Starting phenix.real_space_refine
on Fri Jun  6 11:07:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w3v_32294/06_2025/7w3v_32294.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w3v_32294/06_2025/7w3v_32294.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w3v_32294/06_2025/7w3v_32294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w3v_32294/06_2025/7w3v_32294.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w3v_32294/06_2025/7w3v_32294.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w3v_32294/06_2025/7w3v_32294.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    4755      2.51       5
     N    1197      2.21       5
     O    1499      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7480
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1675
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 5, 'TRANS': 216}
    Chain: "C"
      Number of atoms: 5487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 696, 5487
          Classifications: {'peptide': 696}
          Link IDs: {'PTRANS': 29, 'TRANS': 666}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 94
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 94
          Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 112
          Unusual residues: {'NAG': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
  Time building chain proxies: 4.74, per 1000 atoms: 0.63
  Number of scatterers: 7480
  At special positions: 0
  Unit cell: (92.307, 90.185, 120.954, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1499      8.00
     N    1197      7.00
     C    4755      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  30 " - pdb=" SG  CYS C  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  90 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 621 " - pdb=" SG  CYS C 644 " 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
    ALPHA1-2
      " MAN D   5 " - " MAN D   6 "
    ALPHA1-3
      " BMA D   3 " - " MAN D   8 "
      " MAN D   4 " - " MAN D   7 "
    ALPHA1-6
      " BMA D   3 " - " MAN D   4 "
      " MAN D   4 " - " MAN D   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG B   1 " - " ASN C  73 "
      " NAG C1001 " - " ASN C 159 "
      " NAG C1002 " - " ASN C 234 "
      " NAG C1003 " - " ASN C 261 "
      " NAG C1004 " - " ASN C 532 "
      " NAG C1005 " - " ASN C 542 "
      " NAG C1006 " - " ASN C 562 "
      " NAG C1007 " - " ASN C 591 "
      " NAG C1008 " - " ASN C 660 "
      " NAG D   1 " - " ASN C 143 "
      " NAG E   1 " - " ASN C 311 "
      " NAG F   1 " - " ASN C 481 "
      " NAG G   1 " - " ASN C 647 "
  Time building additional restraints: 2.15
  Conformation dependent library (CDL) restraints added in 812.1 milliseconds
  

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1710

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 11 sheets defined
      16.6% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 95 through 97
      No H-bonds generated for 'chain 'A' and resid 95 through 97'
    Processing helix  chain 'A' and resid 195 through 206
    Processing helix  chain 'C' and resid 31 through 45
      removed outlier: 3.511A  pdb=" N   GLY C  44 " --> pdb=" O   GLU C  40 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU C  45 " --> pdb=" O   PHE C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 62
    Processing helix  chain 'C' and resid 105 through 111
      removed outlier: 3.849A  pdb=" N   LEU C 108 " --> pdb=" O   SER C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 136
      removed outlier: 3.900A  pdb=" N   ILE C 133 " --> pdb=" O   PRO C 130 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   PHE C 136 " --> pdb=" O   ILE C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 160
      removed outlier: 3.667A  pdb=" N   PHE C 157 " --> pdb=" O   PRO C 154 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS C 158 " --> pdb=" O   THR C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 184
      removed outlier: 3.782A  pdb=" N   SER C 182 " --> pdb=" O   THR C 179 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   HIS C 183 " --> pdb=" O   TRP C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 228 through 234
    Processing helix  chain 'C' and resid 256 through 263
      removed outlier: 4.134A  pdb=" N   SER C 263 " --> pdb=" O   PHE C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 285
    Processing helix  chain 'C' and resid 328 through 336
    Processing helix  chain 'C' and resid 337 through 340
      removed outlier: 3.855A  pdb=" N   ARG C 340 " --> pdb=" O   SER C 337 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 337 through 340'
    Processing helix  chain 'C' and resid 406 through 410
    Processing helix  chain 'C' and resid 428 through 434
      removed outlier: 3.914A  pdb=" N   GLY C 432 " --> pdb=" O   GLN C 429 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU C 434 " --> pdb=" O   ILE C 431 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 451 through 458
      removed outlier: 3.634A  pdb=" N   MET C 454 " --> pdb=" O   PRO C 451 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLY C 455 " --> pdb=" O   GLU C 452 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU C 457 " --> pdb=" O   MET C 454 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER C 458 " --> pdb=" O   GLY C 455 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 475 through 480
      removed outlier: 3.551A  pdb=" N   HIS C 478 " --> pdb=" O   THR C 475 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER C 480 " --> pdb=" O   SER C 477 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 617 through 621
      removed outlier: 3.687A  pdb=" N   CYS C 621 " --> pdb=" O   SER C 618 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 644 through 648
    Processing helix  chain 'C' and resid 666 through 672
      removed outlier: 3.723A  pdb=" N   LEU C 672 " --> pdb=" O   LEU C 669 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22
      removed outlier: 6.891A  pdb=" N   ALA A  64 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   ILE A  58 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   THR A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ILE A  63 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   SER A 235 " --> pdb=" O   ILE A  63 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   TRP A  71 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   THR A 227 " --> pdb=" O   TRP A  71 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   LYS A 105 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   PHE A 236 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LYS A 103 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ALA A 238 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31
      removed outlier: 3.561A  pdb=" N   TYR A  34 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93
      removed outlier: 4.300A  pdb=" N   LYS A  92 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   PHE A 124 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU A 217 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ASP A 122 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ALA A 219 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   SER A 120 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   THR A 221 " --> pdb=" O   ASP A 118 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ASP A 118 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ALA A 117 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   ALA A 143 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL A 119 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   GLU A 136 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   PHE A 182 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   MET A 138 " --> pdb=" O   PHE A 182 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   ALA A 184 " --> pdb=" O   MET A 138 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   TRP A 140 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA A 158 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148
    Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 71
      removed outlier: 6.845A  pdb=" N   LEU C  82 " --> pdb=" O   ASP C 118 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 141 through 143
      removed outlier: 6.532A  pdb=" N   LEU C 142 " --> pdb=" O   ASP C 167 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   LEU C 166 " --> pdb=" O   SER C 191 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   LEU C 190 " --> pdb=" O   ASP C 216 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LEU C 215 " --> pdb=" O   HIS C 244 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU C 318 " --> pdb=" O   GLY C 347 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   LEU C 346 " --> pdb=" O   TYR C 370 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP C 394 " --> pdb=" O   LEU C 369 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LEU C 393 " --> pdb=" O   HIS C 417 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU C 416 " --> pdb=" O   ASP C 441 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LEU C 440 " --> pdb=" O   ASP C 464 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE C 463 " --> pdb=" O   ASP C 489 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   LEU C 488 " --> pdb=" O   ASN C 513 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ILE C 512 " --> pdb=" O   ASP C 537 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU C 536 " --> pdb=" O   ASN C 562 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LEU C 561 " --> pdb=" O   ASP C 586 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE C 585 " --> pdb=" O   TYR C 607 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU C 630 " --> pdb=" O   VAL C 653 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU C 654 " --> pdb=" O   TYR C 679 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 152
      removed outlier: 6.354A  pdb=" N   GLY C 151 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   LEU C 173 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 358
      removed outlier: 6.408A  pdb=" N   LEU C 357 " --> pdb=" O   MET C 381 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AB1, first strand: chain 'C' and resid 569 through 570
      removed outlier: 5.632A  pdb=" N   GLY C 570 " --> pdb=" O   SER C 593 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   PHE C 592 " --> pdb=" O   GLN C 612 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE C 614 " --> pdb=" O   PHE C 592 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   GLY C 594 " --> pdb=" O   PHE C 614 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   PHE C 613 " --> pdb=" O   GLN C 636 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER C 638 " --> pdb=" O   PHE C 613 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   GLY C 615 " --> pdb=" O   SER C 638 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   PHE C 637 " --> pdb=" O   ASN C 660 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   SER C 662 " --> pdb=" O   PHE C 637 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   GLY C 639 " --> pdb=" O   SER C 662 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LYS C 664 " --> pdb=" O   GLY C 639 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   PHE C 661 " --> pdb=" O   SER C 684 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   SER C 686 " --> pdb=" O   PHE C 661 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   GLY C 663 " --> pdb=" O   SER C 686 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 781 through 789
      removed outlier: 3.832A  pdb=" N   MET C 781 " --> pdb=" O   TYR C 798 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY C 787 " --> pdb=" O   TYR C 792 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   TYR C 792 " --> pdb=" O   GLY C 787 " (cutoff:3.500A)

    133 hydrogen bonds defined for protein.
    285 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2323
        1.34 -     1.46: 1832
        1.46 -     1.58: 3441
        1.58 -     1.70: 0
        1.70 -     1.81: 42
  Bond restraints: 7638
  Sorted by residual:
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 7.06e+00
  bond pdb=" C1  NAG C1002 "
       pdb=" O5  NAG C1002 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.75e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.67e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.14e+00
  bond pdb=" C1  NAG C1007 "
       pdb=" O5  NAG C1007 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.07e+00
  ... (remaining 7633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 9921
        1.44 -     2.89: 356
        2.89 -     4.33: 57
        4.33 -     5.78: 15
        5.78 -     7.22: 9
  Bond angle restraints: 10358
  Sorted by residual:
  angle pdb=" N   ILE C 620 "
        pdb=" CA  ILE C 620 "
        pdb=" C   ILE C 620 "
      ideal   model   delta    sigma   weight residual
     111.91  108.11    3.80 8.90e-01 1.26e+00 1.82e+01
  angle pdb=" C   PHE C 136 "
        pdb=" N   LYS C 137 "
        pdb=" CA  LYS C 137 "
      ideal   model   delta    sigma   weight residual
     121.54  127.58   -6.04 1.91e+00 2.74e-01 1.00e+01
  angle pdb=" C   LEU C 312 "
        pdb=" N   THR C 313 "
        pdb=" CA  THR C 313 "
      ideal   model   delta    sigma   weight residual
     121.54  126.40   -4.86 1.91e+00 2.74e-01 6.47e+00
  angle pdb=" C   ILE A 215 "
        pdb=" N   THR A 216 "
        pdb=" CA  THR A 216 "
      ideal   model   delta    sigma   weight residual
     122.73  118.78    3.95 1.62e+00 3.81e-01 5.93e+00
  angle pdb=" C   PHE C 250 "
        pdb=" N   SER C 251 "
        pdb=" CA  SER C 251 "
      ideal   model   delta    sigma   weight residual
     121.54  126.08   -4.54 1.91e+00 2.74e-01 5.65e+00
  ... (remaining 10353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.00: 4521
       23.00 -    45.99: 248
       45.99 -    68.99: 34
       68.99 -    91.98: 10
       91.98 -   114.98: 29
  Dihedral angle restraints: 4842
    sinusoidal: 2185
      harmonic: 2657
  Sorted by residual:
  dihedral pdb=" CB  CYS C  30 "
           pdb=" SG  CYS C  30 "
           pdb=" SG  CYS C  64 "
           pdb=" CB  CYS C  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.84   46.16     1      1.00e+01 1.00e-02 2.95e+01
  dihedral pdb=" CA  PHE C 260 "
           pdb=" C   PHE C 260 "
           pdb=" N   ASN C 261 "
           pdb=" CA  ASN C 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.85   21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" C2  NAG E   2 "
           pdb=" C1  NAG E   2 "
           pdb=" O5  NAG E   2 "
           pdb=" C5  NAG E   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   52.02 -114.98     1      3.00e+01 1.11e-03 1.52e+01
  ... (remaining 4839 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1048
       0.063 -    0.126: 177
       0.126 -    0.188: 12
       0.188 -    0.251: 0
       0.251 -    0.314: 4
  Chirality restraints: 1241
  Sorted by residual:
  chirality pdb=" C1  NAG C1003 "
            pdb=" ND2 ASN C 261 "
            pdb=" C2  NAG C1003 "
            pdb=" O5  NAG C1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C1  NAG C1004 "
            pdb=" ND2 ASN C 532 "
            pdb=" C2  NAG C1004 "
            pdb=" O5  NAG C1004 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN C 481 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 1238 not shown)

  Planarity restraints: 1293
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 792 "    0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO C 793 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO C 793 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 793 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 261 "   -0.017 2.00e-02 2.50e+03   1.58e-02 3.12e+00
        pdb=" CG  ASN C 261 "    0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 261 "   -0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 261 "    0.017 2.00e-02 2.50e+03
        pdb=" C1  NAG C1003 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 614 "    0.006 2.00e-02 2.50e+03   9.66e-03 1.63e+00
        pdb=" CG  PHE C 614 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 614 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 614 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 614 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 614 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 614 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1290 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1191
        2.76 -     3.30: 6969
        3.30 -     3.83: 11850
        3.83 -     4.37: 14502
        4.37 -     4.90: 24817
  Nonbonded interactions: 59329
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 101 "
            pdb=" OE2 GLU C 123 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   CYS C 220 "
            pdb=" ND2 ASN C 248 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OH  TYR A  69 "
            pdb=" OH  TYR A 108 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" NZ  LYS A 155 "
            pdb=" O7  NAG D   2 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OD1 ASP C 319 "
            pdb=" OG  SER C 321 "
     model   vdw
     2.304 3.040
  ... (remaining 59324 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 'B'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.670
  Find NCS groups from input model:        0.250
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
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      :  0.004   0.053   7665  Z= 0.178
  Angle     :  0.672   7.220  10436  Z= 0.321
  Chirality :  0.048   0.314   1241
  Planarity :  0.004   0.057   1280
  Dihedral  : 17.079 114.975   3123
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.62 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.27), residues: 910
  helix: -2.30 (0.43), residues: 133
  sheet: -2.16 (0.36), residues: 200
  loop : -1.50 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  28 
 HIS   0.002   0.001   HIS C 417 
 PHE   0.022   0.001   PHE C 614 
 TYR   0.021   0.002   TYR A 108 
 ARG   0.008   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00314 (   13)
  link_NAG-ASN         : angle       2.05242 (   39)
  link_ALPHA1-6        : bond        0.00302 (    2)
  link_ALPHA1-6        : angle       1.68255 (    6)
  link_BETA1-4         : bond        0.00544 (    6)
  link_BETA1-4         : angle       1.90597 (   18)
  link_ALPHA1-2        : bond        0.00202 (    1)
  link_ALPHA1-2        : angle       1.90260 (    3)
  link_ALPHA1-3        : bond        0.00462 (    2)
  link_ALPHA1-3        : angle       1.53095 (    6)
  hydrogen bonds       : bond        0.18587 (  133)
  hydrogen bonds       : angle       6.74611 (  285)
  SS BOND              : bond        0.00284 (    3)
  SS BOND              : angle       1.00021 (    6)
  covalent geometry    : bond        0.00366 ( 7638)
  covalent geometry    : angle       0.65429 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.823 
Fit side-chains
REVERT: A   96 ASN cc_start: 0.7605 (m-40) cc_final: 0.7399 (m110)
REVERT: A  114 THR cc_start: 0.7936 (m) cc_final: 0.7516 (p)
REVERT: C  270 ASP cc_start: 0.6854 (t0) cc_final: 0.6344 (t0)
REVERT: C  676 GLU cc_start: 0.7134 (pt0) cc_final: 0.6780 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2088
  time to fit residues: 50.2633
Evaluate side-chains
  160 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0000
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.9992

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
C  86 ASN
C 122 ASN
C 493 ASN
C 530 GLN
C 650 ASN
** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.097523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.087594 restraints weight = 11636.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 1.97
r_work: 0.3044 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061   7665  Z= 0.365
  Angle     :  0.792  10.805  10436  Z= 0.388
  Chirality :  0.055   0.372   1241
  Planarity :  0.005   0.038   1280
  Dihedral  : 13.817 111.328   1462
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  8.87 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.27), residues: 910
  helix: -2.24 (0.44), residues: 129
  sheet: -1.94 (0.34), residues: 222
  loop : -1.74 (0.25), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  28 
 HIS   0.006   0.002   HIS C 292 
 PHE   0.019   0.002   PHE C 410 
 TYR   0.025   0.003   TYR C 170 
 ARG   0.004   0.000   ARG C  99 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00616 (   13)
  link_NAG-ASN         : angle       2.06834 (   39)
  link_ALPHA1-6        : bond        0.00504 (    2)
  link_ALPHA1-6        : angle       2.41907 (    6)
  link_BETA1-4         : bond        0.00582 (    6)
  link_BETA1-4         : angle       2.34826 (   18)
  link_ALPHA1-2        : bond        0.00252 (    1)
  link_ALPHA1-2        : angle       2.33526 (    3)
  link_ALPHA1-3        : bond        0.00877 (    2)
  link_ALPHA1-3        : angle       1.71648 (    6)
  hydrogen bonds       : bond        0.05150 (  133)
  hydrogen bonds       : angle       5.86795 (  285)
  SS BOND              : bond        0.00457 (    3)
  SS BOND              : angle       1.55044 (    6)
  covalent geometry    : bond        0.00828 ( 7638)
  covalent geometry    : angle       0.77359 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 171
  time to evaluate  : 1.033 
Fit side-chains
REVERT: A   34 TYR cc_start: 0.8241 (m-80) cc_final: 0.7421 (m-80)
REVERT: C   70 ILE cc_start: 0.8668 (mm) cc_final: 0.8390 (mt)
REVERT: C  201 ASN cc_start: 0.7810 (p0) cc_final: 0.7442 (p0)
REVERT: C  270 ASP cc_start: 0.7404 (t0) cc_final: 0.6925 (t0)
REVERT: C  493 ASN cc_start: 0.8299 (m-40) cc_final: 0.8037 (m110)
REVERT: C  559 LYS cc_start: 0.8697 (tttp) cc_final: 0.8482 (tttt)
REVERT: C  676 GLU cc_start: 0.7382 (pt0) cc_final: 0.6917 (pt0)
  outliers start: 12
  outliers final: 8
  residues processed: 175
  average time/residue: 0.2043
  time to fit residues: 47.8834
Evaluate side-chains
  172 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 164
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  286 ASN
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  649 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 88 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
C 422 HIS
C 510 GLN
** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 659 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 = 0.3335 r_free = 0.3335 target = 0.100797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.090796 restraints weight = 11540.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.97
r_work: 0.3088 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7665  Z= 0.156
  Angle     :  0.629   7.738  10436  Z= 0.310
  Chirality :  0.047   0.200   1241
  Planarity :  0.003   0.031   1280
  Dihedral  : 11.292 108.813   1462
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.93 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.27), residues: 910
  helix: -2.10 (0.45), residues: 127
  sheet: -2.05 (0.33), residues: 229
  loop : -1.61 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  41 
 HIS   0.003   0.001   HIS C 292 
 PHE   0.019   0.001   PHE C 132 
 TYR   0.016   0.002   TYR C 533 
 ARG   0.004   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00492 (   13)
  link_NAG-ASN         : angle       1.83325 (   39)
  link_ALPHA1-6        : bond        0.00458 (    2)
  link_ALPHA1-6        : angle       1.74612 (    6)
  link_BETA1-4         : bond        0.00593 (    6)
  link_BETA1-4         : angle       1.89098 (   18)
  link_ALPHA1-2        : bond        0.00069 (    1)
  link_ALPHA1-2        : angle       1.88588 (    3)
  link_ALPHA1-3        : bond        0.01016 (    2)
  link_ALPHA1-3        : angle       1.85648 (    6)
  hydrogen bonds       : bond        0.03681 (  133)
  hydrogen bonds       : angle       5.50611 (  285)
  SS BOND              : bond        0.00404 (    3)
  SS BOND              : angle       1.28839 (    6)
  covalent geometry    : bond        0.00349 ( 7638)
  covalent geometry    : angle       0.61189 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 172
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8180 (m-80) cc_final: 0.7407 (m-80)
REVERT: C  270 ASP cc_start: 0.7323 (t0) cc_final: 0.6862 (t0)
REVERT: C  493 ASN cc_start: 0.8212 (m-40) cc_final: 0.7789 (m110)
REVERT: C  559 LYS cc_start: 0.8660 (tttp) cc_final: 0.8448 (tttt)
REVERT: C  676 GLU cc_start: 0.7409 (pt0) cc_final: 0.6944 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 177
  average time/residue: 0.1970
  time to fit residues: 46.5005
Evaluate side-chains
  173 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  650 ASN
Chi-restraints excluded: chain C residue  653 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 62 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
A 174 ASN
C 248 ASN
C 351 ASN
C 372 GLN
C 422 HIS
C 510 GLN
C 565 ASN
C 650 ASN
** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.100481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.090415 restraints weight = 11512.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.98
r_work: 0.3083 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7665  Z= 0.134
  Angle     :  0.617   9.515  10436  Z= 0.300
  Chirality :  0.047   0.223   1241
  Planarity :  0.003   0.030   1280
  Dihedral  : 10.004  99.596   1462
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.05 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.27), residues: 910
  helix: -2.10 (0.45), residues: 127
  sheet: -2.04 (0.34), residues: 229
  loop : -1.56 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  41 
 HIS   0.004   0.001   HIS C 417 
 PHE   0.014   0.001   PHE C 132 
 TYR   0.016   0.002   TYR C 533 
 ARG   0.005   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00324 (   13)
  link_NAG-ASN         : angle       1.88375 (   39)
  link_ALPHA1-6        : bond        0.00542 (    2)
  link_ALPHA1-6        : angle       1.77380 (    6)
  link_BETA1-4         : bond        0.00553 (    6)
  link_BETA1-4         : angle       2.12664 (   18)
  link_ALPHA1-2        : bond        0.00052 (    1)
  link_ALPHA1-2        : angle       1.83191 (    3)
  link_ALPHA1-3        : bond        0.00960 (    2)
  link_ALPHA1-3        : angle       1.78948 (    6)
  hydrogen bonds       : bond        0.03283 (  133)
  hydrogen bonds       : angle       5.27212 (  285)
  SS BOND              : bond        0.00367 (    3)
  SS BOND              : angle       1.24673 (    6)
  covalent geometry    : bond        0.00303 ( 7638)
  covalent geometry    : angle       0.59776 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8193 (m-80) cc_final: 0.7427 (m-80)
REVERT: C  150 SER cc_start: 0.8911 (t) cc_final: 0.8485 (m)
REVERT: C  270 ASP cc_start: 0.7189 (t0) cc_final: 0.6740 (t0)
REVERT: C  337 SER cc_start: 0.8549 (m) cc_final: 0.8320 (m)
REVERT: C  493 ASN cc_start: 0.8213 (m-40) cc_final: 0.7735 (m110)
REVERT: C  559 LYS cc_start: 0.8638 (tttp) cc_final: 0.8412 (tttt)
REVERT: C  612 GLN cc_start: 0.7784 (mt0) cc_final: 0.7361 (mt0)
REVERT: C  676 GLU cc_start: 0.7419 (pt0) cc_final: 0.6935 (pt0)
  outliers start: 19
  outliers final: 15
  residues processed: 181
  average time/residue: 0.2255
  time to fit residues: 54.2284
Evaluate side-chains
  180 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 CYS
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  372 GLN
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  650 ASN
Chi-restraints excluded: chain C residue  653 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 78 optimal weight:    0.3980
   chunk 20 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
C 372 GLN
C 510 GLN
** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 659 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 = 0.3327 r_free = 0.3327 target = 0.100248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.090236 restraints weight = 11524.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.97
r_work: 0.3084 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7665  Z= 0.148
  Angle     :  0.621   8.994  10436  Z= 0.303
  Chirality :  0.047   0.245   1241
  Planarity :  0.003   0.030   1280
  Dihedral  :  9.590  96.339   1462
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 13.42 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.27), residues: 910
  helix: -2.08 (0.45), residues: 127
  sheet: -2.01 (0.34), residues: 229
  loop : -1.55 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  41 
 HIS   0.005   0.001   HIS C 417 
 PHE   0.019   0.001   PHE C 614 
 TYR   0.017   0.002   TYR C 170 
 ARG   0.005   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00359 (   13)
  link_NAG-ASN         : angle       1.81854 (   39)
  link_ALPHA1-6        : bond        0.00545 (    2)
  link_ALPHA1-6        : angle       1.82008 (    6)
  link_BETA1-4         : bond        0.00506 (    6)
  link_BETA1-4         : angle       2.20779 (   18)
  link_ALPHA1-2        : bond        0.00050 (    1)
  link_ALPHA1-2        : angle       1.91396 (    3)
  link_ALPHA1-3        : bond        0.00924 (    2)
  link_ALPHA1-3        : angle       1.82842 (    6)
  hydrogen bonds       : bond        0.03275 (  133)
  hydrogen bonds       : angle       5.21511 (  285)
  SS BOND              : bond        0.00380 (    3)
  SS BOND              : angle       1.25786 (    6)
  covalent geometry    : bond        0.00335 ( 7638)
  covalent geometry    : angle       0.60130 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8202 (m-80) cc_final: 0.7431 (m-80)
REVERT: C  150 SER cc_start: 0.8926 (t) cc_final: 0.8496 (m)
REVERT: C  270 ASP cc_start: 0.7209 (t0) cc_final: 0.6759 (t0)
REVERT: C  337 SER cc_start: 0.8569 (m) cc_final: 0.8333 (m)
REVERT: C  493 ASN cc_start: 0.8194 (m-40) cc_final: 0.7638 (m110)
REVERT: C  559 LYS cc_start: 0.8663 (tttp) cc_final: 0.8444 (tttt)
REVERT: C  612 GLN cc_start: 0.7795 (mt0) cc_final: 0.7359 (mt0)
REVERT: C  676 GLU cc_start: 0.7456 (pt0) cc_final: 0.6950 (pt0)
  outliers start: 21
  outliers final: 17
  residues processed: 183
  average time/residue: 0.2119
  time to fit residues: 52.1832
Evaluate side-chains
  184 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain C residue   33 LYS
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  630 LEU
Chi-restraints excluded: chain C residue  653 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0770
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
C 349 ASN
C 510 GLN
C 650 ASN
** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.100498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.090490 restraints weight = 11566.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.97
r_work: 0.3086 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7665  Z= 0.154
  Angle     :  0.614   9.278  10436  Z= 0.301
  Chirality :  0.047   0.240   1241
  Planarity :  0.003   0.031   1280
  Dihedral  :  9.155  93.284   1462
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.67 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.27), residues: 910
  helix: -2.06 (0.45), residues: 127
  sheet: -2.02 (0.34), residues: 229
  loop : -1.54 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  28 
 HIS   0.003   0.001   HIS C 417 
 PHE   0.026   0.002   PHE C 384 
 TYR   0.018   0.002   TYR C 170 
 ARG   0.007   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00355 (   13)
  link_NAG-ASN         : angle       1.72205 (   39)
  link_ALPHA1-6        : bond        0.00573 (    2)
  link_ALPHA1-6        : angle       1.84065 (    6)
  link_BETA1-4         : bond        0.00466 (    6)
  link_BETA1-4         : angle       2.27286 (   18)
  link_ALPHA1-2        : bond        0.00024 (    1)
  link_ALPHA1-2        : angle       1.88793 (    3)
  link_ALPHA1-3        : bond        0.00927 (    2)
  link_ALPHA1-3        : angle       1.87148 (    6)
  hydrogen bonds       : bond        0.03249 (  133)
  hydrogen bonds       : angle       5.18476 (  285)
  SS BOND              : bond        0.00386 (    3)
  SS BOND              : angle       1.27310 (    6)
  covalent geometry    : bond        0.00349 ( 7638)
  covalent geometry    : angle       0.59438 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 1.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8203 (m-80) cc_final: 0.7476 (m-80)
REVERT: C   79 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.6948 (t)
REVERT: C  150 SER cc_start: 0.8929 (t) cc_final: 0.8507 (m)
REVERT: C  270 ASP cc_start: 0.7209 (t0) cc_final: 0.6784 (t0)
REVERT: C  279 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7780 (tp40)
REVERT: C  337 SER cc_start: 0.8597 (m) cc_final: 0.8355 (m)
REVERT: C  493 ASN cc_start: 0.8192 (m-40) cc_final: 0.7620 (m110)
REVERT: C  559 LYS cc_start: 0.8618 (tttp) cc_final: 0.8400 (tttt)
REVERT: C  612 GLN cc_start: 0.7808 (mt0) cc_final: 0.7381 (mt0)
REVERT: C  676 GLU cc_start: 0.7459 (pt0) cc_final: 0.6952 (pt0)
  outliers start: 26
  outliers final: 14
  residues processed: 193
  average time/residue: 0.2284
  time to fit residues: 59.7060
Evaluate side-chains
  188 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 173
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  649 THR
Chi-restraints excluded: chain C residue  653 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
A 190 ASN
C 349 ASN
C 650 ASN
** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.099496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.089534 restraints weight = 11499.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.95
r_work: 0.3063 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7665  Z= 0.240
  Angle     :  0.673   6.901  10436  Z= 0.331
  Chirality :  0.050   0.254   1241
  Planarity :  0.004   0.035   1280
  Dihedral  :  9.282  94.320   1462
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.02 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.27), residues: 910
  helix: -2.11 (0.45), residues: 127
  sheet: -1.94 (0.35), residues: 223
  loop : -1.67 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  28 
 HIS   0.008   0.002   HIS C 417 
 PHE   0.030   0.002   PHE C 384 
 TYR   0.023   0.002   TYR C 533 
 ARG   0.006   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00466 (   13)
  link_NAG-ASN         : angle       1.92739 (   39)
  link_ALPHA1-6        : bond        0.00480 (    2)
  link_ALPHA1-6        : angle       2.04012 (    6)
  link_BETA1-4         : bond        0.00449 (    6)
  link_BETA1-4         : angle       2.49265 (   18)
  link_ALPHA1-2        : bond        0.00260 (    1)
  link_ALPHA1-2        : angle       2.13415 (    3)
  link_ALPHA1-3        : bond        0.00859 (    2)
  link_ALPHA1-3        : angle       1.78226 (    6)
  hydrogen bonds       : bond        0.03794 (  133)
  hydrogen bonds       : angle       5.37333 (  285)
  SS BOND              : bond        0.00442 (    3)
  SS BOND              : angle       1.38416 (    6)
  covalent geometry    : bond        0.00545 ( 7638)
  covalent geometry    : angle       0.65146 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8235 (m-80) cc_final: 0.7578 (m-80)
REVERT: C   79 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7266 (t)
REVERT: C  270 ASP cc_start: 0.7420 (t0) cc_final: 0.6970 (t0)
REVERT: C  559 LYS cc_start: 0.8640 (tttp) cc_final: 0.8418 (tttt)
REVERT: C  612 GLN cc_start: 0.7795 (mt0) cc_final: 0.7365 (mt0)
  outliers start: 21
  outliers final: 16
  residues processed: 190
  average time/residue: 0.2018
  time to fit residues: 51.5947
Evaluate side-chains
  190 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain C residue   33 LYS
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  649 THR
Chi-restraints excluded: chain C residue  650 ASN
Chi-restraints excluded: chain C residue  653 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0670
   chunk 22 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
C 349 ASN
** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.099737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.089686 restraints weight = 11543.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 1.96
r_work: 0.3077 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7665  Z= 0.170
  Angle     :  0.640   9.550  10436  Z= 0.316
  Chirality :  0.049   0.320   1241
  Planarity :  0.004   0.037   1280
  Dihedral  :  9.126  94.421   1462
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.41 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.27), residues: 910
  helix: -2.13 (0.44), residues: 127
  sheet: -1.99 (0.34), residues: 233
  loop : -1.59 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  28 
 HIS   0.006   0.001   HIS C 417 
 PHE   0.029   0.002   PHE C 384 
 TYR   0.018   0.002   TYR C 170 
 ARG   0.007   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00398 (   13)
  link_NAG-ASN         : angle       1.81387 (   39)
  link_ALPHA1-6        : bond        0.00552 (    2)
  link_ALPHA1-6        : angle       1.85106 (    6)
  link_BETA1-4         : bond        0.00420 (    6)
  link_BETA1-4         : angle       2.27071 (   18)
  link_ALPHA1-2        : bond        0.00133 (    1)
  link_ALPHA1-2        : angle       1.98510 (    3)
  link_ALPHA1-3        : bond        0.00880 (    2)
  link_ALPHA1-3        : angle       1.87838 (    6)
  hydrogen bonds       : bond        0.03441 (  133)
  hydrogen bonds       : angle       5.32124 (  285)
  SS BOND              : bond        0.00405 (    3)
  SS BOND              : angle       1.30977 (    6)
  covalent geometry    : bond        0.00387 ( 7638)
  covalent geometry    : angle       0.62037 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 TRP cc_start: 0.8874 (m100) cc_final: 0.8339 (m100)
REVERT: A   34 TYR cc_start: 0.8221 (m-80) cc_final: 0.7502 (m-80)
REVERT: C   79 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7324 (t)
REVERT: C  150 SER cc_start: 0.8937 (t) cc_final: 0.8496 (m)
REVERT: C  270 ASP cc_start: 0.7382 (t0) cc_final: 0.6908 (t0)
REVERT: C  279 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7715 (tp40)
REVERT: C  280 ILE cc_start: 0.8429 (mm) cc_final: 0.8038 (tt)
REVERT: C  493 ASN cc_start: 0.8201 (m-40) cc_final: 0.7639 (m110)
REVERT: C  559 LYS cc_start: 0.8657 (tttp) cc_final: 0.8423 (tttt)
REVERT: C  612 GLN cc_start: 0.7767 (mt0) cc_final: 0.7345 (mt0)
  outliers start: 22
  outliers final: 18
  residues processed: 185
  average time/residue: 0.2021
  time to fit residues: 49.9785
Evaluate side-chains
  193 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 174
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  137 LYS
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  630 LEU
Chi-restraints excluded: chain C residue  649 THR
Chi-restraints excluded: chain C residue  653 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0030
   chunk 3 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.9794

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
C 422 HIS
C 650 ASN
** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.098833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.088796 restraints weight = 11656.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.97
r_work: 0.3067 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7665  Z= 0.193
  Angle     :  0.655   8.468  10436  Z= 0.322
  Chirality :  0.049   0.270   1241
  Planarity :  0.004   0.039   1280
  Dihedral  :  9.047  94.123   1462
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.02 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.27), residues: 910
  helix: -2.12 (0.44), residues: 127
  sheet: -1.91 (0.35), residues: 223
  loop : -1.67 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  41 
 HIS   0.006   0.002   HIS C 417 
 PHE   0.029   0.002   PHE C 384 
 TYR   0.019   0.002   TYR C 533 
 ARG   0.007   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (   13)
  link_NAG-ASN         : angle       1.76179 (   39)
  link_ALPHA1-6        : bond        0.00577 (    2)
  link_ALPHA1-6        : angle       1.91527 (    6)
  link_BETA1-4         : bond        0.00405 (    6)
  link_BETA1-4         : angle       2.29211 (   18)
  link_ALPHA1-2        : bond        0.00076 (    1)
  link_ALPHA1-2        : angle       1.94653 (    3)
  link_ALPHA1-3        : bond        0.00834 (    2)
  link_ALPHA1-3        : angle       1.84136 (    6)
  hydrogen bonds       : bond        0.03523 (  133)
  hydrogen bonds       : angle       5.31905 (  285)
  SS BOND              : bond        0.00431 (    3)
  SS BOND              : angle       1.37179 (    6)
  covalent geometry    : bond        0.00441 ( 7638)
  covalent geometry    : angle       0.63691 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 TRP cc_start: 0.8877 (m100) cc_final: 0.8313 (m100)
REVERT: A   34 TYR cc_start: 0.8239 (m-80) cc_final: 0.7523 (m-80)
REVERT: C   79 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7334 (t)
REVERT: C  150 SER cc_start: 0.8927 (t) cc_final: 0.8503 (m)
REVERT: C  270 ASP cc_start: 0.7391 (t0) cc_final: 0.6910 (t0)
REVERT: C  280 ILE cc_start: 0.8429 (mm) cc_final: 0.8057 (tt)
REVERT: C  493 ASN cc_start: 0.8215 (m-40) cc_final: 0.7673 (m110)
REVERT: C  559 LYS cc_start: 0.8639 (tttp) cc_final: 0.8418 (tttt)
REVERT: C  612 GLN cc_start: 0.7799 (mt0) cc_final: 0.7380 (mt0)
  outliers start: 21
  outliers final: 17
  residues processed: 188
  average time/residue: 0.2029
  time to fit residues: 51.1557
Evaluate side-chains
  190 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 172
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  630 LEU
Chi-restraints excluded: chain C residue  650 ASN
Chi-restraints excluded: chain C residue  653 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 48 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0670
   chunk 75 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
C 422 HIS
C 650 ASN
** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.099781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.089623 restraints weight = 11701.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.00
r_work: 0.3093 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7665  Z= 0.113
  Angle     :  0.612   9.326  10436  Z= 0.300
  Chirality :  0.047   0.252   1241
  Planarity :  0.003   0.038   1280
  Dihedral  :  8.739  93.137   1462
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.39 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.28), residues: 910
  helix: -2.11 (0.44), residues: 127
  sheet: -1.95 (0.34), residues: 228
  loop : -1.52 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  41 
 HIS   0.003   0.001   HIS C 417 
 PHE   0.028   0.001   PHE C 384 
 TYR   0.017   0.001   TYR C 580 
 ARG   0.008   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00367 (   13)
  link_NAG-ASN         : angle       1.62402 (   39)
  link_ALPHA1-6        : bond        0.00744 (    2)
  link_ALPHA1-6        : angle       1.70920 (    6)
  link_BETA1-4         : bond        0.00434 (    6)
  link_BETA1-4         : angle       2.11617 (   18)
  link_ALPHA1-2        : bond        0.00003 (    1)
  link_ALPHA1-2        : angle       1.83898 (    3)
  link_ALPHA1-3        : bond        0.00879 (    2)
  link_ALPHA1-3        : angle       1.95301 (    6)
  hydrogen bonds       : bond        0.02970 (  133)
  hydrogen bonds       : angle       5.14357 (  285)
  SS BOND              : bond        0.00353 (    3)
  SS BOND              : angle       1.23283 (    6)
  covalent geometry    : bond        0.00255 ( 7638)
  covalent geometry    : angle       0.59470 (10358)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 TRP cc_start: 0.8881 (m100) cc_final: 0.8345 (m100)
REVERT: A   34 TYR cc_start: 0.8195 (m-80) cc_final: 0.7506 (m-80)
REVERT: C  123 GLU cc_start: 0.7098 (pp20) cc_final: 0.6861 (tm-30)
REVERT: C  150 SER cc_start: 0.8849 (t) cc_final: 0.8440 (m)
REVERT: C  270 ASP cc_start: 0.7377 (t0) cc_final: 0.6912 (t0)
REVERT: C  280 ILE cc_start: 0.8399 (mm) cc_final: 0.8019 (tt)
REVERT: C  337 SER cc_start: 0.8558 (m) cc_final: 0.8323 (m)
REVERT: C  493 ASN cc_start: 0.8184 (m-40) cc_final: 0.7622 (m110)
REVERT: C  559 LYS cc_start: 0.8679 (tttp) cc_final: 0.8452 (tttt)
REVERT: C  612 GLN cc_start: 0.7795 (mt0) cc_final: 0.7388 (mt0)
  outliers start: 18
  outliers final: 15
  residues processed: 188
  average time/residue: 0.2245
  time to fit residues: 57.5503
Evaluate side-chains
  190 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  107 SER
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  598 LEU
Chi-restraints excluded: chain C residue  609 HIS
Chi-restraints excluded: chain C residue  650 ASN
Chi-restraints excluded: chain C residue  653 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 88 optimal weight:    0.0670
   chunk 84 optimal weight:    3.9990
   chunk 15 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
C 422 HIS
** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.099599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.089535 restraints weight = 11638.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.96
r_work: 0.3092 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.223   7665  Z= 0.275
  Angle     :  1.117  59.200  10436  Z= 0.597
  Chirality :  0.058   0.924   1241
  Planarity :  0.004   0.046   1280
  Dihedral  :  8.765  92.347   1462
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.26 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.27), residues: 910
  helix: -2.12 (0.44), residues: 127
  sheet: -1.95 (0.34), residues: 228
  loop : -1.56 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  41 
 HIS   0.004   0.001   HIS C 417 
 PHE   0.027   0.002   PHE C 384 
 TYR   0.013   0.002   TYR C 170 
 ARG   0.008   0.000   ARG C 164 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.06196 (   13)
  link_NAG-ASN         : angle       6.49447 (   39)
  link_ALPHA1-6        : bond        0.00796 (    2)
  link_ALPHA1-6        : angle       1.78428 (    6)
  link_BETA1-4         : bond        0.00612 (    6)
  link_BETA1-4         : angle       2.18121 (   18)
  link_ALPHA1-2        : bond        0.00030 (    1)
  link_ALPHA1-2        : angle       1.86359 (    3)
  link_ALPHA1-3        : bond        0.00930 (    2)
  link_ALPHA1-3        : angle       1.98607 (    6)
  hydrogen bonds       : bond        0.03014 (  133)
  hydrogen bonds       : angle       5.13683 (  285)
  SS BOND              : bond        0.00435 (    3)
  SS BOND              : angle       5.51034 (    6)
  covalent geometry    : bond        0.00505 ( 7638)
  covalent geometry    : angle       1.03317 (10358)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4328.64 seconds
wall clock time: 76 minutes 32.82 seconds (4592.82 seconds total)