cc_final: 0.9116 (mmm)
REVERT: B  120 GLU cc_start: 0.9689 (tt0) cc_final: 0.9348 (mt-10)
REVERT: B  294 MET cc_start: 0.9531 (ppp) cc_final: 0.8864 (ppp)
REVERT: B  376 LEU cc_start: 0.9538 (mt) cc_final: 0.9012 (tt)
REVERT: B  442 MET cc_start: 0.9793 (ttt) cc_final: 0.9409 (tmm)
REVERT: B  455 ASN cc_start: 0.9528 (m110) cc_final: 0.9206 (m110)
REVERT: B  551 TRP cc_start: 0.9378 (t-100) cc_final: 0.9139 (t-100)
REVERT: M  708 TYR cc_start: 0.9641 (t80) cc_final: 0.9409 (t80)
REVERT: M  710 HIS cc_start: 0.9617 (m90) cc_final: 0.9191 (m90)
REVERT: O    6 LEU cc_start: 0.9015 (mt) cc_final: 0.8742 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1171
  time to fit residues: 15.6358
Evaluate side-chains
  74 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 133 optimal weight:    0.3980
   chunk 128 optimal weight:    0.8980
   chunk 130 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 126 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
A 410 GLN
A 589 GLN
B  78 ASN
B 100 HIS
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 263 HIS
B 276 GLN
L   4 GLN
P 710 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.032186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2464 r_free = 0.2464 target = 0.021374 restraints weight = 126679.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2499 r_free = 0.2499 target = 0.022126 restraints weight = 88131.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2526 r_free = 0.2526 target = 0.022720 restraints weight = 67508.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2544 r_free = 0.2544 target = 0.023136 restraints weight = 55483.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.023446 restraints weight = 47874.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12045  Z= 0.129
  Angle     :  0.693   9.352  16380  Z= 0.336
  Chirality :  0.047   0.267   1862
  Planarity :  0.004   0.061   2050
  Dihedral  :  7.812  57.085   2130
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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: -2.36 (0.22), residues: 1372
  helix: -1.43 (0.33), residues: 194
  sheet: -0.99 (0.36), residues: 194
  loop : -1.84 (0.20), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 780 
 TYR   0.024   0.002   TYR N  19 
 PHE   0.014   0.001   PHE L  25 
 TRP   0.016   0.002   TRP B 493 
 HIS   0.010   0.001   HIS P 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (11986)
  covalent geometry    : angle       0.66851 (16234)
  SS BOND              : bond        0.00247 (   31)
  SS BOND              : angle       0.83691 (   62)
  hydrogen bonds       : bond        0.03622 (  230)
  hydrogen bonds       : angle       7.02664 (  591)
  link_BETA1-4         : bond        0.00421 (   10)
  link_BETA1-4         : angle       2.35350 (   30)
  link_BETA1-6         : bond        0.00411 (    6)
  link_BETA1-6         : angle       1.44071 (   18)
  link_NAG-ASN         : bond        0.00385 (   12)
  link_NAG-ASN         : angle       3.17775 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8759 (mmp) cc_final: 0.8283 (mmm)
REVERT: A  101 LEU cc_start: 0.9549 (tp) cc_final: 0.9232 (mt)
REVERT: A  120 GLU cc_start: 0.9568 (tt0) cc_final: 0.8688 (mt-10)
REVERT: A  137 LEU cc_start: 0.9462 (mp) cc_final: 0.9085 (tt)
REVERT: A  294 MET cc_start: 0.8622 (ppp) cc_final: 0.8255 (ppp)
REVERT: A  434 LEU cc_start: 0.9188 (mt) cc_final: 0.8815 (mt)
REVERT: A  442 MET cc_start: 0.9718 (tmm) cc_final: 0.9510 (tmm)
REVERT: A  504 MET cc_start: 0.9632 (mmp) cc_final: 0.9225 (mmp)
REVERT: A  553 MET cc_start: 0.9616 (tpt) cc_final: 0.9303 (tpp)
REVERT: B   11 MET cc_start: 0.9505 (mmp) cc_final: 0.9287 (mmt)
REVERT: B   38 MET cc_start: 0.8776 (mtt) cc_final: 0.8527 (mtt)
REVERT: B   98 MET cc_start: 0.8930 (mmm) cc_final: 0.8591 (mmm)
REVERT: B  101 LEU cc_start: 0.9850 (tp) cc_final: 0.9559 (mp)
REVERT: B  294 MET cc_start: 0.9515 (ppp) cc_final: 0.8965 (ppp)
REVERT: B  376 LEU cc_start: 0.9519 (mt) cc_final: 0.8985 (tt)
REVERT: B  442 MET cc_start: 0.9792 (ttt) cc_final: 0.9406 (tmm)
REVERT: B  455 ASN cc_start: 0.9512 (m110) cc_final: 0.9215 (m110)
REVERT: M  708 TYR cc_start: 0.9639 (t80) cc_final: 0.9363 (t80)
REVERT: M  710 HIS cc_start: 0.9629 (m90) cc_final: 0.9330 (m-70)
REVERT: L   15 LEU cc_start: 0.9774 (mm) cc_final: 0.9526 (pp)
REVERT: O   26 TYR cc_start: 0.8881 (t80) cc_final: 0.8659 (t80)
REVERT: P  706 GLU cc_start: 0.9693 (pt0) cc_final: 0.9155 (pp20)
REVERT: P  707 ASP cc_start: 0.9503 (t70) cc_final: 0.9156 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1053
  time to fit residues: 15.6082
Evaluate side-chains
  78 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 128 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 134 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 119 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 108 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 HIS
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   4 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.031798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2433 r_free = 0.2433 target = 0.020878 restraints weight = 128642.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2470 r_free = 0.2470 target = 0.021624 restraints weight = 90924.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2496 r_free = 0.2496 target = 0.022174 restraints weight = 69432.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.022607 restraints weight = 56979.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2531 r_free = 0.2531 target = 0.022938 restraints weight = 48822.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12045  Z= 0.180
  Angle     :  0.717   8.392  16380  Z= 0.349
  Chirality :  0.047   0.245   1862
  Planarity :  0.005   0.059   2050
  Dihedral  :  7.572  56.913   2130
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.24 %
    Favored  : 87.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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: -2.34 (0.22), residues: 1372
  helix: -1.40 (0.33), residues: 194
  sheet: -0.91 (0.35), residues: 201
  loop : -1.85 (0.20), residues: 977

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  14 
 TYR   0.022   0.002   TYR N  19 
 PHE   0.031   0.002   PHE A  89 
 TRP   0.013   0.002   TRP A 414 
 HIS   0.005   0.001   HIS B   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (11986)
  covalent geometry    : angle       0.69460 (16234)
  SS BOND              : bond        0.00263 (   31)
  SS BOND              : angle       0.85436 (   62)
  hydrogen bonds       : bond        0.03710 (  230)
  hydrogen bonds       : angle       6.97337 (  591)
  link_BETA1-4         : bond        0.00326 (   10)
  link_BETA1-4         : angle       2.34025 (   30)
  link_BETA1-6         : bond        0.00332 (    6)
  link_BETA1-6         : angle       1.51347 (   18)
  link_NAG-ASN         : bond        0.00393 (   12)
  link_NAG-ASN         : angle       3.06851 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8802 (mmp) cc_final: 0.8319 (mmm)
REVERT: A  101 LEU cc_start: 0.9535 (tp) cc_final: 0.9125 (mt)
REVERT: A  120 GLU cc_start: 0.9581 (tt0) cc_final: 0.8802 (mt-10)
REVERT: A  137 LEU cc_start: 0.9450 (mp) cc_final: 0.9100 (tt)
REVERT: A  294 MET cc_start: 0.8621 (ppp) cc_final: 0.8238 (ppp)
REVERT: A  434 LEU cc_start: 0.9246 (mt) cc_final: 0.8880 (mt)
REVERT: A  442 MET cc_start: 0.9689 (tmm) cc_final: 0.9486 (tmm)
REVERT: A  504 MET cc_start: 0.9592 (mmp) cc_final: 0.9091 (mmp)
REVERT: A  553 MET cc_start: 0.9641 (tpt) cc_final: 0.9318 (tpp)
REVERT: B   38 MET cc_start: 0.8706 (mtt) cc_final: 0.8438 (mtt)
REVERT: B  101 LEU cc_start: 0.9845 (tp) cc_final: 0.9641 (mt)
REVERT: B  110 MET cc_start: 0.9403 (mmt) cc_final: 0.9149 (mmm)
REVERT: B  294 MET cc_start: 0.9490 (ppp) cc_final: 0.8891 (ppp)
REVERT: B  376 LEU cc_start: 0.9534 (mt) cc_final: 0.9043 (tt)
REVERT: B  442 MET cc_start: 0.9792 (ttt) cc_final: 0.9372 (tmm)
REVERT: B  455 ASN cc_start: 0.9513 (m110) cc_final: 0.9210 (m110)
REVERT: M  703 LYS cc_start: 0.9607 (tptm) cc_final: 0.9333 (tptm)
REVERT: M  710 HIS cc_start: 0.9637 (m90) cc_final: 0.9233 (m90)
REVERT: L   15 LEU cc_start: 0.9756 (mm) cc_final: 0.9514 (pp)
REVERT: O   26 TYR cc_start: 0.8924 (t80) cc_final: 0.8709 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1056
  time to fit residues: 14.2319
Evaluate side-chains
  71 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 126 optimal weight:    0.0670
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 104 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    2.0126

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 263 HIS
B 276 GLN
L   4 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.032219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.021308 restraints weight = 126680.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2494 r_free = 0.2494 target = 0.022076 restraints weight = 87788.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2519 r_free = 0.2519 target = 0.022612 restraints weight = 67289.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2539 r_free = 0.2539 target = 0.023052 restraints weight = 55546.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.023368 restraints weight = 47776.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.2539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12045  Z= 0.136
  Angle     :  0.676   8.343  16380  Z= 0.329
  Chirality :  0.046   0.252   1862
  Planarity :  0.005   0.070   2050
  Dihedral  :  7.372  54.789   2130
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.47 %
    Twisted General : 0.15 %

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 (0.22), residues: 1372
  helix: -1.22 (0.35), residues: 194
  sheet: -0.86 (0.35), residues: 203
  loop : -1.78 (0.20), residues: 975

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  14 
 TYR   0.045   0.002   TYR M 708 
 PHE   0.063   0.002   PHE P 714 
 TRP   0.013   0.002   TRP B 493 
 HIS   0.004   0.001   HIS B   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11986)
  covalent geometry    : angle       0.65397 (16234)
  SS BOND              : bond        0.00238 (   31)
  SS BOND              : angle       0.79924 (   62)
  hydrogen bonds       : bond        0.03509 (  230)
  hydrogen bonds       : angle       6.74297 (  591)
  link_BETA1-4         : bond        0.00382 (   10)
  link_BETA1-4         : angle       2.23713 (   30)
  link_BETA1-6         : bond        0.00377 (    6)
  link_BETA1-6         : angle       1.45045 (   18)
  link_NAG-ASN         : bond        0.00369 (   12)
  link_NAG-ASN         : angle       2.93162 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.9595 (tp) cc_final: 0.9341 (tp)
REVERT: A   98 MET cc_start: 0.8872 (mmp) cc_final: 0.8429 (mmm)
REVERT: A  101 LEU cc_start: 0.9528 (tp) cc_final: 0.9210 (mt)
REVERT: A  120 GLU cc_start: 0.9537 (tt0) cc_final: 0.8744 (mt-10)
REVERT: A  137 LEU cc_start: 0.9454 (mp) cc_final: 0.9100 (tt)
REVERT: A  294 MET cc_start: 0.8661 (ppp) cc_final: 0.8320 (ppp)
REVERT: A  434 LEU cc_start: 0.9196 (mt) cc_final: 0.8821 (mt)
REVERT: A  442 MET cc_start: 0.9713 (tmm) cc_final: 0.9509 (tmm)
REVERT: A  504 MET cc_start: 0.9618 (mmp) cc_final: 0.9303 (mmp)
REVERT: A  553 MET cc_start: 0.9650 (tpt) cc_final: 0.9328 (tpp)
REVERT: B   38 MET cc_start: 0.8784 (mtt) cc_final: 0.8557 (mtt)
REVERT: B  110 MET cc_start: 0.9409 (mmt) cc_final: 0.9142 (mmm)
REVERT: B  120 GLU cc_start: 0.9690 (tt0) cc_final: 0.9218 (mt-10)
REVERT: B  294 MET cc_start: 0.9489 (ppp) cc_final: 0.8954 (ppp)
REVERT: B  376 LEU cc_start: 0.9515 (mt) cc_final: 0.9038 (tt)
REVERT: B  442 MET cc_start: 0.9802 (ttt) cc_final: 0.9383 (tmm)
REVERT: B  455 ASN cc_start: 0.9505 (m110) cc_final: 0.9209 (m110)
REVERT: M  703 LYS cc_start: 0.9742 (tptm) cc_final: 0.9408 (tppt)
REVERT: M  706 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9223 (pt0)
REVERT: M  710 HIS cc_start: 0.9666 (m90) cc_final: 0.9281 (m90)
REVERT: L   15 LEU cc_start: 0.9756 (mm) cc_final: 0.9526 (pp)
REVERT: O   26 TYR cc_start: 0.8919 (t80) cc_final: 0.8697 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1002
  time to fit residues: 14.0608
Evaluate side-chains
  75 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 133 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 117 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 589 GLN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 263 HIS
B 276 GLN
B 406 GLN
B 431 ASN
L   4 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.031273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2437 r_free = 0.2437 target = 0.020656 restraints weight = 130160.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2473 r_free = 0.2473 target = 0.021402 restraints weight = 90842.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2498 r_free = 0.2498 target = 0.021938 restraints weight = 70016.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.022349 restraints weight = 57700.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2531 r_free = 0.2531 target = 0.022671 restraints weight = 49824.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.4359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12045  Z= 0.210
  Angle     :  0.743   8.511  16380  Z= 0.360
  Chirality :  0.047   0.240   1862
  Planarity :  0.005   0.063   2050
  Dihedral  :  7.486  54.674   2130
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.47 %
    Twisted General : 0.30 %

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: -2.30 (0.22), residues: 1372
  helix: -1.36 (0.34), residues: 200
  sheet: -0.88 (0.35), residues: 205
  loop : -1.82 (0.20), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 488 
 TYR   0.044   0.002   TYR M 708 
 PHE   0.048   0.002   PHE P 714 
 TRP   0.013   0.002   TRP A 414 
 HIS   0.009   0.002   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (11986)
  covalent geometry    : angle       0.72224 (16234)
  SS BOND              : bond        0.00264 (   31)
  SS BOND              : angle       0.87611 (   62)
  hydrogen bonds       : bond        0.03760 (  230)
  hydrogen bonds       : angle       6.86820 (  591)
  link_BETA1-4         : bond        0.00344 (   10)
  link_BETA1-4         : angle       2.30122 (   30)
  link_BETA1-6         : bond        0.00374 (    6)
  link_BETA1-6         : angle       1.55402 (   18)
  link_NAG-ASN         : bond        0.00430 (   12)
  link_NAG-ASN         : angle       2.96131 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8874 (mmp) cc_final: 0.8399 (mmm)
REVERT: A  101 LEU cc_start: 0.9556 (tp) cc_final: 0.9168 (mt)
REVERT: A  120 GLU cc_start: 0.9497 (tt0) cc_final: 0.8691 (mt-10)
REVERT: A  137 LEU cc_start: 0.9440 (mp) cc_final: 0.9083 (tt)
REVERT: A  294 MET cc_start: 0.8602 (ppp) cc_final: 0.8222 (ppp)
REVERT: A  434 LEU cc_start: 0.9256 (mt) cc_final: 0.8896 (mt)
REVERT: A  504 MET cc_start: 0.9547 (mmp) cc_final: 0.8992 (mmp)
REVERT: A  553 MET cc_start: 0.9643 (tpt) cc_final: 0.9309 (tpp)
REVERT: B   38 MET cc_start: 0.8809 (mtt) cc_final: 0.8579 (mtt)
REVERT: B  294 MET cc_start: 0.9495 (ppp) cc_final: 0.8891 (ppp)
REVERT: B  376 LEU cc_start: 0.9530 (mt) cc_final: 0.9044 (tt)
REVERT: B  442 MET cc_start: 0.9800 (ttt) cc_final: 0.9375 (tmm)
REVERT: B  455 ASN cc_start: 0.9499 (m110) cc_final: 0.9201 (m110)
REVERT: M  703 LYS cc_start: 0.9716 (tptm) cc_final: 0.9337 (tppt)
REVERT: M  706 GLU cc_start: 0.9563 (mt-10) cc_final: 0.9250 (pt0)
REVERT: M  710 HIS cc_start: 0.9661 (m90) cc_final: 0.9268 (m90)
REVERT: L   15 LEU cc_start: 0.9739 (mm) cc_final: 0.9453 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1006
  time to fit residues: 12.9488
Evaluate side-chains
  70 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 129 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 66 optimal weight:    0.0050
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 81 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    2.3598

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 589 GLN
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   4 GLN
L  10 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.031637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2446 r_free = 0.2446 target = 0.020829 restraints weight = 126998.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2483 r_free = 0.2483 target = 0.021607 restraints weight = 87534.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2509 r_free = 0.2509 target = 0.022175 restraints weight = 67046.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.022618 restraints weight = 54956.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2544 r_free = 0.2544 target = 0.022954 restraints weight = 47127.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.2527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12045  Z= 0.147
  Angle     :  0.686   8.279  16380  Z= 0.333
  Chirality :  0.047   0.248   1862
  Planarity :  0.004   0.066   2050
  Dihedral  :  7.337  52.923   2130
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.47 %
    Twisted General : 0.30 %

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: -2.21 (0.22), residues: 1372
  helix: -1.22 (0.35), residues: 200
  sheet: -0.77 (0.35), residues: 203
  loop : -1.79 (0.20), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 114 
 TYR   0.039   0.002   TYR M 708 
 PHE   0.044   0.002   PHE P 714 
 TRP   0.013   0.002   TRP B 493 
 HIS   0.008   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (11986)
  covalent geometry    : angle       0.66532 (16234)
  SS BOND              : bond        0.00246 (   31)
  SS BOND              : angle       0.79550 (   62)
  hydrogen bonds       : bond        0.03486 (  230)
  hydrogen bonds       : angle       6.67893 (  591)
  link_BETA1-4         : bond        0.00379 (   10)
  link_BETA1-4         : angle       2.19020 (   30)
  link_BETA1-6         : bond        0.00370 (    6)
  link_BETA1-6         : angle       1.45768 (   18)
  link_NAG-ASN         : bond        0.00362 (   12)
  link_NAG-ASN         : angle       2.88412 (   36)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.9595 (tp) cc_final: 0.9348 (tp)
REVERT: A   98 MET cc_start: 0.8948 (mmp) cc_final: 0.8478 (mmm)
REVERT: A  101 LEU cc_start: 0.9539 (tp) cc_final: 0.9157 (mt)
REVERT: A  120 GLU cc_start: 0.9504 (tt0) cc_final: 0.8700 (mt-10)
REVERT: A  137 LEU cc_start: 0.9449 (mp) cc_final: 0.9101 (tt)
REVERT: A  294 MET cc_start: 0.8585 (ppp) cc_final: 0.8254 (ppp)
REVERT: A  434 LEU cc_start: 0.9209 (mt) cc_final: 0.8846 (mt)
REVERT: A  504 MET cc_start: 0.9608 (mmp) cc_final: 0.9326 (mmp)
REVERT: A  553 MET cc_start: 0.9640 (tpt) cc_final: 0.9304 (tpp)
REVERT: B  110 MET cc_start: 0.9512 (mmt) cc_final: 0.9246 (mmm)
REVERT: B  120 GLU cc_start: 0.9702 (tt0) cc_final: 0.9216 (mt-10)
REVERT: B  294 MET cc_start: 0.9493 (ppp) cc_final: 0.8921 (ppp)
REVERT: B  376 LEU cc_start: 0.9504 (mt) cc_final: 0.9030 (tt)
REVERT: B  442 MET cc_start: 0.9812 (ttt) cc_final: 0.9488 (tmm)
REVERT: B  455 ASN cc_start: 0.9504 (m110) cc_final: 0.9218 (m110)
REVERT: M  703 LYS cc_start: 0.9708 (tptm) cc_final: 0.9346 (tppt)
REVERT: M  706 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9199 (pt0)
REVERT: M  710 HIS cc_start: 0.9679 (m90) cc_final: 0.9286 (m90)
REVERT: L   15 LEU cc_start: 0.9734 (mm) cc_final: 0.9501 (pp)
REVERT: O   26 TYR cc_start: 0.8925 (t80) cc_final: 0.8657 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1009
  time to fit residues: 13.6635
Evaluate side-chains
  73 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 117 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 263 HIS
B 276 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.032483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2467 r_free = 0.2467 target = 0.021492 restraints weight = 125271.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2503 r_free = 0.2503 target = 0.022264 restraints weight = 86487.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.022822 restraints weight = 66373.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2549 r_free = 0.2549 target = 0.023261 restraints weight = 54641.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.023582 restraints weight = 46970.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12045  Z= 0.114
  Angle     :  0.654   7.761  16380  Z= 0.317
  Chirality :  0.046   0.243   1862
  Planarity :  0.004   0.059   2050
  Dihedral  :  6.918  50.561   2130
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.35 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.47 %
    Twisted General : 0.30 %

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: -2.07 (0.23), residues: 1372
  helix: -1.00 (0.36), residues: 200
  sheet: -0.70 (0.35), residues: 204
  loop : -1.71 (0.20), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 345 
 TYR   0.039   0.001   TYR M 708 
 PHE   0.038   0.001   PHE P 714 
 TRP   0.012   0.002   TRP B 493 
 HIS   0.004   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (11986)
  covalent geometry    : angle       0.63548 (16234)
  SS BOND              : bond        0.00203 (   31)
  SS BOND              : angle       0.74821 (   62)
  hydrogen bonds       : bond        0.03307 (  230)
  hydrogen bonds       : angle       6.27293 (  591)
  link_BETA1-4         : bond        0.00410 (   10)
  link_BETA1-4         : angle       2.14193 (   30)
  link_BETA1-6         : bond        0.00391 (    6)
  link_BETA1-6         : angle       1.40862 (   18)
  link_NAG-ASN         : bond        0.00291 (   12)
  link_NAG-ASN         : angle       2.63803 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1929.80 seconds
wall clock time: 34 minutes 20.23 seconds (2060.23 seconds total)