Starting phenix.real_space_refine
on Wed Sep 17 12:19:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vlu_43344/09_2025/8vlu_43344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vlu_43344/09_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_43344/09_2025/8vlu_43344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vlu_43344/09_2025/8vlu_43344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vlu_43344/09_2025/8vlu_43344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vlu_43344/09_2025/8vlu_43344.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1}
          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: {'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1}
          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: {'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'ARG:plan': 4, 'PHE:plan': 1, 'TRP:plan': 1}
          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: 3.07, per 1000 atoms: 0.36
  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: 0.92
  Conformation dependent library (CDL) restraints added in 494.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.27
  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: 1.42

  Time building geometry restraints manager: 1.16 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 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 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.330
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.810
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG B 656 
 TYR   0.012   0.001   TYR A 602 
 PHE   0.015   0.001   PHE A 601 
 TRP   0.008   0.001   TRP A 300 
 HIS   0.005   0.001   HIS A 614 

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

*********************** 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  : 0.325 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 76
  average time/residue: 0.1043
  time to fit residues: 11.0373
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  : 0.337 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.147888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.115744 restraints weight = 20252.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.48
r_work: 0.3137 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    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 = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.0772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8854  Z= 0.201
  Angle     :  0.607   9.136  12140  Z= 0.302
  Chirality :  0.044   0.197   1418
  Planarity :  0.004   0.040   1468
  Dihedral  :  9.552  60.995   1440
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.67 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.25), residues: 1092
  helix:  1.60 (0.22), residues: 532
  sheet: -0.17 (0.50), residues: 108
  loop : -1.26 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 379 
 TYR   0.015   0.002   TYR A 570 
 PHE   0.020   0.002   PHE A 512 
 TRP   0.012   0.001   TRP A 300 
 HIS   0.006   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 8841)
  covalent geometry    : angle       0.60184 (12107)
  SS BOND              : bond        0.00145 (    6)
  SS BOND              : angle       0.87593 (   12)
  hydrogen bonds       : bond        0.04085 (  474)
  hydrogen bonds       : angle       5.01266 ( 1377)
  link_NAG-ASN         : bond        0.00330 (    7)
  link_NAG-ASN         : angle       2.00242 (   21)

*********************** 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
  91 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.318 
Fit side-chains
  outliers start: 14
  outliers final: 8
  residues processed: 86
  average time/residue: 0.1040
  time to fit residues: 12.4190
Evaluate side-chains
  75 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  478 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 73 optimal weight:    0.0970
   chunk 6 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 555 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.147324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.115494 restraints weight = 19484.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.40
r_work: 0.3169 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    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 = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8854  Z= 0.170
  Angle     :  0.584   9.198  12140  Z= 0.289
  Chirality :  0.043   0.180   1418
  Planarity :  0.004   0.046   1468
  Dihedral  :  8.817  56.912   1440
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.26 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.25), residues: 1092
  helix:  1.63 (0.22), residues: 532
  sheet: -0.16 (0.50), residues: 106
  loop : -1.27 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 656 
 TYR   0.015   0.001   TYR B 570 
 PHE   0.017   0.001   PHE A 512 
 TRP   0.010   0.001   TRP A 647 
 HIS   0.006   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 8841)
  covalent geometry    : angle       0.57883 (12107)
  SS BOND              : bond        0.00168 (    6)
  SS BOND              : angle       0.77813 (   12)
  hydrogen bonds       : bond        0.03792 (  474)
  hydrogen bonds       : angle       4.85439 ( 1377)
  link_NAG-ASN         : bond        0.00280 (    7)
  link_NAG-ASN         : angle       1.99238 (   21)

*********************** 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
  83 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.297 
Fit side-chains
REVERT: B  333 CYS cc_start: 0.7412 (t) cc_final: 0.6453 (m)
REVERT: B  663 ILE cc_start: 0.6819 (mm) cc_final: 0.6330 (mm)
  outliers start: 12
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0809
  time to fit residues: 9.5636
Evaluate side-chains
  73 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 36 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   chunk 103 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 13 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.149711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.121018 restraints weight = 27023.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.60
r_work: 0.3143 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3129
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3129
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.0999

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= 0.175
  Angle     :  0.593   9.248  12140  Z= 0.291
  Chirality :  0.043   0.170   1418
  Planarity :  0.004   0.043   1468
  Dihedral  :  8.353  58.885   1438
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 10.84 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.25), residues: 1092
  helix:  1.64 (0.22), residues: 531
  sheet: -0.15 (0.50), residues: 106
  loop : -1.28 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 656 
 TYR   0.016   0.001   TYR A 570 
 PHE   0.017   0.001   PHE A 512 
 TRP   0.010   0.001   TRP A 647 
 HIS   0.006   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8841)
  covalent geometry    : angle       0.58690 (12107)
  SS BOND              : bond        0.00248 (    6)
  SS BOND              : angle       0.75566 (   12)
  hydrogen bonds       : bond        0.03731 (  474)
  hydrogen bonds       : angle       4.81362 ( 1377)
  link_NAG-ASN         : bond        0.00266 (    7)
  link_NAG-ASN         : angle       2.05559 (   21)

*********************** 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
  88 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.332 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7181 (p90)
REVERT: B  333 CYS cc_start: 0.7437 (t) cc_final: 0.6508 (m)
REVERT: B  605 MET cc_start: 0.8475 (mtt) cc_final: 0.8005 (mtt)
REVERT: B  663 ILE cc_start: 0.6839 (mm) cc_final: 0.6324 (mm)
  outliers start: 19
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0915
  time to fit residues: 10.9827
Evaluate side-chains
  79 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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 A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  552 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 96 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    7.9990
   chunk 89 optimal weight:    0.4980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.145740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.115556 restraints weight = 22577.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.52
r_work: 0.3150 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1097

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= 0.201
  Angle     :  0.605   9.865  12140  Z= 0.299
  Chirality :  0.043   0.163   1418
  Planarity :  0.004   0.042   1468
  Dihedral  :  8.274  59.786   1438
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.66 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.25), residues: 1092
  helix:  1.56 (0.22), residues: 531
  sheet: -0.23 (0.50), residues: 106
  loop : -1.31 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 656 
 TYR   0.017   0.001   TYR B 570 
 PHE   0.019   0.001   PHE A 512 
 TRP   0.011   0.001   TRP A 647 
 HIS   0.008   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 8841)
  covalent geometry    : angle       0.59832 (12107)
  SS BOND              : bond        0.00199 (    6)
  SS BOND              : angle       0.78224 (   12)
  hydrogen bonds       : bond        0.03778 (  474)
  hydrogen bonds       : angle       4.87191 ( 1377)
  link_NAG-ASN         : bond        0.00262 (    7)
  link_NAG-ASN         : angle       2.18901 (   21)

*********************** 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: 18
    poor density    : 70
  time to evaluate  : 0.395 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7007 (p90)
REVERT: B  199 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6708 (mm)
REVERT: B  333 CYS cc_start: 0.7448 (t) cc_final: 0.6504 (m)
REVERT: B  605 MET cc_start: 0.8400 (mtt) cc_final: 0.7920 (mtt)
REVERT: B  663 ILE cc_start: 0.6733 (mm) cc_final: 0.6243 (mm)
  outliers start: 18
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0940
  time to fit residues: 11.4073
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  : 0.289 
-------------------------------------------------------------------------------
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  150 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  183 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0970
   chunk 9 optimal weight:    4.9990
   chunk 89 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.147616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.118173 restraints weight = 21455.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.44
r_work: 0.3161 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8854  Z= 0.177
  Angle     :  0.589  10.538  12140  Z= 0.290
  Chirality :  0.043   0.151   1418
  Planarity :  0.004   0.040   1468
  Dihedral  :  8.168  59.463   1438
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.25), residues: 1092
  helix:  1.62 (0.22), residues: 531
  sheet: -0.22 (0.50), residues: 106
  loop : -1.33 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 656 
 TYR   0.016   0.001   TYR B 570 
 PHE   0.017   0.001   PHE A 512 
 TRP   0.010   0.001   TRP A 647 
 HIS   0.007   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 8841)
  covalent geometry    : angle       0.58276 (12107)
  SS BOND              : bond        0.00181 (    6)
  SS BOND              : angle       0.73693 (   12)
  hydrogen bonds       : bond        0.03695 (  474)
  hydrogen bonds       : angle       4.82282 ( 1377)
  link_NAG-ASN         : bond        0.00259 (    7)
  link_NAG-ASN         : angle       2.16418 (   21)

*********************** 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
  87 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.358 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7041 (p90)
REVERT: B  199 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6742 (mm)
REVERT: B  333 CYS cc_start: 0.7409 (t) cc_final: 0.6479 (m)
REVERT: B  605 MET cc_start: 0.8413 (mtt) cc_final: 0.7967 (mtt)
REVERT: B  663 ILE cc_start: 0.6781 (mm) cc_final: 0.6270 (mm)
  outliers start: 17
  outliers final: 11
  residues processed: 84
  average time/residue: 0.0950
  time to fit residues: 11.4633
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  : 0.334 
-------------------------------------------------------------------------------
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  183 VAL
Chi-restraints excluded: chain A residue  478 ASP
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 48 optimal weight:    0.9980
   chunk 67 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 102 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 68 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0170
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.6618

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.147597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.119541 restraints weight = 25492.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.39
r_work: 0.3168 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8854  Z= 0.177
  Angle     :  0.588  10.874  12140  Z= 0.289
  Chirality :  0.042   0.148   1418
  Planarity :  0.004   0.040   1468
  Dihedral  :  8.107  59.955   1438
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.16 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 11.42 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.25), residues: 1092
  helix:  1.64 (0.22), residues: 531
  sheet: -0.26 (0.50), residues: 106
  loop : -1.33 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 656 
 TYR   0.016   0.001   TYR B 570 
 PHE   0.017   0.001   PHE A 512 
 TRP   0.010   0.001   TRP A 647 
 HIS   0.008   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 8841)
  covalent geometry    : angle       0.58155 (12107)
  SS BOND              : bond        0.00182 (    6)
  SS BOND              : angle       0.73520 (   12)
  hydrogen bonds       : bond        0.03675 (  474)
  hydrogen bonds       : angle       4.81194 ( 1377)
  link_NAG-ASN         : bond        0.00257 (    7)
  link_NAG-ASN         : angle       2.14987 (   21)

*********************** 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
  93 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.336 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7032 (p90)
REVERT: B  199 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6732 (mm)
REVERT: B  333 CYS cc_start: 0.7476 (t) cc_final: 0.6480 (m)
REVERT: B  605 MET cc_start: 0.8344 (mtt) cc_final: 0.7895 (mtt)
REVERT: B  663 ILE cc_start: 0.6776 (mm) cc_final: 0.6271 (mm)
  outliers start: 23
  outliers final: 16
  residues processed: 87
  average time/residue: 0.0945
  time to fit residues: 11.8385
Evaluate side-chains
  86 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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  153 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain A residue   85 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  183 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 50 optimal weight:    0.1980
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0970
   chunk 71 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 13 optimal weight:    9.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 140 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.118866 restraints weight = 20948.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.81
r_work: 0.3172 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    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 = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8854  Z= 0.126
  Angle     :  0.551  10.448  12140  Z= 0.271
  Chirality :  0.041   0.139   1418
  Planarity :  0.004   0.040   1468
  Dihedral  :  7.756  64.131   1438
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.06 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.00 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.25), residues: 1092
  helix:  1.85 (0.22), residues: 531
  sheet: -0.34 (0.49), residues: 108
  loop : -1.31 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 656 
 TYR   0.015   0.001   TYR B 570 
 PHE   0.014   0.001   PHE B 601 
 TRP   0.008   0.001   TRP A 647 
 HIS   0.008   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8841)
  covalent geometry    : angle       0.54586 (12107)
  SS BOND              : bond        0.00156 (    6)
  SS BOND              : angle       0.70102 (   12)
  hydrogen bonds       : bond        0.03492 (  474)
  hydrogen bonds       : angle       4.64462 ( 1377)
  link_NAG-ASN         : bond        0.00270 (    7)
  link_NAG-ASN         : angle       1.91046 (   21)

*********************** 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
  89 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.324 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7090 (p90)
REVERT: B  199 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6917 (mm)
REVERT: B  333 CYS cc_start: 0.7414 (t) cc_final: 0.6497 (m)
REVERT: B  605 MET cc_start: 0.8397 (mtt) cc_final: 0.7934 (mtt)
REVERT: B  663 ILE cc_start: 0.6811 (mm) cc_final: 0.6285 (mm)
  outliers start: 20
  outliers final: 11
  residues processed: 85
  average time/residue: 0.0955
  time to fit residues: 11.5633
Evaluate side-chains
  82 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  153 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 24 optimal weight:    0.3980
   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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.147729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117389 restraints weight = 20459.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.65
r_work: 0.3174 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    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 = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1182

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= 0.184
  Angle     :  0.585  10.569  12140  Z= 0.290
  Chirality :  0.043   0.148   1418
  Planarity :  0.004   0.039   1468
  Dihedral  :  7.849  80.173   1438
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.06 %
    Favored  : 94.84 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.25), residues: 1092
  helix:  1.72 (0.22), residues: 531
  sheet: -0.41 (0.48), residues: 109
  loop : -1.32 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 656 
 TYR   0.019   0.001   TYR A 155 
 PHE   0.018   0.001   PHE A 512 
 TRP   0.011   0.001   TRP A 647 
 HIS   0.009   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 8841)
  covalent geometry    : angle       0.57879 (12107)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       0.74309 (   12)
  hydrogen bonds       : bond        0.03670 (  474)
  hydrogen bonds       : angle       4.75660 ( 1377)
  link_NAG-ASN         : bond        0.00250 (    7)
  link_NAG-ASN         : angle       2.07679 (   21)

*********************** 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
  85 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.318 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.6991 (p90)
REVERT: B  199 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6808 (mm)
REVERT: B  333 CYS cc_start: 0.7450 (t) cc_final: 0.6477 (m)
REVERT: B  605 MET cc_start: 0.8407 (mtt) cc_final: 0.7957 (mtt)
REVERT: B  663 ILE cc_start: 0.6780 (mm) cc_final: 0.6265 (mm)
REVERT: A  156 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7645 (ttm110)
  outliers start: 17
  outliers final: 12
  residues processed: 79
  average time/residue: 0.1067
  time to fit residues: 11.7020
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  : 0.307 
-------------------------------------------------------------------------------
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  153 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain A residue   85 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  571 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0270
   chunk 75 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 98 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 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 = 0.149210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.120469 restraints weight = 24275.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.31
r_work: 0.3195 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8854  Z= 0.152
  Angle     :  0.561  10.679  12140  Z= 0.277
  Chirality :  0.042   0.145   1418
  Planarity :  0.004   0.043   1468
  Dihedral  :  7.686  83.959   1438
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.16 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.59 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.25), residues: 1092
  helix:  1.79 (0.22), residues: 531
  sheet: -0.43 (0.48), residues: 108
  loop : -1.32 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 656 
 TYR   0.021   0.001   TYR A 155 
 PHE   0.015   0.001   PHE A 512 
 TRP   0.009   0.001   TRP A 647 
 HIS   0.008   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8841)
  covalent geometry    : angle       0.55493 (12107)
  SS BOND              : bond        0.00175 (    6)
  SS BOND              : angle       0.72393 (   12)
  hydrogen bonds       : bond        0.03523 (  474)
  hydrogen bonds       : angle       4.66678 ( 1377)
  link_NAG-ASN         : bond        0.00260 (    7)
  link_NAG-ASN         : angle       1.97380 (   21)

********************** 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
  81 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.325 
Fit side-chains
REVERT: B  135 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.6946 (p90)
REVERT: B  199 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6849 (mm)
REVERT: B  333 CYS cc_start: 0.7420 (t) cc_final: 0.6494 (m)
REVERT: B  605 MET cc_start: 0.8358 (mtt) cc_final: 0.7909 (mtt)
REVERT: B  663 ILE cc_start: 0.6805 (mm) cc_final: 0.6308 (mm)
REVERT: A  153 LEU cc_start: 0.8092 (mt) cc_final: 0.7875 (mt)
REVERT: A  156 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7726 (ttm110)
  outliers start: 13
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1043
  time to fit residues: 11.2853
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  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  135 HIS
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  107 CYS
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 102 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3675 r_free = 0.3675 target = 0.148340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.119469 restraints weight = 21704.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.39
r_work: 0.3186 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    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 = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8854  Z= 0.169
  Angle     :  0.574  10.743  12140  Z= 0.284
  Chirality :  0.042   0.154   1418
  Planarity :  0.004   0.042   1468
  Dihedral  :  7.627  74.316   1438
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.97 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.25), residues: 1092
  helix:  1.75 (0.22), residues: 531
  sheet: -0.44 (0.48), residues: 109
  loop : -1.30 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 656 
 TYR   0.016   0.001   TYR B 570 
 PHE   0.016   0.001   PHE A 512 
 TRP   0.010   0.001   TRP A 647 
 HIS   0.008   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 8841)
  covalent geometry    : angle       0.56749 (12107)
  SS BOND              : bond        0.00168 (    6)
  SS BOND              : angle       0.74846 (   12)
  hydrogen bonds       : bond        0.03594 (  474)
  hydrogen bonds       : angle       4.70729 ( 1377)
  link_NAG-ASN         : bond        0.00247 (    7)
  link_NAG-ASN         : angle       2.05534 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2454.58 seconds
wall clock time: 42 minutes 48.48 seconds (2568.48 seconds total)