Starting phenix.real_space_refine
on Mon May 12 01:45:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vlu_43344/05_2025/8vlu_43344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vlu_43344/05_2025/8vlu_43344.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vlu_43344/05_2025/8vlu_43344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vlu_43344/05_2025/8vlu_43344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vlu_43344/05_2025/8vlu_43344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vlu_43344/05_2025/8vlu_43344.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      38      5.16       5
     C    5666      2.51       5
     N    1385      2.21       5
     O    1501      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8596
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4201
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 546, 4181
          Classifications: {'peptide': 546}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 26, 'TRANS': 519}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 80
      Conformer: "B"
        Number of residues, atoms: 546, 4181
          Classifications: {'peptide': 546}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 26, 'TRANS': 519}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 80
          bond proxies already assigned to first conformer: 4278
    Chain: "A"
      Number of atoms: 4201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4201
          Classifications: {'peptide': 550}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 26, 'TRANS': 523}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 173
          Unresolved non-hydrogen angles: 214
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 92
    Chain: "B"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 90
          Unusual residues: {'COA': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 104
          Unusual residues: {'COA': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ALYS B 100 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B 100 " occ=0.50
    residue:
      pdb=" N  AARG B 267 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 267 " occ=0.50
  Time building chain proxies: 8.87, per 1000 atoms: 1.03
  Number of scatterers: 8596
  At special positions: 0
  Unit cell: (105.69, 81.3, 106.503, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       6     15.00
     O    1501      8.00
     N    1385      7.00
     C    5666      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 104 " - pdb=" SG  CYS B 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 151 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 443 " - pdb=" SG  CYS B 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 104 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 462 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A  94 "
      " NAG A 702 " - " ASN A 162 "
      " NAG A 703 " - " ASN A 461 "
      " NAG A 705 " - " ASN A 142 "
      " NAG B 701 " - " ASN B 162 "
      " NAG B 703 " - " ASN B  94 "
      " NAG B 704 " - " ASN B 142 "
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2034

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      53.0% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'B' and resid 197 through 228
    Processing helix  chain 'B' and resid 269 through 287
    Processing helix  chain 'B' and resid 288 through 292
      removed outlier: 3.570A  pdb=" N   TYR B 292 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 330
    Processing helix  chain 'B' and resid 334 through 356
    Processing helix  chain 'B' and resid 375 through 394
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 438
    Processing helix  chain 'B' and resid 454 through 458
      removed outlier: 3.670A  pdb=" N   LYS B 458 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 475
    Processing helix  chain 'B' and resid 486 through 491
    Processing helix  chain 'B' and resid 502 through 524
      removed outlier: 4.214A  pdb=" N   ASN B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 551
      removed outlier: 3.506A  pdb=" N   ILE B 531 " --> pdb=" O   ARG B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 590
      Proline residue:  B 587  - end of helix
    Processing helix  chain 'B' and resid 602 through 605
    Processing helix  chain 'B' and resid 606 through 617
    Processing helix  chain 'B' and resid 632 through 657
    Processing helix  chain 'A' and resid 194 through 220
    Processing helix  chain 'A' and resid 269 through 287
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.541A  pdb=" N   TYR A 292 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TRP A 293 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LYS A 296 " --> pdb=" O   TRP A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 308 through 332
    Processing helix  chain 'A' and resid 334 through 357
    Processing helix  chain 'A' and resid 375 through 394
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 417 through 437
    Processing helix  chain 'A' and resid 454 through 458
      removed outlier: 3.647A  pdb=" N   LYS A 458 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 475
      removed outlier: 3.607A  pdb=" N   ASP A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 4.099A  pdb=" N   VAL A 488 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 524
      removed outlier: 4.275A  pdb=" N   ASN A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 551
      removed outlier: 3.650A  pdb=" N   ILE A 531 " --> pdb=" O   ARG A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 590
      Proline residue:  A 587  - end of helix
    Processing helix  chain 'A' and resid 597 through 606
      removed outlier: 4.453A  pdb=" N   TYR A 602 " --> pdb=" O   THR A 598 " (cutoff:3.500A)
      Proline residue:  A 603  - end of helix
    Processing helix  chain 'A' and resid 606 through 617
    Processing helix  chain 'A' and resid 632 through 657
    Processing sheet with id=AA1, first strand: chain 'B' and resid 125 through 132
      removed outlier: 7.289A  pdb=" N   LEU B 165 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   LEU B  85 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   HIS B  87 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 110 through 115
      removed outlier: 6.818A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   ASN B 114 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   LEU B  95 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   CYS B 151 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 132
      removed outlier: 3.505A  pdb=" N   ALA A 127 " --> pdb=" O   ILE A  86 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA A 182 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS A 168 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 115
      removed outlier: 6.845A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   ASN A 114 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   LEU A  95 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   CYS A 151 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1377 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: 2.36

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2587
        1.35 -     1.48: 2455
        1.48 -     1.61: 3743
        1.61 -     1.74: 2
        1.74 -     1.87: 54
  Bond restraints: 8841
  Sorted by residual:
  bond pdb=" O3B COA B 702 "
       pdb=" P3B COA B 702 "
    ideal  model  delta    sigma   weight residual
    1.683  1.868 -0.185 2.00e-02 2.50e+03 8.59e+01
  bond pdb=" O3B COA A 704 "
       pdb=" P3B COA A 704 "
    ideal  model  delta    sigma   weight residual
    1.683  1.831 -0.148 2.00e-02 2.50e+03 5.50e+01
  bond pdb=" O6A COA B 702 "
       pdb=" P2A COA B 702 "
    ideal  model  delta    sigma   weight residual
    1.620  1.766 -0.146 2.00e-02 2.50e+03 5.31e+01
  bond pdb=" O6A COA A 704 "
       pdb=" P2A COA A 704 "
    ideal  model  delta    sigma   weight residual
    1.620  1.765 -0.145 2.00e-02 2.50e+03 5.23e+01
  bond pdb=" CCP COA B 702 "
       pdb=" O6A COA B 702 "
    ideal  model  delta    sigma   weight residual
    1.431  1.346  0.085 2.00e-02 2.50e+03 1.80e+01
  ... (remaining 8836 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 11965
        2.68 -     5.35: 104
        5.35 -     8.03: 31
        8.03 -    10.71: 5
       10.71 -    13.39: 2
  Bond angle restraints: 12107
  Sorted by residual:
  angle pdb=" O1A COA A 704 "
        pdb=" P1A COA A 704 "
        pdb=" O3A COA A 704 "
      ideal   model   delta    sigma   weight residual
     110.50   97.11   13.39 3.00e+00 1.11e-01 1.99e+01
  angle pdb=" O1A COA B 702 "
        pdb=" P1A COA B 702 "
        pdb=" O3A COA B 702 "
      ideal   model   delta    sigma   weight residual
     110.50   97.33   13.17 3.00e+00 1.11e-01 1.93e+01
  angle pdb=" C   LEU A 268 "
        pdb=" N   ARG A 269 "
        pdb=" CA  ARG A 269 "
      ideal   model   delta    sigma   weight residual
     121.54  129.05   -7.51 1.91e+00 2.74e-01 1.55e+01
  angle pdb=" C   SER B 299 "
        pdb=" N   TRP B 300 "
        pdb=" CA  TRP B 300 "
      ideal   model   delta    sigma   weight residual
     121.54  127.92   -6.38 1.91e+00 2.74e-01 1.12e+01
  angle pdb=" O4A COA B 702 "
        pdb=" P2A COA B 702 "
        pdb=" O6A COA B 702 "
      ideal   model   delta    sigma   weight residual
     110.27  100.98    9.29 3.00e+00 1.11e-01 9.58e+00
  ... (remaining 12102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 4546
       17.01 -    34.02: 505
       34.02 -    51.03: 124
       51.03 -    68.03: 36
       68.03 -    85.04: 18
  Dihedral angle restraints: 5229
    sinusoidal: 2052
      harmonic: 3177
  Sorted by residual:
  dihedral pdb=" CB  CYS A 104 "
           pdb=" SG  CYS A 104 "
           pdb=" SG  CYS A 107 "
           pdb=" CB  CYS A 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.33   81.67     1      1.00e+01 1.00e-02 8.21e+01
  dihedral pdb=" CB  CYS A 443 "
           pdb=" SG  CYS A 443 "
           pdb=" SG  CYS A 462 "
           pdb=" CB  CYS A 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.67  -73.67     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" CB  CYS B 443 "
           pdb=" SG  CYS B 443 "
           pdb=" SG  CYS B 462 "
           pdb=" CB  CYS B 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.09  -70.09     1      1.00e+01 1.00e-02 6.33e+01
  ... (remaining 5226 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1319
       0.082 -    0.164: 95
       0.164 -    0.246: 0
       0.246 -    0.328: 1
       0.328 -    0.410: 3
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CAP COA B 702 "
            pdb=" C9P COA B 702 "
            pdb=" CBP COA B 702 "
            pdb=" OAP COA B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.09   -0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" CAP COA A 704 "
            pdb=" C9P COA A 704 "
            pdb=" CBP COA A 704 "
            pdb=" OAP COA A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.10   -0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" C2B COA B 702 "
            pdb=" C1B COA B 702 "
            pdb=" C3B COA B 702 "
            pdb=" O2B COA B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.75    0.35 2.00e-01 2.50e+01 3.02e+00
  ... (remaining 1415 not shown)

  Planarity restraints: 1475
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 269 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.82e+00
        pdb=" C   ARG B 269 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ARG B 269 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   SER B 270 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 269 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   ARG A 269 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ARG A 269 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER A 270 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 418 "    0.033 5.00e-02 4.00e+02   4.89e-02 3.82e+00
        pdb=" N   PRO B 419 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 419 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 419 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1472 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 147
        2.69 -     3.24: 8538
        3.24 -     3.79: 14361
        3.79 -     4.35: 18795
        4.35 -     4.90: 31684
  Nonbonded interactions: 73525
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 546 "
            pdb=" OG1 THR B 573 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OG1 THR A 133 "
            pdb=" O   PHE A 157 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG1 THR B 133 "
            pdb=" O   PHE B 157 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OD1 ASN B 358 "
            pdb=" NE2 GLN B 378 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   ILE A 355 "
            pdb=" OH  TYR A 361 "
     model   vdw
     2.271 3.040
  ... (remaining 73520 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 77 through 99 or resid 101 through 146 or (resid 147 throu \ 
gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ 
ough 167 or (resid 168 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 169 through 170 or resid 176 through 184 or (resid 185 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 186 through 189 or (resid 190  \ 
through 193 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 
4 through 199 or (resid 200 and (name N or name CA or name C or name O or name C \ 
B )) or resid 201 through 205 or (resid 206 through 207 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 208 through 266 or resid 268 through 6 \ 
57 or (resid 658 and (name N or name CA or name C or name O or name CB )) or res \ 
id 659 through 663 or resid 701 or resid 703))
  selection = (chain 'B' and (resid 77 through 88 or (resid 89 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 90 through 99 or resid 101 through 190 or (re \ 
sid 191 through 193 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 194 through 210 or (resid 211 through 227 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 265 through 266 or resid 268 through 336 or (r \ 
esid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 t \ 
hrough 369 or (resid 370 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 371 through 395 or (resid 396 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 397 through 663 or resid 701 or resid 703))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.180
  Set stop_for_unknowns flag:              0.010
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.020
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
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   0.185   8854  Z= 0.276
  Angle     :  0.700  13.386  12140  Z= 0.310
  Chirality :  0.046   0.410   1418
  Planarity :  0.004   0.049   1468
  Dihedral  : 16.179  85.042   3177
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  8.74 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.25), residues: 1092
  helix:  1.89 (0.22), residues: 517
  sheet: -0.32 (0.49), residues: 115
  loop : -1.36 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 300 
 HIS   0.005   0.001   HIS A 614 
 PHE   0.015   0.001   PHE A 601 
 TYR   0.012   0.001   TYR A 602 
 ARG   0.002   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00336 (    7)
  link_NAG-ASN         : angle       1.60599 (   21)
  hydrogen bonds       : bond        0.13086 (  474)
  hydrogen bonds       : angle       5.80761 ( 1377)
  SS BOND              : bond        0.00088 (    6)
  SS BOND              : angle       0.97976 (   12)
  covalent geometry    : bond        0.00562 ( 8841)
  covalent geometry    : angle       0.69659 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.836 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 76
  average time/residue: 0.2145
  time to fit residues: 22.8695
Evaluate side-chains
  73 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0010
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0970
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.4980
   overall best weight:    0.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 401 HIS
B 562 ASN
A 184 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN
A 640 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.152036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.121016 restraints weight = 22722.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 3.17
r_work: 0.3122 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.0631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8854  Z= 0.133
  Angle     :  0.551   8.369  12140  Z= 0.275
  Chirality :  0.042   0.181   1418
  Planarity :  0.004   0.039   1468
  Dihedral  :  9.512  61.286   1440
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.44 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.25), residues: 1092
  helix:  1.88 (0.22), residues: 532
  sheet: -0.21 (0.49), residues: 114
  loop : -1.20 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 300 
 HIS   0.005   0.001   HIS A 614 
 PHE   0.014   0.001   PHE A 512 
 TYR   0.013   0.001   TYR A 602 
 ARG   0.001   0.000   ARG B 275 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00354 (    7)
  link_NAG-ASN         : angle       1.69821 (   21)
  hydrogen bonds       : bond        0.03847 (  474)
  hydrogen bonds       : angle       4.83351 ( 1377)
  SS BOND              : bond        0.00110 (    6)
  SS BOND              : angle       0.77517 (   12)
  covalent geometry    : bond        0.00309 ( 8841)
  covalent geometry    : angle       0.54703 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.850 
Fit side-chains
  outliers start: 13
  outliers final: 5
  residues processed: 87
  average time/residue: 0.2052
  time to fit residues: 25.2056
Evaluate side-chains
  74 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain A residue   79 MET
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  167 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0770
   chunk 39 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 562 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.146114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.115231 restraints weight = 23973.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.90
r_work: 0.3105 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.0824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8854  Z= 0.158
  Angle     :  0.570   8.400  12140  Z= 0.283
  Chirality :  0.042   0.175   1418
  Planarity :  0.004   0.042   1468
  Dihedral  :  8.782  56.203   1438
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.14 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1092
  helix:  1.81 (0.22), residues: 532
  sheet: -0.10 (0.50), residues: 106
  loop : -1.22 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 647 
 HIS   0.006   0.001   HIS A 614 
 PHE   0.021   0.001   PHE A 601 
 TYR   0.014   0.001   TYR A 570 
 ARG   0.007   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    7)
  link_NAG-ASN         : angle       1.85664 (   21)
  hydrogen bonds       : bond        0.03739 (  474)
  hydrogen bonds       : angle       4.76099 ( 1377)
  SS BOND              : bond        0.00173 (    6)
  SS BOND              : angle       0.73289 (   12)
  covalent geometry    : bond        0.00377 ( 8841)
  covalent geometry    : angle       0.56548 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.857 
Fit side-chains
REVERT: B  333 CYS cc_start: 0.7312 (t) cc_final: 0.6323 (m)
  outliers start: 13
  outliers final: 8
  residues processed: 86
  average time/residue: 0.1717
  time to fit residues: 22.0659
Evaluate side-chains
  78 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  562 ASN
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  478 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0870
   chunk 102 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0370
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.5436

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
A 140 GLN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.145064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.115369 restraints weight = 25380.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.53
r_work: 0.3120 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8854  Z= 0.158
  Angle     :  0.576   8.919  12140  Z= 0.283
  Chirality :  0.042   0.171   1418
  Planarity :  0.004   0.042   1468
  Dihedral  :  8.398  57.870   1438
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.42 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.25), residues: 1092
  helix:  1.79 (0.22), residues: 532
  sheet: -0.14 (0.50), residues: 106
  loop : -1.25 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 647 
 HIS   0.006   0.001   HIS A 614 
 PHE   0.020   0.001   PHE A 601 
 TYR   0.014   0.001   TYR B 570 
 ARG   0.005   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00282 (    7)
  link_NAG-ASN         : angle       1.90002 (   21)
  hydrogen bonds       : bond        0.03657 (  474)
  hydrogen bonds       : angle       4.72355 ( 1377)
  SS BOND              : bond        0.00159 (    6)
  SS BOND              : angle       0.71398 (   12)
  covalent geometry    : bond        0.00379 ( 8841)
  covalent geometry    : angle       0.57080 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.846 
Fit side-chains
REVERT: B  333 CYS cc_start: 0.7338 (t) cc_final: 0.6388 (m)
REVERT: A  156 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7645 (ttm110)
  outliers start: 13
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1684
  time to fit residues: 19.8102
Evaluate side-chains
  74 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  478 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 101 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 562 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.144041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.115186 restraints weight = 27211.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.62
r_work: 0.3111 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   8854  Z= 0.196
  Angle     :  0.605   9.836  12140  Z= 0.298
  Chirality :  0.043   0.164   1418
  Planarity :  0.004   0.041   1468
  Dihedral  :  8.261  59.184   1438
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.19 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.25), residues: 1092
  helix:  1.67 (0.22), residues: 531
  sheet: -0.18 (0.50), residues: 106
  loop : -1.29 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 647 
 HIS   0.007   0.001   HIS A 614 
 PHE   0.021   0.001   PHE A 601 
 TYR   0.017   0.001   TYR B 570 
 ARG   0.004   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00274 (    7)
  link_NAG-ASN         : angle       2.10648 (   21)
  hydrogen bonds       : bond        0.03759 (  474)
  hydrogen bonds       : angle       4.81928 ( 1377)
  SS BOND              : bond        0.00184 (    6)
  SS BOND              : angle       0.78085 (   12)
  covalent geometry    : bond        0.00479 ( 8841)
  covalent geometry    : angle       0.59861 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.847 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.6924 (p90)
REVERT: B  199 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6833 (mm)
REVERT: B  333 CYS cc_start: 0.7356 (t) cc_final: 0.6412 (m)
REVERT: B  605 MET cc_start: 0.8233 (mtt) cc_final: 0.7745 (mtt)
REVERT: B  663 ILE cc_start: 0.6633 (mm) cc_final: 0.6135 (mm)
REVERT: A  156 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7543 (ttm110)
  outliers start: 17
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1971
  time to fit residues: 23.8204
Evaluate side-chains
  82 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  135 HIS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  562 ASN
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  552 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 65 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 562 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116751 restraints weight = 20943.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.73
r_work: 0.3162 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   8854  Z= 0.198
  Angle     :  0.603  10.820  12140  Z= 0.298
  Chirality :  0.043   0.154   1418
  Planarity :  0.004   0.043   1468
  Dihedral  :  8.220  59.998   1438
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.31 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.25), residues: 1092
  helix:  1.61 (0.22), residues: 531
  sheet: -0.20 (0.50), residues: 106
  loop : -1.30 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 647 
 HIS   0.008   0.001   HIS A 614 
 PHE   0.020   0.001   PHE A 601 
 TYR   0.017   0.001   TYR A 570 
 ARG   0.004   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00259 (    7)
  link_NAG-ASN         : angle       2.16982 (   21)
  hydrogen bonds       : bond        0.03742 (  474)
  hydrogen bonds       : angle       4.84273 ( 1377)
  SS BOND              : bond        0.00193 (    6)
  SS BOND              : angle       0.77614 (   12)
  covalent geometry    : bond        0.00484 ( 8841)
  covalent geometry    : angle       0.59673 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.916 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7025 (p90)
REVERT: B  199 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6829 (mm)
REVERT: B  333 CYS cc_start: 0.7449 (t) cc_final: 0.6511 (m)
REVERT: B  605 MET cc_start: 0.8422 (mtt) cc_final: 0.7964 (mtt)
REVERT: B  663 ILE cc_start: 0.6767 (mm) cc_final: 0.6257 (mm)
REVERT: A  156 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7713 (ttm110)
  outliers start: 17
  outliers final: 11
  residues processed: 82
  average time/residue: 0.1967
  time to fit residues: 23.6862
Evaluate side-chains
  79 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  135 HIS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  571 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 13 optimal weight:    9.9990
   chunk 108 optimal weight:    0.2980
   chunk 63 optimal weight:    5.9990
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 562 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.149169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.118718 restraints weight = 21366.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.82
r_work: 0.3179 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8854  Z= 0.151
  Angle     :  0.566  10.745  12140  Z= 0.279
  Chirality :  0.042   0.144   1418
  Planarity :  0.004   0.042   1468
  Dihedral  :  7.921  58.693   1438
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.25 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.77 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.25), residues: 1092
  helix:  1.76 (0.22), residues: 531
  sheet: -0.23 (0.50), residues: 106
  loop : -1.29 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 647 
 HIS   0.008   0.001   HIS A 614 
 PHE   0.021   0.001   PHE A 601 
 TYR   0.015   0.001   TYR B 570 
 ARG   0.004   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00265 (    7)
  link_NAG-ASN         : angle       2.00203 (   21)
  hydrogen bonds       : bond        0.03555 (  474)
  hydrogen bonds       : angle       4.70996 ( 1377)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       0.71516 (   12)
  covalent geometry    : bond        0.00363 ( 8841)
  covalent geometry    : angle       0.56021 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.819 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.6981 (p90)
REVERT: B  199 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6771 (mm)
REVERT: B  333 CYS cc_start: 0.7360 (t) cc_final: 0.6458 (m)
REVERT: B  605 MET cc_start: 0.8356 (mtt) cc_final: 0.7886 (mtt)
REVERT: B  663 ILE cc_start: 0.6721 (mm) cc_final: 0.6212 (mm)
REVERT: A  156 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7505 (ttm110)
  outliers start: 17
  outliers final: 9
  residues processed: 84
  average time/residue: 0.2096
  time to fit residues: 24.8292
Evaluate side-chains
  78 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  135 HIS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  571 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 562 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.147856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.117024 restraints weight = 19270.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.24
r_work: 0.3163 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3041
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3041
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   8854  Z= 0.186
  Angle     :  0.592  10.643  12140  Z= 0.292
  Chirality :  0.043   0.149   1418
  Planarity :  0.004   0.041   1468
  Dihedral  :  7.919  66.837   1438
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.25 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.00 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1092
  helix:  1.68 (0.22), residues: 531
  sheet: -0.28 (0.50), residues: 106
  loop : -1.30 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 647 
 HIS   0.009   0.001   HIS A 614 
 PHE   0.020   0.001   PHE A 601 
 TYR   0.024   0.001   TYR A 155 
 ARG   0.003   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00257 (    7)
  link_NAG-ASN         : angle       2.09789 (   21)
  hydrogen bonds       : bond        0.03658 (  474)
  hydrogen bonds       : angle       4.77596 ( 1377)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       0.75466 (   12)
  covalent geometry    : bond        0.00454 ( 8841)
  covalent geometry    : angle       0.58590 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.828 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7167 (p90)
REVERT: B  199 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6875 (mm)
REVERT: B  333 CYS cc_start: 0.7427 (t) cc_final: 0.6525 (m)
REVERT: B  605 MET cc_start: 0.8556 (mtt) cc_final: 0.8102 (mtt)
REVERT: B  663 ILE cc_start: 0.6897 (mm) cc_final: 0.6371 (mm)
REVERT: A  156 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7749 (ttm110)
  outliers start: 17
  outliers final: 12
  residues processed: 81
  average time/residue: 0.2133
  time to fit residues: 24.5194
Evaluate side-chains
  80 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  135 HIS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain A residue   79 MET
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  571 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 47 optimal weight:    0.3980
   chunk 57 optimal weight:    0.5980
   chunk 25 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 99 optimal weight:    0.5980
   chunk 83 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 105 optimal weight:    0.1980
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 562 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.149428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.118626 restraints weight = 19037.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.23
r_work: 0.3197 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3057
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3057
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8854  Z= 0.140
  Angle     :  0.562  10.580  12140  Z= 0.277
  Chirality :  0.041   0.141   1418
  Planarity :  0.004   0.042   1468
  Dihedral  :  7.771  76.406   1438
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.97 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.00 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.25), residues: 1092
  helix:  1.81 (0.22), residues: 531
  sheet: -0.35 (0.49), residues: 108
  loop : -1.30 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 647 
 HIS   0.009   0.001   HIS A 614 
 PHE   0.019   0.001   PHE A 601 
 TYR   0.026   0.001   TYR A 155 
 ARG   0.004   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00260 (    7)
  link_NAG-ASN         : angle       1.98914 (   21)
  hydrogen bonds       : bond        0.03542 (  474)
  hydrogen bonds       : angle       4.68368 ( 1377)
  SS BOND              : bond        0.00155 (    6)
  SS BOND              : angle       0.70747 (   12)
  covalent geometry    : bond        0.00332 ( 8841)
  covalent geometry    : angle       0.55614 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.991 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7091 (p90)
REVERT: B  199 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6862 (mm)
REVERT: B  333 CYS cc_start: 0.7387 (t) cc_final: 0.6522 (m)
REVERT: B  605 MET cc_start: 0.8507 (mtt) cc_final: 0.8057 (mtt)
REVERT: B  663 ILE cc_start: 0.6862 (mm) cc_final: 0.6336 (mm)
REVERT: A  153 LEU cc_start: 0.8165 (mt) cc_final: 0.7959 (mt)
  outliers start: 16
  outliers final: 10
  residues processed: 81
  average time/residue: 0.2083
  time to fit residues: 24.4228
Evaluate side-chains
  79 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  135 HIS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  478 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0470
   chunk 82 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 562 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.148715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.119596 restraints weight = 22843.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.35
r_work: 0.3192 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3063
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8854  Z= 0.167
  Angle     :  0.579  10.689  12140  Z= 0.285
  Chirality :  0.042   0.145   1418
  Planarity :  0.004   0.041   1468
  Dihedral  :  7.793  85.144   1438
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.88 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.24 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.25), residues: 1092
  helix:  1.76 (0.22), residues: 531
  sheet: -0.35 (0.49), residues: 108
  loop : -1.30 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 647 
 HIS   0.009   0.001   HIS A 614 
 PHE   0.019   0.001   PHE A 601 
 TYR   0.025   0.001   TYR A 155 
 ARG   0.003   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00263 (    7)
  link_NAG-ASN         : angle       2.01858 (   21)
  hydrogen bonds       : bond        0.03577 (  474)
  hydrogen bonds       : angle       4.71859 ( 1377)
  SS BOND              : bond        0.00170 (    6)
  SS BOND              : angle       0.74440 (   12)
  covalent geometry    : bond        0.00405 ( 8841)
  covalent geometry    : angle       0.57342 (12107)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.813 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.6928 (p90)
REVERT: B  199 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6815 (mm)
REVERT: B  333 CYS cc_start: 0.7347 (t) cc_final: 0.6481 (m)
REVERT: B  605 MET cc_start: 0.8419 (mtt) cc_final: 0.7946 (mtt)
REVERT: B  663 ILE cc_start: 0.6789 (mm) cc_final: 0.6271 (mm)
REVERT: A  153 LEU cc_start: 0.8070 (mt) cc_final: 0.7835 (mt)
REVERT: A  156 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7858 (ttm110)
  outliers start: 14
  outliers final: 11
  residues processed: 80
  average time/residue: 0.2059
  time to fit residues: 23.3179
Evaluate side-chains
  81 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  135 HIS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  571 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 67 optimal weight:    7.9990
   chunk 88 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0070
   chunk 83 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 99 optimal weight:    0.5980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 562 ASN
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.148944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.118919 restraints weight = 16551.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.06
r_work: 0.3205 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8854  Z= 0.158
  Angle     :  0.575  10.862  12140  Z= 0.283
  Chirality :  0.042   0.144   1418
  Planarity :  0.004   0.041   1468
  Dihedral  :  7.764  87.888   1438
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.97 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.89 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1092
  helix:  1.78 (0.22), residues: 531
  sheet: -0.37 (0.49), residues: 108
  loop : -1.30 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 647 
 HIS   0.009   0.001   HIS A 614 
 PHE   0.019   0.001   PHE A 601 
 TYR   0.024   0.001   TYR A 155 
 ARG   0.003   0.000   ARG B 656 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00260 (    7)
  link_NAG-ASN         : angle       2.00009 (   21)
  hydrogen bonds       : bond        0.03563 (  474)
  hydrogen bonds       : angle       4.69961 ( 1377)
  SS BOND              : bond        0.00167 (    6)
  SS BOND              : angle       0.74456 (   12)
  covalent geometry    : bond        0.00383 ( 8841)
  covalent geometry    : angle       0.56875 (12107)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4819.08 seconds
wall clock time: 85 minutes 0.19 seconds (5100.19 seconds total)