Starting phenix.real_space_refine
on Wed May 14 22:47:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gce_29932/05_2025/8gce_29932.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gce_29932/05_2025/8gce_29932.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gce_29932/05_2025/8gce_29932.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gce_29932/05_2025/8gce_29932.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gce_29932/05_2025/8gce_29932.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gce_29932/05_2025/8gce_29932.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     Mg      1      5.21       5
     S      98      5.16       5
     C    7697      2.51       5
     N    2116      2.21       5
     O    2425      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12343
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 7007
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 912, 6966
          Classifications: {'peptide': 912}
          Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 850}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 912, 6966
          Classifications: {'peptide': 912}
          Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 850}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 7082
    Chain: "B"
      Number of atoms: 5195
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 676, 5191
          Classifications: {'peptide': 676}
          Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 643}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 676, 5191
          Classifications: {'peptide': 676}
          Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 643}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 5277
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 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: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 32
          Unusual residues: {' CA': 4, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' MG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 72
    residue:
      pdb=" N  AGLN A 177 " occ=0.51
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 177 " occ=0.49
    residue:
      pdb=" N  AARG A 276 " occ=0.92
      ... (20 atoms not shown)
      pdb=" NH2BARG A 276 " occ=0.08
    residue:
      pdb=" N  AHIS A 587 " occ=0.40
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 587 " occ=0.60
    residue:
      pdb=" N   PRO B 605 " occ=0.71
      ... (5 atoms not shown)
      pdb=" CD  PRO B 605 " occ=0.71
    residue:
      pdb=" N   ASP B 606 " occ=0.49
      ... (6 atoms not shown)
      pdb=" OD2 ASP B 606 " occ=0.49
    residue:
      pdb=" N   ALA B 607 " occ=0.70
      ... (3 atoms not shown)
      pdb=" CB  ALA B 607 " occ=0.70
    residue:
      pdb=" N   CYS B 608 " occ=0.50
      ... (4 atoms not shown)
      pdb=" SG  CYS B 608 " occ=0.50
    residue:
      pdb=" N   THR B 609 " occ=0.56
      ... (5 atoms not shown)
      pdb=" CG2 THR B 609 " occ=0.56
    residue:
      pdb=" N   PHE B 610 " occ=0.93
      ... (9 atoms not shown)
      pdb=" CZ  PHE B 610 " occ=0.93
    residue:
      pdb=" N   LYS B 611 " occ=0.77
      ... (7 atoms not shown)
      pdb=" NZ  LYS B 611 " occ=0.77
    residue:
      pdb=" N   LYS B 612 " occ=0.67
      ... (7 atoms not shown)
      pdb=" NZ  LYS B 612 " occ=0.67
    residue:
      pdb=" N   GLU B 613 " occ=0.76
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 613 " occ=0.76
    ... (remaining 60 not shown)
  Time building chain proxies: 13.00, per 1000 atoms: 1.05
  Number of scatterers: 12343
  At special positions: 0
  Unit cell: (104.86, 123.05, 129.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      6     19.99
     S      98     16.00
     Mg      1     11.99
     O    2425      8.00
     N    2116      7.00
     C    7697      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=36, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  56 " - pdb=" SG  CYS A  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 130 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 167 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 473 " - pdb=" SG  CYS A 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 490 " - pdb=" SG  CYS A 545 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 602 " - pdb=" SG  CYS A 608 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 674 " - pdb=" SG  CYS A 687 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 826 " - pdb=" SG  CYS A 890 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 880 " - pdb=" SG  CYS A 885 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   5 " - pdb=" SG  CYS B  23 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  13 " - pdb=" SG  CYS B 435 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  16 " - pdb=" SG  CYS B  38 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  26 " - pdb=" SG  CYS B  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 374 " - pdb=" SG  CYS B 386 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 406 " - pdb=" SG  CYS B 433 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 437 " - pdb=" SG  CYS B 457 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 448 " - pdb=" SG  CYS B 460 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 462 " - pdb=" SG  CYS B 471 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 473 " - pdb=" SG  CYS B 503 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 501 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 495 " - pdb=" SG  CYS B 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 508 " - pdb=" SG  CYS B 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 523 " - pdb=" SG  CYS B 544 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 528 " - pdb=" SG  CYS B 542 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 536 " - pdb=" SG  CYS B 547 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 549 " - pdb=" SG  CYS B 558 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 560 " - pdb=" SG  CYS B 583 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 567 " - pdb=" SG  CYS B 581 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 575 " - pdb=" SG  CYS B 586 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 588 " - pdb=" SG  CYS B 598 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 601 " - pdb=" SG  CYS B 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 608 " - pdb=" SG  CYS B 655 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 614 " - pdb=" SG  CYS B 635 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 631 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A1105 " - " ASN A  15 "
      " NAG A1106 " - " ASN A 570 "
      " NAG C   1 " - " ASN B 371 "
      " NAG D   1 " - " ASN B 320 "
      " NAG E   1 " - " ASN B  99 "
  Time building additional restraints: 3.27
  Conformation dependent library (CDL) restraints added in 3.3 seconds
  

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2920

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 25 sheets defined
      10.2% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 199 through 204
      removed outlier: 3.545A  pdb=" N   ILE A 203 " --> pdb=" O   PRO A 199 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE A 204 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 199 through 204'
    Processing helix  chain 'A' and resid 910 through 916
      removed outlier: 3.567A  pdb=" N   GLN A 916 " --> pdb=" O   PRO A 912 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 9
      removed outlier: 3.557A  pdb=" N   ARG B   8 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY B   9 " --> pdb=" O   CYS B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 20
      removed outlier: 4.195A  pdb=" N   SER B  20 " --> pdb=" O   CYS B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 47
    Processing helix  chain 'B' and resid 50 through 52
      No H-bonds generated for 'chain 'B' and resid 50 through 52'
    Processing helix  chain 'B' and resid 121 through 123
      No H-bonds generated for 'chain 'B' and resid 121 through 123'
    Processing helix  chain 'B' and resid 124 through 132
    Processing helix  chain 'B' and resid 135 through 143
      removed outlier: 3.943A  pdb=" N   GLN B 141 " --> pdb=" O   LYS B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 173
      removed outlier: 3.636A  pdb=" N   LEU B 173 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 209
      removed outlier: 3.948A  pdb=" N   ASN B 204 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS B 208 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   LYS B 209 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 232
      removed outlier: 4.309A  pdb=" N   ALA B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 258 through 264
      removed outlier: 3.642A  pdb=" N   ARG B 261 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU B 262 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 286
      removed outlier: 4.383A  pdb=" N   THR B 285 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 302
    Processing helix  chain 'B' and resid 314 through 319
    Processing helix  chain 'B' and resid 339 through 354
    Processing helix  chain 'B' and resid 493 through 497
    Processing helix  chain 'B' and resid 534 through 538
    Processing helix  chain 'B' and resid 612 through 617
    Processing helix  chain 'B' and resid 630 through 635
      removed outlier: 4.039A  pdb=" N   TYR B 634 " --> pdb=" O   THR B 630 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   CYS B 635 " --> pdb=" O   CYS B 631 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 630 through 635'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10
      removed outlier: 3.865A  pdb=" N   THR A   9 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26
      removed outlier: 3.612A  pdb=" N   HIS A  26 " --> pdb=" O   ALA A  34 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54
      removed outlier: 4.900A  pdb=" N   VAL A  53 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76
      removed outlier: 4.399A  pdb=" N   GLU A  75 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 257
      removed outlier: 6.522A  pdb=" N   VAL A 267 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ARG A 279 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE A 269 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296
      removed outlier: 3.810A  pdb=" N   LEU A 345 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315
    Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364
      removed outlier: 5.866A  pdb=" N   ASP A 373 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLN A 405 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523
      removed outlier: 3.672A  pdb=" N   LEU A 522 " --> pdb=" O   PHE A 551 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 551 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A 544 " --> pdb=" O   VAL A 491 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL A 491 " --> pdb=" O   ILE A 544 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 494 " --> pdb=" O   LYS A 455 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   VAL A 454 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N  AHIS A 587 " --> pdb=" O   VAL A 454 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474
      removed outlier: 4.678A  pdb=" N   CYS A 473 " --> pdb=" O   VAL A 482 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   VAL A 482 " --> pdb=" O   CYS A 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 536
      removed outlier: 4.143A  pdb=" N   ASN A 505 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   SER A 572 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLU A 507 " --> pdb=" O   ASN A 570 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ASN A 570 " --> pdb=" O   GLU A 507 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   GLN A 509 " --> pdb=" O   SER A 568 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   SER A 568 " --> pdb=" O   GLN A 509 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 612 through 615
      removed outlier: 3.683A  pdb=" N   MET A 703 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER A 706 " --> pdb=" O   HIS A 658 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 648 through 652
      removed outlier: 4.232A  pdb=" N   GLN A 720 " --> pdb=" O   HIS A 652 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 749 through 755
      removed outlier: 3.581A  pdb=" N   GLU A 749 " --> pdb=" O   HIS A 787 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   HIS A 787 " --> pdb=" O   GLU A 749 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ARG A 751 " --> pdb=" O   GLU A 785 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA A 907 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   HIS A 782 " --> pdb=" O   VAL A 905 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 905 " --> pdb=" O   HIS A 782 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   TYR A 784 " --> pdb=" O   VAL A 903 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL A 903 " --> pdb=" O   TYR A 784 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   MET A 902 " --> pdb=" O   PRO A 820 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   THR A 904 " --> pdb=" O   ILE A 818 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   ILE A 818 " --> pdb=" O   THR A 904 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   LEU A 906 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE A 908 " --> pdb=" O   TYR A 814 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   TYR A 814 " --> pdb=" O   PHE A 908 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 825 through 829
      removed outlier: 4.338A  pdb=" N   GLN A 825 " --> pdb=" O   ASP A 891 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A 887 " --> pdb=" O   GLN A 829 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   GLU A 894 " --> pdb=" O   ASN A 795 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ASN A 795 " --> pdb=" O   GLU A 894 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   GLY A 796 " --> pdb=" O   SER A 933 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A 933 " --> pdb=" O   GLY A 796 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   HIS A 802 " --> pdb=" O   HIS A 927 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   HIS A 927 " --> pdb=" O   HIS A 802 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 39
    Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 65
      removed outlier: 3.815A  pdb=" N   ARG B  62 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ARG B  87 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE B  88 " --> pdb=" O   GLN B 428 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   THR B 430 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LEU B  90 " --> pdb=" O   THR B 430 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B 414 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 102
    Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 197
      removed outlier: 5.923A  pdb=" N   THR B 195 " --> pdb=" O   PHE B 153 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   PHE B 153 " --> pdb=" O   THR B 195 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B 151 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 499 through 502
    Processing sheet with id=AC4, first strand: chain 'B' and resid 540 through 543
    Processing sheet with id=AC5, first strand: chain 'B' and resid 581 through 582
    Processing sheet with id=AC6, first strand: chain 'B' and resid 638 through 639
      removed outlier: 6.184A  pdb=" N   GLU B 638 " --> pdb=" O   LEU B 679 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'B' and resid 655 through 658
      removed outlier: 3.673A  pdb=" N   TYR B 657 " --> pdb=" O   VAL B 665 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL B 665 " --> pdb=" O   TYR B 657 " (cutoff:3.500A)

    244 hydrogen bonds defined for protein.
    632 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: 3.92

  Time building geometry restraints manager: 3.81 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 2145
        1.31 -     1.44: 3267
        1.44 -     1.58: 7063
        1.58 -     1.71: 1
        1.71 -     1.85: 123
  Bond restraints: 12599
  Sorted by residual:
  bond pdb=" CA  SER A 664 "
       pdb=" CB  SER A 664 "
    ideal  model  delta    sigma   weight residual
    1.530  1.363  0.167 1.69e-02 3.50e+03 9.75e+01
  bond pdb=" CA  LEU A 689 "
       pdb=" C   LEU A 689 "
    ideal  model  delta    sigma   weight residual
    1.523  1.422  0.101 1.34e-02 5.57e+03 5.66e+01
  bond pdb=" CA  ALA A 662 "
       pdb=" C   ALA A 662 "
    ideal  model  delta    sigma   weight residual
    1.523  1.429  0.094 1.34e-02 5.57e+03 4.90e+01
  bond pdb=" CA  ASN A 665 "
       pdb=" C   ASN A 665 "
    ideal  model  delta    sigma   weight residual
    1.524  1.427  0.096 1.59e-02 3.96e+03 3.67e+01
  bond pdb=" CA  ALA A 662 "
       pdb=" CB  ALA A 662 "
    ideal  model  delta    sigma   weight residual
    1.530  1.439  0.091 1.69e-02 3.50e+03 2.90e+01
  ... (remaining 12594 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.77: 17022
        5.77 -    11.54: 76
       11.54 -    17.31: 16
       17.31 -    23.08: 7
       23.08 -    28.85: 1
  Bond angle restraints: 17122
  Sorted by residual:
  angle pdb=" N   GLN A  18 "
        pdb=" CA  GLN A  18 "
        pdb=" C   GLN A  18 "
      ideal   model   delta    sigma   weight residual
     110.41   92.07   18.34 1.18e+00 7.18e-01 2.42e+02
  angle pdb=" C   ASN A 691 "
        pdb=" N   PRO A 692 "
        pdb=" CA  PRO A 692 "
      ideal   model   delta    sigma   weight residual
     119.84  101.42   18.42 1.25e+00 6.40e-01 2.17e+02
  angle pdb=" C   ARG A 661 "
        pdb=" CA  ARG A 661 "
        pdb=" CB  ARG A 661 "
      ideal   model   delta    sigma   weight residual
     110.42   81.57   28.85 1.99e+00 2.53e-01 2.10e+02
  angle pdb=" N   ASN A 665 "
        pdb=" CA  ASN A 665 "
        pdb=" C   ASN A 665 "
      ideal   model   delta    sigma   weight residual
     112.97   98.69   14.28 1.06e+00 8.90e-01 1.82e+02
  angle pdb=" N   LEU A 689 "
        pdb=" CA  LEU A 689 "
        pdb=" CB  LEU A 689 "
      ideal   model   delta    sigma   weight residual
     110.49   88.84   21.65 1.69e+00 3.50e-01 1.64e+02
  ... (remaining 17117 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.51: 7211
       24.51 -    49.02: 525
       49.02 -    73.53: 72
       73.53 -    98.04: 15
       98.04 -   122.55: 9
  Dihedral angle restraints: 7832
    sinusoidal: 3269
      harmonic: 4563
  Sorted by residual:
  dihedral pdb=" CA  ASN A 691 "
           pdb=" C   ASN A 691 "
           pdb=" N   PRO A 692 "
           pdb=" CA  PRO A 692 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -57.45 -122.55     0      5.00e+00 4.00e-02 6.01e+02
  dihedral pdb=" C   ARG A 661 "
           pdb=" N   ARG A 661 "
           pdb=" CA  ARG A 661 "
           pdb=" CB  ARG A 661 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -83.31  -39.29     0      2.50e+00 1.60e-01 2.47e+02
  dihedral pdb=" N   LEU A 689 "
           pdb=" C   LEU A 689 "
           pdb=" CA  LEU A 689 "
           pdb=" CB  LEU A 689 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   90.01   32.79     0      2.50e+00 1.60e-01 1.72e+02
  ... (remaining 7829 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.215: 1899
       0.215 -    0.431: 16
       0.431 -    0.646: 3
       0.646 -    0.862: 1
       0.862 -    1.077: 3
  Chirality restraints: 1922
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.32   -1.08 2.00e-02 2.50e+03 2.90e+03
  chirality pdb=" C1  BMA D   3 "
            pdb=" O4  NAG D   2 "
            pdb=" C2  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-02 2.50e+03 2.38e+02
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 4.37e+01
  ... (remaining 1919 not shown)

  Planarity restraints: 2264
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.365 2.00e-02 2.50e+03   3.08e-01 1.19e+03
        pdb=" C7  NAG C   1 "    0.096 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "   -0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.539 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "   -0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "    0.333 2.00e-02 2.50e+03   2.89e-01 1.04e+03
        pdb=" C7  NAG C   2 "   -0.073 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.079 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "   -0.514 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "    0.175 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "    0.336 2.00e-02 2.50e+03   2.86e-01 1.02e+03
        pdb=" C7  NAG D   1 "   -0.086 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.177 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "   -0.501 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.074 2.00e-02 2.50e+03
  ... (remaining 2261 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.25: 25
        2.25 -     2.91: 5679
        2.91 -     3.57: 17632
        3.57 -     4.24: 28454
        4.24 -     4.90: 46088
  Nonbonded interactions: 97878
  Sorted by model distance:
  nonbonded pdb=" N   LEU A 689 "
            pdb=" OD1 ASN A 691 "
     model   vdw
     1.584 3.120
  nonbonded pdb=" CA  LEU A 689 "
            pdb=" OD1 ASN A 691 "
     model   vdw
     1.759 3.470
  nonbonded pdb=" C   LEU A 689 "
            pdb=" OD1 ASN A 691 "
     model   vdw
     1.847 3.270
  nonbonded pdb=" N   ASN A 665 "
            pdb=" O   GLY A 700 "
     model   vdw
     1.909 3.120
  nonbonded pdb=" OE2 GLU B 220 "
            pdb="MG    MG B2001 "
     model   vdw
     1.982 2.170
  ... (remaining 97873 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.98
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:             3.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     38.190
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5559
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      :  0.007   0.167  12645  Z= 0.408
  Angle     :  1.166  28.849  17224  Z= 0.661
  Chirality :  0.077   1.077   1922
  Planarity :  0.015   0.308   2259
  Dihedral  : 16.738 122.547   4804
  Min Nonbonded Distance : 1.584

Molprobity Statistics.
  All-atom Clashscore : 31.98
  Ramachandran Plot:
    Outliers :  1.59 %
    Allowed  :  9.58 %
    Favored  : 88.83 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.57 %
    Favored  : 79.04 %
  Cbeta Deviations :  1.03 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.08 %
    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: -2.30 (0.20), residues: 1587
  helix: -2.13 (0.43), residues: 122
  sheet: -0.83 (0.26), residues: 425
  loop : -1.84 (0.18), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 113 
 HIS   0.007   0.001   HIS B 274 
 PHE   0.037   0.002   PHE A 669 
 TYR   0.029   0.002   TYR B 164 
 ARG   0.038   0.001   ARG A 661 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01894 (    5)
  link_NAG-ASN         : angle       3.50567 (   15)
  link_BETA1-4         : bond        0.00816 (    5)
  link_BETA1-4         : angle       4.24233 (   15)
  hydrogen bonds       : bond        0.28179 (  244)
  hydrogen bonds       : angle      11.08730 (  632)
  SS BOND              : bond        0.00443 (   36)
  SS BOND              : angle       1.62065 (   72)
  covalent geometry    : bond        0.00693 (12599)
  covalent geometry    : angle       1.15296 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 162
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLN cc_start: 0.7898 (mt0) cc_final: 0.7512 (tt0)
REVERT: A  112 HIS cc_start: 0.4661 (m90) cc_final: 0.4455 (m170)
REVERT: A  121 GLU cc_start: 0.2824 (mp0) cc_final: 0.2220 (tt0)
REVERT: A  124 LYS cc_start: 0.2962 (mtmm) cc_final: 0.2582 (mtmm)
REVERT: A  164 LYS cc_start: 0.5149 (pttt) cc_final: 0.4624 (pttm)
REVERT: A  449 ARG cc_start: 0.5775 (mpp80) cc_final: 0.4968 (mtp180)
REVERT: A  489 MET cc_start: 0.5934 (ppp) cc_final: 0.5655 (tpt)
REVERT: A  660 MET cc_start: 0.4302 (mmm) cc_final: 0.3346 (mmt)
REVERT: A  691 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6490 (m110)
REVERT: A  835 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.0928 (mt)
REVERT: A  837 VAL cc_start: 0.1859 (OUTLIER) cc_final: 0.1241 (m)
  outliers start: 45
  outliers final: 18
  residues processed: 202
  average time/residue: 0.2689
  time to fit residues: 75.9657
Evaluate side-chains
  115 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 PRO
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  676 GLN
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  688 GLU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  691 ASN
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  313 ASN
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  507 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:    3.9990
   chunk 119 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 123 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   chunk 75 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9980
   chunk 143 optimal weight:    8.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
A 629 ASN
A 665 ASN
A 808 GLN
A 833 ASN
B  79 GLN
B 255 HIS
B 319 GLN
** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.228266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.200866 restraints weight = 35698.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.4617 rms_B_bonded: 5.26
r_work (final): 0.4617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4614 r_free = 0.4614    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4611 r_free = 0.4611    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|
r_final: 0.4611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5512
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.125  12645  Z= 0.300
  Angle     :  0.977  12.005  17224  Z= 0.491
  Chirality :  0.055   0.472   1922
  Planarity :  0.007   0.069   2259
  Dihedral  : 10.163  83.278   1968
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 20.57
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.58 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.43 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.08 %
    Twisted General : 0.13 %

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 (0.20), residues: 1587
  helix: -2.30 (0.42), residues: 117
  sheet: -1.21 (0.25), residues: 441
  loop : -1.98 (0.18), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP B 553 
 HIS   0.010   0.001   HIS A 112 
 PHE   0.029   0.004   PHE B 153 
 TYR   0.027   0.003   TYR A 190 
 ARG   0.012   0.001   ARG A 661 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01162 (    5)
  link_NAG-ASN         : angle       4.31579 (   15)
  link_BETA1-4         : bond        0.01115 (    5)
  link_BETA1-4         : angle       4.10631 (   15)
  hydrogen bonds       : bond        0.05738 (  244)
  hydrogen bonds       : angle       8.24106 (  632)
  SS BOND              : bond        0.00511 (   36)
  SS BOND              : angle       1.78533 (   72)
  covalent geometry    : bond        0.00690 (12599)
  covalent geometry    : angle       0.95650 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 114
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 ASN cc_start: 0.7020 (OUTLIER) cc_final: 0.6728 (m-40)
REVERT: A  121 GLU cc_start: 0.2878 (mp0) cc_final: 0.2361 (tt0)
REVERT: A  667 GLU cc_start: 0.4751 (OUTLIER) cc_final: 0.3361 (mm-30)
REVERT: A  681 GLU cc_start: 0.3587 (OUTLIER) cc_final: 0.3333 (mt-10)
REVERT: A  895 MET cc_start: -0.0843 (ttt) cc_final: -0.1330 (ttt)
REVERT: A  902 MET cc_start: 0.6619 (pmm) cc_final: 0.5030 (tmm)
REVERT: B  304 ILE cc_start: 0.5807 (mm) cc_final: 0.5594 (mm)
REVERT: B  459 VAL cc_start: 0.4073 (OUTLIER) cc_final: 0.3740 (p)
  outliers start: 51
  outliers final: 27
  residues processed: 153
  average time/residue: 0.2148
  time to fit residues: 49.4009
Evaluate side-chains
  124 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 93
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  178 TYR
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  568 MET
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 152 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 148 optimal weight:    0.9990
   chunk 114 optimal weight:    0.5980
   chunk 51 optimal weight:    7.9990
   chunk 106 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 54 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9990
   chunk 151 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN
A 808 GLN
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 449 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.230863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.193361 restraints weight = 44843.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.4539 rms_B_bonded: 3.99
r_work: 0.4069 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       40 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
r_final: 0.4051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  12645  Z= 0.179
  Angle     :  0.792  10.222  17224  Z= 0.395
  Chirality :  0.049   0.312   1922
  Planarity :  0.005   0.075   2259
  Dihedral  :  7.988  59.960   1943
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.39 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.12 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.08 %
    Twisted General : 0.13 %

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: -2.42 (0.20), residues: 1587
  helix: -2.01 (0.42), residues: 122
  sheet: -1.16 (0.24), residues: 453
  loop : -1.83 (0.19), residues: 1012

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 238 
 HIS   0.004   0.001   HIS A  26 
 PHE   0.019   0.002   PHE A 669 
 TYR   0.020   0.002   TYR A 380 
 ARG   0.006   0.001   ARG B  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01087 (    5)
  link_NAG-ASN         : angle       2.90809 (   15)
  link_BETA1-4         : bond        0.00892 (    5)
  link_BETA1-4         : angle       3.23171 (   15)
  hydrogen bonds       : bond        0.04291 (  244)
  hydrogen bonds       : angle       7.33128 (  632)
  SS BOND              : bond        0.00392 (   36)
  SS BOND              : angle       1.37425 (   72)
  covalent geometry    : bond        0.00409 (12599)
  covalent geometry    : angle       0.77911 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.1150 (OUTLIER) cc_final: -0.0108 (mt)
REVERT: A  121 GLU cc_start: 0.3028 (mp0) cc_final: 0.2779 (tt0)
REVERT: A  164 LYS cc_start: 0.5919 (pttt) cc_final: 0.5557 (ptpp)
REVERT: A  208 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.6200 (mmp80)
REVERT: A  489 MET cc_start: 0.7662 (ppp) cc_final: 0.7334 (ppp)
REVERT: A  520 ARG cc_start: 0.5824 (mmt180) cc_final: 0.5462 (mpt-90)
REVERT: A  667 GLU cc_start: 0.4521 (OUTLIER) cc_final: 0.3247 (mm-30)
REVERT: A  671 ARG cc_start: -0.0647 (OUTLIER) cc_final: -0.0943 (tmm-80)
REVERT: A  681 GLU cc_start: 0.3351 (OUTLIER) cc_final: 0.2951 (mt-10)
REVERT: A  709 ASN cc_start: 0.2032 (m-40) cc_final: 0.1742 (p0)
REVERT: A  902 MET cc_start: 0.6887 (pmm) cc_final: 0.5023 (tmm)
REVERT: B  205 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6294 (mp0)
REVERT: B  344 ILE cc_start: 0.5222 (OUTLIER) cc_final: 0.4512 (mt)
REVERT: B  557 TYR cc_start: 0.5470 (t80) cc_final: 0.4939 (t80)
  outliers start: 31
  outliers final: 14
  residues processed: 132
  average time/residue: 0.2164
  time to fit residues: 42.9928
Evaluate side-chains
  106 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  698 GLN
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  587 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 82 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 139 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.229752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.193522 restraints weight = 53441.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.4540 rms_B_bonded: 4.15
r_work: 0.4008 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4006 r_free = 0.4006    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4007 r_free = 0.4007    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.4007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6530
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12645  Z= 0.202
  Angle     :  0.790  10.018  17224  Z= 0.395
  Chirality :  0.050   0.473   1922
  Planarity :  0.005   0.069   2259
  Dihedral  :  7.396  58.706   1943
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 15.89
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.90 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.46 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.08 %
    Twisted General : 0.13 %

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: -2.43 (0.20), residues: 1587
  helix: -1.88 (0.43), residues: 121
  sheet: -1.23 (0.24), residues: 448
  loop : -1.83 (0.19), residues: 1018

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 553 
 HIS   0.005   0.001   HIS B 255 
 PHE   0.020   0.002   PHE A 669 
 TYR   0.023   0.002   TYR B 318 
 ARG   0.007   0.001   ARG B 489 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00958 (    5)
  link_NAG-ASN         : angle       2.54554 (   15)
  link_BETA1-4         : bond        0.00837 (    5)
  link_BETA1-4         : angle       3.17739 (   15)
  hydrogen bonds       : bond        0.04069 (  244)
  hydrogen bonds       : angle       7.11325 (  632)
  SS BOND              : bond        0.00370 (   36)
  SS BOND              : angle       1.32024 (   72)
  covalent geometry    : bond        0.00470 (12599)
  covalent geometry    : angle       0.77861 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 92
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.1553 (OUTLIER) cc_final: 0.0110 (mt)
REVERT: A  121 GLU cc_start: 0.3251 (mp0) cc_final: 0.3013 (tt0)
REVERT: A  195 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6767 (mp)
REVERT: A  208 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6384 (mmp80)
REVERT: A  315 GLU cc_start: 0.5747 (mt-10) cc_final: 0.3765 (tt0)
REVERT: A  489 MET cc_start: 0.7744 (ppp) cc_final: 0.7416 (ppp)
REVERT: A  549 MET cc_start: 0.4175 (tpt) cc_final: 0.3947 (tpt)
REVERT: A  681 GLU cc_start: 0.3189 (OUTLIER) cc_final: 0.2787 (mt-10)
REVERT: A  709 ASN cc_start: 0.2085 (m-40) cc_final: 0.1812 (p0)
REVERT: A  827 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5251 (m-80)
REVERT: A  902 MET cc_start: 0.6930 (pmm) cc_final: 0.5091 (tmm)
REVERT: B  205 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6373 (mp0)
REVERT: B  344 ILE cc_start: 0.5098 (OUTLIER) cc_final: 0.4317 (mt)
REVERT: B  520 TYR cc_start: 0.1242 (m-10) cc_final: 0.1015 (p90)
REVERT: B  553 TRP cc_start: 0.4689 (m100) cc_final: 0.4111 (m100)
REVERT: B  557 TYR cc_start: 0.5371 (t80) cc_final: 0.4909 (t80)
  outliers start: 54
  outliers final: 27
  residues processed: 140
  average time/residue: 0.2115
  time to fit residues: 45.3174
Evaluate side-chains
  121 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 87
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  698 GLN
Chi-restraints excluded: chain A residue  827 PHE
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  287 MET
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  621 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 71 optimal weight:   30.0000
   chunk 141 optimal weight:   10.0000
   chunk 53 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 138 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 107 optimal weight:    0.6980
   chunk 73 optimal weight:   20.0000
   chunk 1 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  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 ASN
B 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.231135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.195420 restraints weight = 50981.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.4566 rms_B_bonded: 3.96
r_work: 0.4072 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4053
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4053 r_free = 0.4053    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4054 r_free = 0.4054    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.4054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12645  Z= 0.156
  Angle     :  0.735  11.227  17224  Z= 0.366
  Chirality :  0.047   0.382   1922
  Planarity :  0.005   0.068   2259
  Dihedral  :  6.475  59.585   1936
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.57 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.82 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.08 %
    Twisted General : 0.13 %

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: -2.28 (0.20), residues: 1587
  helix: -1.63 (0.45), residues: 121
  sheet: -1.11 (0.24), residues: 456
  loop : -1.74 (0.19), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 235 
 HIS   0.004   0.001   HIS A  26 
 PHE   0.024   0.002   PHE A  87 
 TYR   0.031   0.002   TYR B 318 
 ARG   0.005   0.000   ARG B  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00703 (    5)
  link_NAG-ASN         : angle       2.21290 (   15)
  link_BETA1-4         : bond        0.00796 (    5)
  link_BETA1-4         : angle       2.85862 (   15)
  hydrogen bonds       : bond        0.03373 (  244)
  hydrogen bonds       : angle       6.71202 (  632)
  SS BOND              : bond        0.00614 (   36)
  SS BOND              : angle       1.32568 (   72)
  covalent geometry    : bond        0.00358 (12599)
  covalent geometry    : angle       0.72479 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 96
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.1614 (OUTLIER) cc_final: 0.0455 (mt)
REVERT: A  195 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6696 (mp)
REVERT: A  208 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6296 (mmp80)
REVERT: A  315 GLU cc_start: 0.5627 (mt-10) cc_final: 0.3635 (tt0)
REVERT: A  367 ASP cc_start: 0.7191 (p0) cc_final: 0.6967 (p0)
REVERT: A  489 MET cc_start: 0.7823 (ppp) cc_final: 0.7424 (ppp)
REVERT: A  681 GLU cc_start: 0.3033 (OUTLIER) cc_final: 0.2529 (mt-10)
REVERT: A  827 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5449 (m-80)
REVERT: A  902 MET cc_start: 0.6830 (pmm) cc_final: 0.4970 (tmm)
REVERT: B  205 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6236 (mp0)
REVERT: B  520 TYR cc_start: 0.1068 (m-10) cc_final: 0.0794 (p90)
REVERT: B  553 TRP cc_start: 0.4775 (m100) cc_final: 0.4237 (m100)
REVERT: B  557 TYR cc_start: 0.5476 (t80) cc_final: 0.4925 (t80)
  outliers start: 41
  outliers final: 26
  residues processed: 132
  average time/residue: 0.2199
  time to fit residues: 44.2755
Evaluate side-chains
  112 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  698 GLN
Chi-restraints excluded: chain A residue  827 PHE
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  178 TYR
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  287 MET
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  587 VAL
Chi-restraints excluded: chain B residue  621 ASP
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 126 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 108 optimal weight:    0.6980
   chunk 157 optimal weight:    0.7980
   chunk 111 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0670
   chunk 105 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.8520

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 591 HIS
A 665 ASN
B 106 GLN
B 539 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.230389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.194304 restraints weight = 46543.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.4555 rms_B_bonded: 3.80
r_work: 0.4046 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4032 r_free = 0.4032    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4032 r_free = 0.4032    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.4032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6469
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12645  Z= 0.161
  Angle     :  0.731  10.613  17224  Z= 0.363
  Chirality :  0.047   0.325   1922
  Planarity :  0.005   0.069   2259
  Dihedral  :  6.066  54.130   1930
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.58 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 19.71 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.08 %
    Twisted General : 0.13 %

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: -2.23 (0.20), residues: 1587
  helix: -1.49 (0.46), residues: 121
  sheet: -1.04 (0.24), residues: 451
  loop : -1.74 (0.19), residues: 1015

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 238 
 HIS   0.005   0.001   HIS A  26 
 PHE   0.015   0.002   PHE B 188 
 TYR   0.040   0.002   TYR A 380 
 ARG   0.004   0.000   ARG B 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00659 (    5)
  link_NAG-ASN         : angle       2.05246 (   15)
  link_BETA1-4         : bond        0.00797 (    5)
  link_BETA1-4         : angle       2.71377 (   15)
  hydrogen bonds       : bond        0.03343 (  244)
  hydrogen bonds       : angle       6.52630 (  632)
  SS BOND              : bond        0.00313 (   36)
  SS BOND              : angle       1.33599 (   72)
  covalent geometry    : bond        0.00371 (12599)
  covalent geometry    : angle       0.72065 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 91
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.1627 (OUTLIER) cc_final: 0.0044 (mt)
REVERT: A  208 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6342 (mmp80)
REVERT: A  315 GLU cc_start: 0.5580 (mt-10) cc_final: 0.3639 (tt0)
REVERT: A  489 MET cc_start: 0.7782 (ppp) cc_final: 0.7457 (ppp)
REVERT: A  681 GLU cc_start: 0.2706 (OUTLIER) cc_final: 0.2282 (mt-10)
REVERT: A  827 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.5590 (m-80)
REVERT: A  902 MET cc_start: 0.6763 (pmm) cc_final: 0.5064 (tmm)
REVERT: B   22 MET cc_start: 0.5777 (tpt) cc_final: 0.5254 (mpp)
REVERT: B  205 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6479 (mp0)
REVERT: B  431 PHE cc_start: 0.5237 (m-10) cc_final: 0.4760 (m-10)
REVERT: B  553 TRP cc_start: 0.5025 (m100) cc_final: 0.4324 (m100)
REVERT: B  557 TYR cc_start: 0.5408 (t80) cc_final: 0.4872 (t80)
REVERT: B  568 MET cc_start: 0.4903 (mtp) cc_final: 0.4643 (mtp)
  outliers start: 41
  outliers final: 29
  residues processed: 129
  average time/residue: 0.2278
  time to fit residues: 44.6287
Evaluate side-chains
  117 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 83
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  827 PHE
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  287 MET
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  587 VAL
Chi-restraints excluded: chain B residue  621 ASP
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 85 optimal weight:   20.0000
   chunk 27 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0980
   chunk 80 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   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  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.231413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.200185 restraints weight = 63444.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.4613 rms_B_bonded: 3.90
r_work: 0.4051 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4046 r_free = 0.4046    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4046 r_free = 0.4046    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.4046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6439
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12645  Z= 0.146
  Angle     :  0.712  10.840  17224  Z= 0.353
  Chirality :  0.046   0.328   1922
  Planarity :  0.005   0.066   2259
  Dihedral  :  5.904  55.802   1929
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.44 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.59 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.08 %
    Twisted General : 0.13 %

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: -2.09 (0.20), residues: 1587
  helix: -1.41 (0.47), residues: 121
  sheet: -0.94 (0.24), residues: 448
  loop : -1.65 (0.19), residues: 1018

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A  26 
 PHE   0.015   0.002   PHE B  56 
 TYR   0.027   0.002   TYR B 318 
 ARG   0.004   0.000   ARG B  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00616 (    5)
  link_NAG-ASN         : angle       1.91349 (   15)
  link_BETA1-4         : bond        0.00755 (    5)
  link_BETA1-4         : angle       2.56166 (   15)
  hydrogen bonds       : bond        0.03168 (  244)
  hydrogen bonds       : angle       6.34170 (  632)
  SS BOND              : bond        0.00330 (   36)
  SS BOND              : angle       1.26258 (   72)
  covalent geometry    : bond        0.00336 (12599)
  covalent geometry    : angle       0.70263 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 87
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.1340 (OUTLIER) cc_final: -0.0226 (mp)
REVERT: A  195 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6692 (mp)
REVERT: A  208 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6315 (mmp80)
REVERT: A  315 GLU cc_start: 0.5698 (mt-10) cc_final: 0.3740 (tt0)
REVERT: A  479 LYS cc_start: 0.4930 (tptt) cc_final: 0.4020 (tppt)
REVERT: A  489 MET cc_start: 0.7673 (ppp) cc_final: 0.7367 (ppp)
REVERT: A  681 GLU cc_start: 0.2657 (OUTLIER) cc_final: 0.2174 (mt-10)
REVERT: A  827 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.5456 (m-80)
REVERT: A  902 MET cc_start: 0.6829 (pmm) cc_final: 0.5150 (tmm)
REVERT: B   22 MET cc_start: 0.5683 (tpt) cc_final: 0.5153 (mpp)
REVERT: B  205 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6403 (mp0)
REVERT: B  431 PHE cc_start: 0.5336 (m-10) cc_final: 0.4879 (m-10)
REVERT: B  553 TRP cc_start: 0.4896 (m100) cc_final: 0.4340 (m100)
REVERT: B  557 TYR cc_start: 0.5500 (t80) cc_final: 0.4902 (t80)
REVERT: B  568 MET cc_start: 0.4793 (mtp) cc_final: 0.4560 (mtp)
  outliers start: 36
  outliers final: 25
  residues processed: 121
  average time/residue: 0.2281
  time to fit residues: 41.8731
Evaluate side-chains
  113 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  827 PHE
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  587 VAL
Chi-restraints excluded: chain B residue  621 ASP
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 79 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 143 optimal weight:    6.9990
   chunk 80 optimal weight:    9.9990
   chunk 149 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0870
   chunk 27 optimal weight:    0.2980
   chunk 145 optimal weight:    9.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4894 r_free = 0.4894 target = 0.231904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.196374 restraints weight = 52618.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.4562 rms_B_bonded: 4.16
r_work: 0.4023 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4017 r_free = 0.4017    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4018 r_free = 0.4018    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.4018
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6485
moved from start:          0.3929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12645  Z= 0.150
  Angle     :  0.707  11.011  17224  Z= 0.350
  Chirality :  0.046   0.294   1922
  Planarity :  0.005   0.063   2259
  Dihedral  :  5.846  56.823   1929
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.01 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.29 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.08 %
    Twisted General : 0.13 %

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: -2.08 (0.21), residues: 1587
  helix: -1.35 (0.47), residues: 122
  sheet: -0.99 (0.25), residues: 448
  loop : -1.62 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 235 
 HIS   0.004   0.001   HIS A  26 
 PHE   0.013   0.002   PHE B 188 
 TYR   0.027   0.002   TYR B 318 
 ARG   0.009   0.001   ARG A 724 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00596 (    5)
  link_NAG-ASN         : angle       1.81903 (   15)
  link_BETA1-4         : bond        0.00728 (    5)
  link_BETA1-4         : angle       2.53913 (   15)
  hydrogen bonds       : bond        0.03126 (  244)
  hydrogen bonds       : angle       6.22440 (  632)
  SS BOND              : bond        0.00307 (   36)
  SS BOND              : angle       1.31928 (   72)
  covalent geometry    : bond        0.00347 (12599)
  covalent geometry    : angle       0.69787 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 87
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.1454 (OUTLIER) cc_final: -0.0172 (mp)
REVERT: A  162 TRP cc_start: 0.3985 (t-100) cc_final: 0.3711 (t-100)
REVERT: A  195 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6698 (mp)
REVERT: A  202 ASP cc_start: 0.7280 (m-30) cc_final: 0.7010 (t0)
REVERT: A  208 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6320 (mmp80)
REVERT: A  315 GLU cc_start: 0.5583 (mt-10) cc_final: 0.3688 (tt0)
REVERT: A  479 LYS cc_start: 0.5050 (tptt) cc_final: 0.4023 (tppt)
REVERT: A  681 GLU cc_start: 0.2449 (OUTLIER) cc_final: 0.1983 (mt-10)
REVERT: A  827 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.5568 (m-80)
REVERT: A  902 MET cc_start: 0.6803 (pmm) cc_final: 0.5174 (tmm)
REVERT: B   22 MET cc_start: 0.5947 (tpt) cc_final: 0.5355 (mpp)
REVERT: B  205 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6534 (mp0)
REVERT: B  431 PHE cc_start: 0.5517 (m-10) cc_final: 0.4962 (m-10)
REVERT: B  444 ASN cc_start: 0.7272 (m-40) cc_final: 0.7056 (m110)
REVERT: B  553 TRP cc_start: 0.4703 (m100) cc_final: 0.4213 (m100)
REVERT: B  557 TYR cc_start: 0.5468 (t80) cc_final: 0.4803 (t80)
REVERT: B  568 MET cc_start: 0.4788 (mtp) cc_final: 0.4556 (mtp)
  outliers start: 38
  outliers final: 28
  residues processed: 123
  average time/residue: 0.2190
  time to fit residues: 41.2082
Evaluate side-chains
  112 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 78
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  827 PHE
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  587 VAL
Chi-restraints excluded: chain B residue  621 ASP
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 96 optimal weight:    9.9990
   chunk 127 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 111 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 ASN
** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.231618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.195540 restraints weight = 45302.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.4557 rms_B_bonded: 3.90
r_work: 0.4040 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4031 r_free = 0.4031    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4031 r_free = 0.4031    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.4031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6490
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12645  Z= 0.156
  Angle     :  0.721  10.928  17224  Z= 0.356
  Chirality :  0.046   0.294   1922
  Planarity :  0.005   0.045   2259
  Dihedral  :  5.844  58.199   1929
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.88 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.66 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.07 (0.21), residues: 1587
  helix: -1.34 (0.47), residues: 122
  sheet: -0.98 (0.25), residues: 450
  loop : -1.61 (0.19), residues: 1015

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 129 
 HIS   0.008   0.001   HIS B 509 
 PHE   0.013   0.002   PHE B 431 
 TYR   0.040   0.002   TYR A 380 
 ARG   0.005   0.001   ARG B 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00582 (    5)
  link_NAG-ASN         : angle       1.81338 (   15)
  link_BETA1-4         : bond        0.00713 (    5)
  link_BETA1-4         : angle       2.49409 (   15)
  hydrogen bonds       : bond        0.03232 (  244)
  hydrogen bonds       : angle       6.16792 (  632)
  SS BOND              : bond        0.00293 (   36)
  SS BOND              : angle       1.31941 (   72)
  covalent geometry    : bond        0.00363 (12599)
  covalent geometry    : angle       0.71225 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.1485 (OUTLIER) cc_final: -0.0087 (mp)
REVERT: A  162 TRP cc_start: 0.3812 (t-100) cc_final: 0.3546 (t-100)
REVERT: A  202 ASP cc_start: 0.7131 (m-30) cc_final: 0.6907 (t0)
REVERT: A  208 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6290 (mmp80)
REVERT: A  315 GLU cc_start: 0.5685 (mt-10) cc_final: 0.3741 (tt0)
REVERT: A  479 LYS cc_start: 0.5086 (tptt) cc_final: 0.3998 (tppt)
REVERT: A  577 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7157 (tt0)
REVERT: A  681 GLU cc_start: 0.2472 (OUTLIER) cc_final: 0.2000 (mt-10)
REVERT: A  827 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.5649 (m-80)
REVERT: A  902 MET cc_start: 0.6751 (pmm) cc_final: 0.5233 (tmm)
REVERT: B   22 MET cc_start: 0.6099 (tpt) cc_final: 0.5494 (mpp)
REVERT: B  205 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6557 (mp0)
REVERT: B  431 PHE cc_start: 0.5579 (m-10) cc_final: 0.4956 (m-80)
REVERT: B  444 ASN cc_start: 0.7238 (m-40) cc_final: 0.7036 (m110)
REVERT: B  553 TRP cc_start: 0.4626 (m100) cc_final: 0.4244 (m100)
REVERT: B  557 TYR cc_start: 0.5401 (t80) cc_final: 0.4730 (t80)
  outliers start: 38
  outliers final: 29
  residues processed: 119
  average time/residue: 0.2320
  time to fit residues: 41.8093
Evaluate side-chains
  118 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 83
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  577 GLU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  827 PHE
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  587 VAL
Chi-restraints excluded: chain B residue  621 ASP
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 33 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 147 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 78 optimal weight:   20.0000
   chunk 64 optimal weight:    9.9990
   chunk 124 optimal weight:    0.8980
   chunk 48 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 145 optimal weight:    0.0370
   overall best weight:    1.2662

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 ASN
A 722 GLN
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4869 r_free = 0.4869 target = 0.228931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.195038 restraints weight = 53748.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.4562 rms_B_bonded: 4.18
r_work (final): 0.4562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4562 r_free = 0.4562    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4558 r_free = 0.4558    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
r_final: 0.4558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5611
moved from start:          0.4321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12645  Z= 0.195
  Angle     :  0.764  11.001  17224  Z= 0.379
  Chirality :  0.047   0.289   1922
  Planarity :  0.005   0.045   2259
  Dihedral  :  6.067  59.325   1929
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.22 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.32 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.16 (0.21), residues: 1587
  helix: -1.43 (0.47), residues: 121
  sheet: -1.06 (0.25), residues: 445
  loop : -1.66 (0.19), residues: 1021

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 260 
 HIS   0.013   0.001   HIS B 509 
 PHE   0.015   0.002   PHE B 203 
 TYR   0.042   0.002   TYR A 380 
 ARG   0.007   0.001   ARG B 214 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00631 (    5)
  link_NAG-ASN         : angle       1.91202 (   15)
  link_BETA1-4         : bond        0.00730 (    5)
  link_BETA1-4         : angle       2.57858 (   15)
  hydrogen bonds       : bond        0.03496 (  244)
  hydrogen bonds       : angle       6.26951 (  632)
  SS BOND              : bond        0.00320 (   36)
  SS BOND              : angle       1.40823 (   72)
  covalent geometry    : bond        0.00453 (12599)
  covalent geometry    : angle       0.75469 (17122)

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.1365 (OUTLIER) cc_final: 0.0250 (mt)
REVERT: A  142 GLU cc_start: 0.5831 (mp0) cc_final: 0.4921 (tt0)
REVERT: A  162 TRP cc_start: 0.3014 (t-100) cc_final: 0.2691 (t-100)
REVERT: A  195 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6485 (mp)
REVERT: A  208 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6256 (mmp80)
REVERT: A  315 GLU cc_start: 0.5519 (mt-10) cc_final: 0.3596 (tt0)
REVERT: A  479 LYS cc_start: 0.4034 (tptt) cc_final: 0.3760 (tppt)
REVERT: A  681 GLU cc_start: 0.2764 (OUTLIER) cc_final: 0.2115 (mt-10)
REVERT: A  827 PHE cc_start: 0.4479 (OUTLIER) cc_final: 0.3663 (m-80)
REVERT: A  902 MET cc_start: 0.6179 (pmm) cc_final: 0.5335 (tmm)
REVERT: B  205 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6046 (mp0)
  outliers start: 33
  outliers final: 26
  residues processed: 112
  average time/residue: 0.2049
  time to fit residues: 35.5186
Evaluate side-chains
  105 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 73
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  681 GLU
Chi-restraints excluded: chain A residue  827 PHE
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  587 VAL
Chi-restraints excluded: chain B residue  621 ASP
Chi-restraints excluded: chain B residue  653 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0020
   chunk 110 optimal weight:    0.6980
   chunk 89 optimal weight:   50.0000
   chunk 62 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 134 optimal weight:    7.9990
   chunk 122 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   overall best weight:    0.8990

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 ASN
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 559 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.230776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.194701 restraints weight = 51631.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.4544 rms_B_bonded: 4.28
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4544 r_free = 0.4544    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4543 r_free = 0.4543    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
r_final: 0.4543
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5635
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12645  Z= 0.162
  Angle     :  0.731  10.843  17224  Z= 0.362
  Chirality :  0.047   0.284   1922
  Planarity :  0.005   0.045   2259
  Dihedral  :  5.763  50.704   1925
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.01 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.32 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.09 (0.21), residues: 1587
  helix: -1.36 (0.48), residues: 122
  sheet: -1.00 (0.25), residues: 440
  loop : -1.62 (0.19), residues: 1025

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 553 
 HIS   0.011   0.001   HIS B 509 
 PHE   0.014   0.002   PHE B 188 
 TYR   0.039   0.002   TYR A 380 
 ARG   0.006   0.001   ARG A 519 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00582 (    5)
  link_NAG-ASN         : angle       1.80380 (   15)
  link_BETA1-4         : bond        0.00717 (    5)
  link_BETA1-4         : angle       2.44129 (   15)
  hydrogen bonds       : bond        0.03245 (  244)
  hydrogen bonds       : angle       6.09110 (  632)
  SS BOND              : bond        0.00291 (   36)
  SS BOND              : angle       1.27875 (   72)
  covalent geometry    : bond        0.00375 (12599)
  covalent geometry    : angle       0.72290 (17122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6313.75 seconds
wall clock time: 109 minutes 59.73 seconds (6599.73 seconds total)