Starting phenix.real_space_refine
on Wed Mar  4 04:32:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vjm_21219/03_2026/6vjm_21219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vjm_21219/03_2026/6vjm_21219.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vjm_21219/03_2026/6vjm_21219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vjm_21219/03_2026/6vjm_21219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vjm_21219/03_2026/6vjm_21219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vjm_21219/03_2026/6vjm_21219.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.008 sd=   0.083
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6837      2.51       5
     N    1759      2.21       5
     O    1979      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10629
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 684, 5267
          Classifications: {'peptide': 684}
          Incomplete info: {'truncation_to_alanine': 53}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 195
          Unresolved non-hydrogen angles: 243
          Unresolved non-hydrogen dihedrals: 158
          Unresolved non-hydrogen chiralities: 24
          Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 88
    Chain: "B"
      Number of atoms: 5212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 685, 5212
          Classifications: {'peptide': 685}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 656}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 237
          Unresolved non-hydrogen angles: 296
          Unresolved non-hydrogen dihedrals: 192
          Unresolved non-hydrogen chiralities: 29
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 4, 'PHE:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 98
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 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: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.11, per 1000 atoms: 0.20
  Number of scatterers: 10629
  At special positions: 0
  Unit cell: (83.16, 106.92, 168.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1979      8.00
     N    1759      7.00
     C    6837      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 663 " - pdb=" SG  CYS A 761 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 108 " - pdb=" SG  CYS B 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 237 " - pdb=" SG  CYS B 266 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 265 " - pdb=" SG  CYS B 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 553 " - pdb=" SG  CYS B 648 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A1006 " - " ASN A 409 "
      " NAG B1002 " - " ASN B 453 "
      " NAG C   1 " - " ASN A 440 "
      " NAG D   1 " - " ASN A 482 "
      " NAG E   1 " - " ASN A 514 "
      " NAG F   1 " - " ASN B 404 "
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 414.9 milliseconds
  

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2566

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 11 sheets defined
      54.0% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 184 through 201
      removed outlier: 3.701A  pdb=" N   GLN A 189 " --> pdb=" O   GLY A 185 " (cutoff:3.500A)
      Proline residue:  A 190  - end of helix
    Processing helix  chain 'A' and resid 221 through 234
      removed outlier: 3.756A  pdb=" N   LYS A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 257
      removed outlier: 3.521A  pdb=" N   ALA A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 260
      No H-bonds generated for 'chain 'A' and resid 258 through 260'
    Processing helix  chain 'A' and resid 271 through 276
      removed outlier: 3.662A  pdb=" N   SER A 275 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASN A 276 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 292
      removed outlier: 3.707A  pdb=" N   LEU A 292 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 289 through 292'
    Processing helix  chain 'A' and resid 293 through 305
      removed outlier: 4.043A  pdb=" N   TRP A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 331
      removed outlier: 4.272A  pdb=" N   THR A 322 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASP A 324 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ASP A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 334
      No H-bonds generated for 'chain 'A' and resid 332 through 334'
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.627A  pdb=" N   VAL A 351 " --> pdb=" O   PRO A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 381
      removed outlier: 4.156A  pdb=" N   LYS A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 419
    Processing helix  chain 'A' and resid 442 through 454
    Processing helix  chain 'A' and resid 467 through 485
      removed outlier: 4.107A  pdb=" N   TYR A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASP A 472 " --> pdb=" O   PRO A 468 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU A 477 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 515
      removed outlier: 3.657A  pdb=" N   SER A 515 " --> pdb=" O   ARG A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 615
      removed outlier: 3.634A  pdb=" N   VAL A 595 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 644
    Processing helix  chain 'A' and resid 658 through 693
      removed outlier: 4.385A  pdb=" N   LYS A 684 " --> pdb=" O   SER A 680 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ILE A 685 " --> pdb=" O   MET A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 732
      removed outlier: 4.264A  pdb=" N   ASP A 721 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   VAL A 722 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LEU A 723 " --> pdb=" O   GLY A 719 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL A 731 " --> pdb=" O   ILE A 727 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP A 732 " --> pdb=" O   TRP A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 791
      removed outlier: 3.616A  pdb=" N   TYR A 789 " --> pdb=" O   ILE A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 801 through 825
      removed outlier: 3.781A  pdb=" N   VAL A 814 " --> pdb=" O   TYR A 810 " (cutoff:3.500A)
      Proline residue:  A 821  - end of helix
    Processing helix  chain 'A' and resid 832 through 853
    Processing helix  chain 'A' and resid 853 through 861
      removed outlier: 3.901A  pdb=" N   MET A 857 " --> pdb=" O   PHE A 853 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ARG A 859 " --> pdb=" O   PRO A 855 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 861 " --> pdb=" O   MET A 857 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 91
      removed outlier: 3.891A  pdb=" N   ILE B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      Proline residue:  B  79  - end of helix
    Processing helix  chain 'B' and resid 109 through 124
    Processing helix  chain 'B' and resid 135 through 146
      removed outlier: 4.105A  pdb=" N   ILE B 142 " --> pdb=" O   VAL B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 165
      removed outlier: 4.129A  pdb=" N   ASP B 165 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 181
    Processing helix  chain 'B' and resid 182 through 193
      removed outlier: 3.836A  pdb=" N   TYR B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 220
      removed outlier: 3.701A  pdb=" N   THR B 216 " --> pdb=" O   ARG B 212 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY B 217 " --> pdb=" O   ASN B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 246
      removed outlier: 4.004A  pdb=" N   SER B 239 " --> pdb=" O   ASP B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 269
      removed outlier: 3.791A  pdb=" N   ALA B 260 " --> pdb=" O   ASP B 256 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA B 261 " --> pdb=" O   GLN B 257 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LYS B 262 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLU B 269 " --> pdb=" O   CYS B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 292
      removed outlier: 3.869A  pdb=" N   GLU B 291 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLN B 292 " --> pdb=" O   TRP B 289 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 288 through 292'
    Processing helix  chain 'B' and resid 304 through 309
      removed outlier: 4.159A  pdb=" N   ALA B 309 " --> pdb=" O   LYS B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 346
      removed outlier: 4.227A  pdb=" N   ARG B 346 " --> pdb=" O   TYR B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 378
      removed outlier: 3.913A  pdb=" N   ILE B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   TRP B 363 " --> pdb=" O   TYR B 359 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   GLU B 374 " --> pdb=" O   GLN B 370 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   THR B 375 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 405
      removed outlier: 3.931A  pdb=" N   GLU B 405 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 509
      removed outlier: 4.195A  pdb=" N   ILE B 484 " --> pdb=" O   PRO B 480 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU B 485 " --> pdb=" O   LEU B 481 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ILE B 490 " --> pdb=" O   SER B 486 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   LEU B 491 " --> pdb=" O   ALA B 487 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY B 492 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   MET B 493 " --> pdb=" O   THR B 489 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 542
      removed outlier: 3.508A  pdb=" N   PHE B 535 " --> pdb=" O   TYR B 531 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   GLY B 538 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU B 539 " --> pdb=" O   PHE B 535 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ASP B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLY B 541 " --> pdb=" O   PHE B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 550
      removed outlier: 3.743A  pdb=" N   PHE B 549 " --> pdb=" O   GLU B 546 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLU B 550 " --> pdb=" O   LYS B 547 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 546 through 550'
    Processing helix  chain 'B' and resid 551 through 583
      removed outlier: 3.867A  pdb=" N   VAL B 555 " --> pdb=" O   THR B 551 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TRP B 558 " --> pdb=" O   THR B 554 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ILE B 559 " --> pdb=" O   VAL B 555 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   LYS B 574 " --> pdb=" O   ALA B 570 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   THR B 575 " --> pdb=" O   MET B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 619
      removed outlier: 3.641A  pdb=" N   MET B 604 " --> pdb=" O   ILE B 600 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP B 619 " --> pdb=" O   TRP B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 678
      removed outlier: 4.023A  pdb=" N   PHE B 670 " --> pdb=" O   LEU B 666 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   GLY B 671 " --> pdb=" O   LEU B 667 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   CYS B 672 " --> pdb=" O   MET B 668 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   TRP B 676 " --> pdb=" O   CYS B 672 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU B 677 " --> pdb=" O   PHE B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 681
      No H-bonds generated for 'chain 'B' and resid 679 through 681'
    Processing helix  chain 'B' and resid 691 through 712
      removed outlier: 4.573A  pdb=" N   MET B 702 " --> pdb=" O   ASN B 698 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE B 704 " --> pdb=" O   GLY B 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 718 through 741
      removed outlier: 4.384A  pdb=" N   THR B 733 " --> pdb=" O   ILE B 729 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   LEU B 736 " --> pdb=" O   SER B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 742 through 748
    Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 175
      removed outlier: 3.689A  pdb=" N   HIS A 216 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242
      removed outlier: 6.082A  pdb=" N   LEU A 242 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 343
      removed outlier: 7.374A  pdb=" N   ILE A 309 " --> pdb=" O   PHE A 339 " (cutoff:3.500A)
      removed outlier: 8.503A  pdb=" N   GLN A 341 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR A 311 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   PHE A 343 " --> pdb=" O   THR A 311 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   GLN A 313 " --> pdb=" O   PHE A 343 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ILE A 361 " --> pdb=" O   LYS A 308 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE A 362 " --> pdb=" O   PHE A 391 " (cutoff:3.500A)
      removed outlier: 8.814A  pdb=" N   ILE A 393 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
      removed outlier: 8.736A  pdb=" N   GLY A 364 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   TRP A 390 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   THR A 425 " --> pdb=" O   TRP A 390 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   LEU A 392 " --> pdb=" O   THR A 425 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   HIS A 422 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE A 539 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 517 through 520
      removed outlier: 3.501A  pdb=" N   PHE A 518 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 578 through 583
      removed outlier: 3.701A  pdb=" N   SER A 753 " --> pdb=" O   THR A 578 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 735 through 736
    Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105
      removed outlier: 8.625A  pdb=" N   PHE B 131 " --> pdb=" O   SER B  57 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   MET B  59 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   GLN B 153 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 225 through 230
      removed outlier: 3.581A  pdb=" N   SER B 227 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   THR B 200 " --> pdb=" O   SER B 227 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   THR B 229 " --> pdb=" O   THR B 200 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   THR B 202 " --> pdb=" O   THR B 229 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ILE B 250 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   TRP B 279 " --> pdb=" O   ILE B 315 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   VAL B 317 " --> pdb=" O   TRP B 279 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ILE B 281 " --> pdb=" O   VAL B 317 " (cutoff:3.500A)
      removed outlier: 9.648A  pdb=" N   PHE B 319 " --> pdb=" O   ILE B 281 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   TYR B 314 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE B 431 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   GLN B 430 " --> pdb=" O   LYS B 438 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   LYS B 438 " --> pdb=" O   GLN B 430 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 408 through 410
      removed outlier: 3.691A  pdb=" N   PHE B 408 " --> pdb=" O   VAL B 415 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 442 through 443
      removed outlier: 3.616A  pdb=" N   THR B 448 " --> pdb=" O   ASN B 443 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 472 through 474
      removed outlier: 6.451A  pdb=" N   GLN B 473 " --> pdb=" O   LEU B 644 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   GLU B 646 " --> pdb=" O   GLN B 473 " (cutoff:3.500A)

    531 hydrogen bonds defined for protein.
    1569 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3356
        1.35 -     1.47: 2723
        1.47 -     1.59: 4711
        1.59 -     1.71: 0
        1.71 -     1.83: 84
  Bond restraints: 10874
  Sorted by residual:
  bond pdb=" N   LEU A 705 "
       pdb=" CA  LEU A 705 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.17e-02 7.31e+03 9.69e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.95e+00
  bond pdb=" C1  NAG A1006 "
       pdb=" O5  NAG A1006 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.70e+00
  bond pdb=" CA  VAL A 349 "
       pdb=" CB  VAL A 349 "
    ideal  model  delta    sigma   weight residual
    1.534  1.551 -0.016 6.80e-03 2.16e+04 5.82e+00
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.88e+00
  ... (remaining 10869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 14399
        2.44 -     4.88: 315
        4.88 -     7.32: 50
        7.32 -     9.76: 21
        9.76 -    12.20: 5
  Bond angle restraints: 14790
  Sorted by residual:
  angle pdb=" C   THR A 704 "
        pdb=" N   LEU A 705 "
        pdb=" CA  LEU A 705 "
      ideal   model   delta    sigma   weight residual
     121.19  130.65   -9.46 1.59e+00 3.96e-01 3.54e+01
  angle pdb=" C   GLN A 357 "
        pdb=" N   ASP A 358 "
        pdb=" CA  ASP A 358 "
      ideal   model   delta    sigma   weight residual
     121.54  131.41   -9.87 1.91e+00 2.74e-01 2.67e+01
  angle pdb=" C   GLN A 658 "
        pdb=" N   PHE A 659 "
        pdb=" CA  PHE A 659 "
      ideal   model   delta    sigma   weight residual
     120.09  126.20   -6.11 1.25e+00 6.40e-01 2.39e+01
  angle pdb=" C   ASN B 650 "
        pdb=" N   THR B 651 "
        pdb=" CA  THR B 651 "
      ideal   model   delta    sigma   weight residual
     121.54  130.86   -9.32 1.91e+00 2.74e-01 2.38e+01
  angle pdb=" C   PHE A 645 "
        pdb=" N   PRO A 646 "
        pdb=" CA  PRO A 646 "
      ideal   model   delta    sigma   weight residual
     121.91  116.28    5.63 1.35e+00 5.49e-01 1.74e+01
  ... (remaining 14785 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 5868
       17.39 -    34.77: 581
       34.77 -    52.16: 108
       52.16 -    69.55: 22
       69.55 -    86.93: 4
  Dihedral angle restraints: 6583
    sinusoidal: 2601
      harmonic: 3982
  Sorted by residual:
  dihedral pdb=" CB  CYS B 108 "
           pdb=" SG  CYS B 108 "
           pdb=" SG  CYS B 135 "
           pdb=" CB  CYS B 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -24.79  -61.21     1      1.00e+01 1.00e-02 4.98e+01
  dihedral pdb=" CB  CYS A 663 "
           pdb=" SG  CYS A 663 "
           pdb=" SG  CYS A 761 "
           pdb=" CB  CYS A 761 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -33.83  -52.17     1      1.00e+01 1.00e-02 3.71e+01
  dihedral pdb=" CA  THR A 704 "
           pdb=" C   THR A 704 "
           pdb=" N   LEU A 705 "
           pdb=" CA  LEU A 705 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.45  -29.55     0      5.00e+00 4.00e-02 3.49e+01
  ... (remaining 6580 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1403
       0.073 -    0.146: 277
       0.146 -    0.219: 29
       0.219 -    0.292: 2
       0.292 -    0.366: 2
  Chirality restraints: 1713
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 440 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.03   -0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" C1  NAG A1006 "
            pdb=" ND2 ASN A 409 "
            pdb=" C2  NAG A1006 "
            pdb=" O5  NAG A1006 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CA  PHE A 645 "
            pdb=" N   PHE A 645 "
            pdb=" C   PHE A 645 "
            pdb=" CB  PHE A 645 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1710 not shown)

  Planarity restraints: 1866
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 320 "    0.045 5.00e-02 4.00e+02   6.85e-02 7.51e+00
        pdb=" N   PRO B 321 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO B 321 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 321 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 467 "   -0.036 5.00e-02 4.00e+02   5.32e-02 4.53e+00
        pdb=" N   PRO A 468 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 468 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 468 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  95 "   -0.034 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO B  96 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B  96 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  96 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1863 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3336
        2.82 -     3.34: 9929
        3.34 -     3.86: 17923
        3.86 -     4.38: 19020
        4.38 -     4.90: 31950
  Nonbonded interactions: 82158
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 721 "
            pdb=" OH  TYR A 776 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ILE B 452 "
            pdb=" OG1 THR B 455 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OH  TYR A 379 "
            pdb=" OE1 GLU A 414 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OG  SER A 443 "
            pdb=" OE1 GLN A 444 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   SER A 247 "
            pdb=" OG  SER A 250 "
     model   vdw
     2.314 3.040
  ... (remaining 82153 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 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.750
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
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      :  0.005   0.056  10892  Z= 0.239
  Angle     :  0.974  18.863  14837  Z= 0.497
  Chirality :  0.058   0.366   1713
  Planarity :  0.006   0.069   1860
  Dihedral  : 14.174  86.933   3996
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 10.53 %
    Favored  : 89.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.38 (0.18), residues: 1357
  helix: -2.44 (0.14), residues: 674
  sheet: -2.27 (0.35), residues: 182
  loop : -3.64 (0.22), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 453 
 TYR   0.019   0.002   TYR B 663 
 PHE   0.022   0.002   PHE A 645 
 TRP   0.015   0.002   TRP B 558 
 HIS   0.006   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (10874)
  covalent geometry    : angle       0.92971 (14790)
  SS BOND              : bond        0.00253 (    7)
  SS BOND              : angle       1.82670 (   14)
  hydrogen bonds       : bond        0.10465 (  531)
  hydrogen bonds       : angle       6.19622 ( 1569)
  link_BETA1-4         : bond        0.00784 (    4)
  link_BETA1-4         : angle       6.59087 (   12)
  link_BETA1-6         : bond        0.00180 (    1)
  link_BETA1-6         : angle       3.36015 (    3)
  link_NAG-ASN         : bond        0.01201 (    6)
  link_NAG-ASN         : angle       6.23252 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.8978 (tt) cc_final: 0.8524 (mp)
REVERT: A  178 MET cc_start: 0.8771 (mmt) cc_final: 0.8267 (mmm)
REVERT: A  582 LYS cc_start: 0.8865 (tttt) cc_final: 0.8544 (tmtt)
REVERT: A  807 MET cc_start: 0.8096 (tpt) cc_final: 0.7843 (tpt)
REVERT: B  435 ARG cc_start: 0.9344 (ptp90) cc_final: 0.9143 (mtm-85)
REVERT: B  604 MET cc_start: 0.7595 (ptt) cc_final: 0.7312 (ptp)
  outliers start: 2
  outliers final: 1
  residues processed: 129
  average time/residue: 0.1081
  time to fit residues: 19.9051
Evaluate side-chains
  90 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.1980
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 293 HIS
A 353 ASN
A 508 GLN
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 HIS
B 126 ASN
B 192 HIS
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 GLN
B 401 ASN
B 414 GLN
B 430 GLN
B 503 ASN
B 506 ASN
B 698 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.071166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.060563 restraints weight = 60643.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.061969 restraints weight = 37086.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.062886 restraints weight = 25856.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.063590 restraints weight = 19780.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.064058 restraints weight = 16141.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10892  Z= 0.124
  Angle     :  0.693  13.353  14837  Z= 0.337
  Chirality :  0.045   0.378   1713
  Planarity :  0.005   0.066   1860
  Dihedral  :  6.075  47.561   1692
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.51 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.21), residues: 1357
  helix: -0.72 (0.19), residues: 676
  sheet: -2.05 (0.35), residues: 199
  loop : -3.24 (0.24), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 304 
 TYR   0.021   0.001   TYR B 169 
 PHE   0.021   0.001   PHE A 645 
 TRP   0.011   0.001   TRP A 395 
 HIS   0.003   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10874)
  covalent geometry    : angle       0.65730 (14790)
  SS BOND              : bond        0.00199 (    7)
  SS BOND              : angle       1.12757 (   14)
  hydrogen bonds       : bond        0.03939 (  531)
  hydrogen bonds       : angle       4.96849 ( 1569)
  link_BETA1-4         : bond        0.00522 (    4)
  link_BETA1-4         : angle       4.59325 (   12)
  link_BETA1-6         : bond        0.00384 (    1)
  link_BETA1-6         : angle       2.37785 (    3)
  link_NAG-ASN         : bond        0.00883 (    6)
  link_NAG-ASN         : angle       4.97854 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.8988 (tt) cc_final: 0.8644 (mt)
REVERT: A  178 MET cc_start: 0.8756 (mmt) cc_final: 0.8206 (mmm)
REVERT: A  582 LYS cc_start: 0.8850 (tttt) cc_final: 0.8532 (tmtt)
REVERT: A  846 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6878 (m-80)
REVERT: B  259 MET cc_start: 0.8191 (tpp) cc_final: 0.7936 (mtt)
REVERT: B  320 GLU cc_start: 0.8210 (tp30) cc_final: 0.7986 (tp30)
REVERT: B  628 TYR cc_start: 0.9026 (t80) cc_final: 0.8570 (t80)
  outliers start: 27
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0874
  time to fit residues: 16.9148
Evaluate side-chains
  112 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  682 PHE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0980
   chunk 74 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 96 optimal weight:    0.9980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 631 ASN
B  87 GLN
B 126 ASN
B 180 ASN
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.070811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.060175 restraints weight = 62220.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.061574 restraints weight = 37599.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.062522 restraints weight = 26103.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.063173 restraints weight = 19872.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.063657 restraints weight = 16253.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10892  Z= 0.134
  Angle     :  0.675  12.714  14837  Z= 0.329
  Chirality :  0.045   0.358   1713
  Planarity :  0.004   0.051   1860
  Dihedral  :  5.876  47.982   1692
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.73 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.22), residues: 1357
  helix: -0.05 (0.20), residues: 674
  sheet: -2.06 (0.34), residues: 208
  loop : -3.00 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 304 
 TYR   0.018   0.001   TYR B 169 
 PHE   0.021   0.001   PHE A 645 
 TRP   0.011   0.001   TRP B 558 
 HIS   0.004   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10874)
  covalent geometry    : angle       0.64205 (14790)
  SS BOND              : bond        0.00301 (    7)
  SS BOND              : angle       1.05640 (   14)
  hydrogen bonds       : bond        0.03783 (  531)
  hydrogen bonds       : angle       4.78093 ( 1569)
  link_BETA1-4         : bond        0.00487 (    4)
  link_BETA1-4         : angle       4.25320 (   12)
  link_BETA1-6         : bond        0.00131 (    1)
  link_BETA1-6         : angle       2.07698 (    3)
  link_NAG-ASN         : bond        0.00843 (    6)
  link_NAG-ASN         : angle       4.87023 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.8987 (tt) cc_final: 0.8643 (mt)
REVERT: A  178 MET cc_start: 0.8746 (mmt) cc_final: 0.8194 (mmm)
REVERT: A  415 MET cc_start: 0.7571 (mmt) cc_final: 0.6963 (mmt)
REVERT: A  582 LYS cc_start: 0.8864 (tttt) cc_final: 0.8542 (tmtt)
REVERT: A  810 TYR cc_start: 0.7827 (m-80) cc_final: 0.7623 (m-80)
REVERT: A  846 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6952 (m-80)
REVERT: B  403 MET cc_start: 0.8997 (tpt) cc_final: 0.8777 (tpp)
  outliers start: 28
  outliers final: 16
  residues processed: 119
  average time/residue: 0.0803
  time to fit residues: 14.7958
Evaluate side-chains
  110 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  645 PHE
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  481 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 129 optimal weight:    0.7980
   chunk 68 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 90 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 128 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 658 GLN
B 180 ASN
** B 257 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 = 0.3529 r_free = 0.3529 target = 0.070047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.059462 restraints weight = 62749.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.060851 restraints weight = 37949.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.061778 restraints weight = 26391.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.062390 restraints weight = 20240.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.062881 restraints weight = 16674.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10892  Z= 0.161
  Angle     :  0.689  12.462  14837  Z= 0.337
  Chirality :  0.046   0.352   1713
  Planarity :  0.004   0.050   1860
  Dihedral  :  5.887  48.307   1692
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.40 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.23), residues: 1357
  helix:  0.20 (0.20), residues: 675
  sheet: -1.96 (0.35), residues: 201
  loop : -2.93 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 457 
 TYR   0.017   0.002   TYR B 663 
 PHE   0.021   0.002   PHE A 645 
 TRP   0.013   0.001   TRP B 558 
 HIS   0.004   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (10874)
  covalent geometry    : angle       0.65566 (14790)
  SS BOND              : bond        0.00236 (    7)
  SS BOND              : angle       2.03891 (   14)
  hydrogen bonds       : bond        0.03868 (  531)
  hydrogen bonds       : angle       4.75392 ( 1569)
  link_BETA1-4         : bond        0.00374 (    4)
  link_BETA1-4         : angle       3.98497 (   12)
  link_BETA1-6         : bond        0.00134 (    1)
  link_BETA1-6         : angle       2.14287 (    3)
  link_NAG-ASN         : bond        0.00834 (    6)
  link_NAG-ASN         : angle       4.84685 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.8997 (tt) cc_final: 0.8643 (mt)
REVERT: A  178 MET cc_start: 0.8777 (mmt) cc_final: 0.8297 (mmm)
REVERT: A  415 MET cc_start: 0.7541 (mmt) cc_final: 0.6995 (mmt)
REVERT: A  582 LYS cc_start: 0.8854 (tttt) cc_final: 0.8530 (tmtt)
REVERT: A  810 TYR cc_start: 0.7914 (m-80) cc_final: 0.7640 (m-80)
REVERT: A  846 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6998 (m-80)
REVERT: B  320 GLU cc_start: 0.8290 (tp30) cc_final: 0.8028 (tp30)
REVERT: B  459 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7644 (pt0)
REVERT: B  630 MET cc_start: 0.9375 (pmm) cc_final: 0.9094 (pmm)
  outliers start: 32
  outliers final: 24
  residues processed: 119
  average time/residue: 0.0799
  time to fit residues: 15.0230
Evaluate side-chains
  116 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  645 PHE
Chi-restraints excluded: chain A residue  682 PHE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  459 GLN
Chi-restraints excluded: chain B residue  481 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 134 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 93 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0980
   chunk 65 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 422 HIS
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 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 = 0.3517 r_free = 0.3517 target = 0.069523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.059124 restraints weight = 62083.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.060492 restraints weight = 37369.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.061376 restraints weight = 25894.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.062020 restraints weight = 19868.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.062498 restraints weight = 16265.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10892  Z= 0.164
  Angle     :  0.693  12.396  14837  Z= 0.339
  Chirality :  0.046   0.348   1713
  Planarity :  0.004   0.049   1860
  Dihedral  :  5.898  48.688   1692
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 17.80 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.23), residues: 1357
  helix:  0.30 (0.20), residues: 674
  sheet: -1.96 (0.34), residues: 206
  loop : -2.83 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 304 
 TYR   0.016   0.001   TYR B 663 
 PHE   0.021   0.002   PHE A 645 
 TRP   0.014   0.001   TRP B 558 
 HIS   0.004   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10874)
  covalent geometry    : angle       0.66102 (14790)
  SS BOND              : bond        0.00257 (    7)
  SS BOND              : angle       2.01812 (   14)
  hydrogen bonds       : bond        0.03875 (  531)
  hydrogen bonds       : angle       4.72206 ( 1569)
  link_BETA1-4         : bond        0.00350 (    4)
  link_BETA1-4         : angle       3.75852 (   12)
  link_BETA1-6         : bond        0.00184 (    1)
  link_BETA1-6         : angle       2.23477 (    3)
  link_NAG-ASN         : bond        0.00833 (    6)
  link_NAG-ASN         : angle       4.80624 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 93
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.8791 (mmt) cc_final: 0.8249 (mmm)
REVERT: A  194 MET cc_start: 0.9085 (mmm) cc_final: 0.8869 (mmm)
REVERT: A  415 MET cc_start: 0.7406 (mmt) cc_final: 0.6899 (mmt)
REVERT: A  582 LYS cc_start: 0.8847 (tttt) cc_final: 0.8517 (tmtt)
REVERT: A  846 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.7029 (m-80)
REVERT: B  459 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7621 (pt0)
REVERT: B  571 MET cc_start: 0.8016 (tpp) cc_final: 0.7754 (tpt)
REVERT: B  630 MET cc_start: 0.9328 (pmm) cc_final: 0.8917 (pmm)
  outliers start: 39
  outliers final: 28
  residues processed: 122
  average time/residue: 0.0780
  time to fit residues: 15.0491
Evaluate side-chains
  120 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  645 PHE
Chi-restraints excluded: chain A residue  682 PHE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  454 ASP
Chi-restraints excluded: chain B residue  459 GLN
Chi-restraints excluded: chain B residue  468 THR
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain B residue  605 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 119 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 117 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 132 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 92 optimal weight:   10.0000
   chunk 122 optimal weight:    6.9990
   chunk 134 optimal weight:    5.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 353 ASN
A 457 HIS
A 735 HIS
B 180 ASN
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.067061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.056670 restraints weight = 64629.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.058034 restraints weight = 38587.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.058921 restraints weight = 26532.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.059581 restraints weight = 20315.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.060032 restraints weight = 16574.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  10892  Z= 0.293
  Angle     :  0.811  12.056  14837  Z= 0.407
  Chirality :  0.049   0.352   1713
  Planarity :  0.005   0.067   1860
  Dihedral  :  6.473  49.251   1692
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.55 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.23), residues: 1357
  helix: -0.02 (0.20), residues: 672
  sheet: -2.07 (0.34), residues: 204
  loop : -2.83 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 346 
 TYR   0.022   0.002   TYR B 663 
 PHE   0.030   0.003   PHE B 501 
 TRP   0.028   0.002   TRP B 558 
 HIS   0.004   0.001   HIS A 689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 (10874)
  covalent geometry    : angle       0.78226 (14790)
  SS BOND              : bond        0.00634 (    7)
  SS BOND              : angle       2.21373 (   14)
  hydrogen bonds       : bond        0.04710 (  531)
  hydrogen bonds       : angle       5.15920 ( 1569)
  link_BETA1-4         : bond        0.00337 (    4)
  link_BETA1-4         : angle       3.86327 (   12)
  link_BETA1-6         : bond        0.00040 (    1)
  link_BETA1-6         : angle       2.74003 (    3)
  link_NAG-ASN         : bond        0.00923 (    6)
  link_NAG-ASN         : angle       4.94979 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 91
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.8833 (mmt) cc_final: 0.8278 (mmm)
REVERT: A  582 LYS cc_start: 0.8864 (tttt) cc_final: 0.8514 (tmtt)
REVERT: A  846 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6884 (m-80)
REVERT: B  153 GLN cc_start: 0.8340 (tp40) cc_final: 0.8058 (tp40)
REVERT: B  320 GLU cc_start: 0.8422 (tp30) cc_final: 0.8178 (tp30)
REVERT: B  403 MET cc_start: 0.8990 (tpt) cc_final: 0.8757 (tpp)
REVERT: B  571 MET cc_start: 0.8090 (tpp) cc_final: 0.7645 (tpp)
REVERT: B  630 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8908 (pmm)
  outliers start: 42
  outliers final: 31
  residues processed: 126
  average time/residue: 0.0767
  time to fit residues: 15.3586
Evaluate side-chains
  118 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  682 PHE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  454 ASP
Chi-restraints excluded: chain B residue  468 THR
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain B residue  605 LEU
Chi-restraints excluded: chain B residue  630 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0770
   chunk 17 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 125 optimal weight:    0.1980
   chunk 29 optimal weight:    9.9990
   overall best weight:    0.5740

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 647 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.070196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.059715 restraints weight = 62152.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.061104 restraints weight = 37462.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.062026 restraints weight = 25899.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.062685 restraints weight = 19713.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.063119 restraints weight = 16103.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  10892  Z= 0.117
  Angle     :  0.701  12.883  14837  Z= 0.334
  Chirality :  0.046   0.348   1713
  Planarity :  0.004   0.048   1860
  Dihedral  :  5.854  49.425   1692
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.32 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.23), residues: 1357
  helix:  0.35 (0.20), residues: 675
  sheet: -1.81 (0.35), residues: 199
  loop : -2.76 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 304 
 TYR   0.015   0.001   TYR A 810 
 PHE   0.025   0.001   PHE A 645 
 TRP   0.012   0.001   TRP A 395 
 HIS   0.005   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10874)
  covalent geometry    : angle       0.67220 (14790)
  SS BOND              : bond        0.00417 (    7)
  SS BOND              : angle       1.82156 (   14)
  hydrogen bonds       : bond        0.03786 (  531)
  hydrogen bonds       : angle       4.62220 ( 1569)
  link_BETA1-4         : bond        0.00546 (    4)
  link_BETA1-4         : angle       3.37014 (   12)
  link_BETA1-6         : bond        0.00419 (    1)
  link_BETA1-6         : angle       2.08538 (    3)
  link_NAG-ASN         : bond        0.00855 (    6)
  link_NAG-ASN         : angle       4.74789 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 100
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.8701 (mmt) cc_final: 0.8246 (mmm)
REVERT: A  415 MET cc_start: 0.7383 (mmt) cc_final: 0.7169 (mmm)
REVERT: A  582 LYS cc_start: 0.8846 (tttt) cc_final: 0.8491 (tmtt)
REVERT: A  678 TYR cc_start: 0.6742 (t80) cc_final: 0.6418 (t80)
REVERT: A  846 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6947 (m-80)
REVERT: B   59 MET cc_start: 0.7785 (pmm) cc_final: 0.7451 (pmm)
REVERT: B  153 GLN cc_start: 0.8289 (tp40) cc_final: 0.7966 (tp40)
REVERT: B  320 GLU cc_start: 0.8303 (tp30) cc_final: 0.8047 (tp30)
REVERT: B  459 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7630 (pt0)
REVERT: B  519 MET cc_start: 0.7454 (ttm) cc_final: 0.6844 (mmm)
REVERT: B  571 MET cc_start: 0.8141 (tpp) cc_final: 0.7803 (tpp)
REVERT: B  630 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8809 (mpp)
REVERT: B  647 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7756 (m-70)
REVERT: B  702 MET cc_start: 0.8937 (mmm) cc_final: 0.8703 (mmm)
  outliers start: 34
  outliers final: 24
  residues processed: 126
  average time/residue: 0.0719
  time to fit residues: 14.4910
Evaluate side-chains
  119 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  645 PHE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  454 ASP
Chi-restraints excluded: chain B residue  459 GLN
Chi-restraints excluded: chain B residue  468 THR
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain B residue  630 MET
Chi-restraints excluded: chain B residue  647 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 84 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 133 optimal weight:    0.1980
   chunk 102 optimal weight:    0.9990
   chunk 128 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 21 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 180 ASN
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 647 HIS
B 698 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.070482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.060010 restraints weight = 61765.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.061394 restraints weight = 37146.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.062310 restraints weight = 25738.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.062978 restraints weight = 19632.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.063411 restraints weight = 16021.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10892  Z= 0.116
  Angle     :  0.705  12.528  14837  Z= 0.332
  Chirality :  0.046   0.345   1713
  Planarity :  0.004   0.049   1860
  Dihedral  :  5.702  49.441   1692
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.06 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.23), residues: 1357
  helix:  0.52 (0.20), residues: 675
  sheet: -1.68 (0.35), residues: 199
  loop : -2.80 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 714 
 TYR   0.012   0.001   TYR B 663 
 PHE   0.027   0.001   PHE A 645 
 TRP   0.012   0.001   TRP A 395 
 HIS   0.011   0.001   HIS B 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10874)
  covalent geometry    : angle       0.67794 (14790)
  SS BOND              : bond        0.00244 (    7)
  SS BOND              : angle       1.38378 (   14)
  hydrogen bonds       : bond        0.03613 (  531)
  hydrogen bonds       : angle       4.53516 ( 1569)
  link_BETA1-4         : bond        0.00469 (    4)
  link_BETA1-4         : angle       3.24242 (   12)
  link_BETA1-6         : bond        0.00293 (    1)
  link_BETA1-6         : angle       2.05619 (    3)
  link_NAG-ASN         : bond        0.00830 (    6)
  link_NAG-ASN         : angle       4.74705 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.8674 (mmt) cc_final: 0.8236 (mmm)
REVERT: A  582 LYS cc_start: 0.8862 (tttt) cc_final: 0.8524 (tmtt)
REVERT: A  678 TYR cc_start: 0.6772 (t80) cc_final: 0.6378 (t80)
REVERT: A  681 MET cc_start: 0.8660 (tpt) cc_final: 0.8408 (tpt)
REVERT: A  846 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.7118 (m-80)
REVERT: B  153 GLN cc_start: 0.8332 (tp40) cc_final: 0.8013 (tp40)
REVERT: B  272 MET cc_start: 0.8907 (mmm) cc_final: 0.8698 (mmm)
REVERT: B  320 GLU cc_start: 0.8350 (tp30) cc_final: 0.8067 (tp30)
REVERT: B  459 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7597 (pt0)
REVERT: B  571 MET cc_start: 0.8103 (tpp) cc_final: 0.7796 (tpp)
REVERT: B  630 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8756 (mpp)
REVERT: B  647 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7779 (m-70)
REVERT: B  702 MET cc_start: 0.8904 (mmm) cc_final: 0.8522 (mmt)
  outliers start: 31
  outliers final: 24
  residues processed: 117
  average time/residue: 0.0780
  time to fit residues: 14.3817
Evaluate side-chains
  120 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  645 PHE
Chi-restraints excluded: chain A residue  653 HIS
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  789 TYR
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  454 ASP
Chi-restraints excluded: chain B residue  459 GLN
Chi-restraints excluded: chain B residue  468 THR
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain B residue  630 MET
Chi-restraints excluded: chain B residue  647 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 114 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 113 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 124 optimal weight:   10.0000
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 647 HIS ** 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 = 0.3513 r_free = 0.3513 target = 0.068522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.058296 restraints weight = 63850.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.059654 restraints weight = 38009.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.060539 restraints weight = 26113.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061182 restraints weight = 19863.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.061648 restraints weight = 16250.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  10892  Z= 0.260
  Angle     :  0.794  11.970  14837  Z= 0.392
  Chirality :  0.049   0.345   1713
  Planarity :  0.005   0.057   1860
  Dihedral  :  6.216  49.493   1692
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.44 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.23), residues: 1357
  helix:  0.31 (0.20), residues: 668
  sheet: -1.96 (0.35), residues: 204
  loop : -2.80 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 453 
 TYR   0.023   0.002   TYR A 776 
 PHE   0.029   0.002   PHE A 645 
 TRP   0.030   0.002   TRP B 558 
 HIS   0.012   0.001   HIS B 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 (10874)
  covalent geometry    : angle       0.76871 (14790)
  SS BOND              : bond        0.00486 (    7)
  SS BOND              : angle       1.56525 (   14)
  hydrogen bonds       : bond        0.04342 (  531)
  hydrogen bonds       : angle       4.95125 ( 1569)
  link_BETA1-4         : bond        0.00270 (    4)
  link_BETA1-4         : angle       3.34396 (   12)
  link_BETA1-6         : bond        0.00070 (    1)
  link_BETA1-6         : angle       2.44026 (    3)
  link_NAG-ASN         : bond        0.00880 (    6)
  link_NAG-ASN         : angle       4.87827 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 90
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.8770 (mmt) cc_final: 0.8278 (mmm)
REVERT: A  582 LYS cc_start: 0.8816 (tttt) cc_final: 0.8459 (tmtt)
REVERT: A  846 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.7038 (m-80)
REVERT: B  153 GLN cc_start: 0.8420 (tp40) cc_final: 0.8131 (tp40)
REVERT: B  571 MET cc_start: 0.8153 (tpp) cc_final: 0.7768 (tpp)
REVERT: B  630 MET cc_start: 0.9090 (pmm) cc_final: 0.8760 (mpp)
REVERT: B  702 MET cc_start: 0.8956 (mmm) cc_final: 0.8587 (mmt)
  outliers start: 33
  outliers final: 27
  residues processed: 117
  average time/residue: 0.0816
  time to fit residues: 15.1813
Evaluate side-chains
  117 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  682 PHE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  454 ASP
Chi-restraints excluded: chain B residue  468 THR
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain B residue  655 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 100 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 86 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   chunk 124 optimal weight:    7.9990
   chunk 114 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 180 ASN
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 647 HIS ** 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 = 0.3510 r_free = 0.3510 target = 0.068438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.058314 restraints weight = 63224.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.059663 restraints weight = 37635.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.060576 restraints weight = 25879.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061207 restraints weight = 19648.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.061672 restraints weight = 16014.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  10892  Z= 0.230
  Angle     :  0.786  11.969  14837  Z= 0.385
  Chirality :  0.049   0.344   1713
  Planarity :  0.004   0.051   1860
  Dihedral  :  6.312  49.940   1692
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.71 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.23), residues: 1357
  helix:  0.18 (0.20), residues: 672
  sheet: -1.95 (0.34), residues: 202
  loop : -2.83 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 453 
 TYR   0.022   0.002   TYR A 776 
 PHE   0.031   0.002   PHE A 645 
 TRP   0.030   0.002   TRP B 558 
 HIS   0.004   0.001   HIS A 689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (10874)
  covalent geometry    : angle       0.76077 (14790)
  SS BOND              : bond        0.00305 (    7)
  SS BOND              : angle       1.71443 (   14)
  hydrogen bonds       : bond        0.04337 (  531)
  hydrogen bonds       : angle       5.00968 ( 1569)
  link_BETA1-4         : bond        0.00325 (    4)
  link_BETA1-4         : angle       3.27523 (   12)
  link_BETA1-6         : bond        0.00083 (    1)
  link_BETA1-6         : angle       2.38318 (    3)
  link_NAG-ASN         : bond        0.00867 (    6)
  link_NAG-ASN         : angle       4.83948 (   18)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.8735 (mmt) cc_final: 0.8182 (mmm)
REVERT: A  582 LYS cc_start: 0.8779 (tttt) cc_final: 0.8410 (tmtt)
REVERT: A  846 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6944 (m-80)
REVERT: B  153 GLN cc_start: 0.8412 (tp40) cc_final: 0.8115 (tp40)
REVERT: B  571 MET cc_start: 0.8184 (tpp) cc_final: 0.7829 (tpp)
REVERT: B  630 MET cc_start: 0.9082 (pmm) cc_final: 0.8766 (mpp)
REVERT: B  702 MET cc_start: 0.9005 (mmm) cc_final: 0.8626 (mmt)
  outliers start: 33
  outliers final: 30
  residues processed: 117
  average time/residue: 0.0804
  time to fit residues: 14.9678
Evaluate side-chains
  120 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  645 PHE
Chi-restraints excluded: chain A residue  682 PHE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  180 ASN
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  448 THR
Chi-restraints excluded: chain B residue  454 ASP
Chi-restraints excluded: chain B residue  468 THR
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain B residue  655 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 71 optimal weight:    0.1980
   chunk 122 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 111 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 647 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.070410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.060288 restraints weight = 60333.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.061691 restraints weight = 35833.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.062595 restraints weight = 24547.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.063306 restraints weight = 18574.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.063809 restraints weight = 14985.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10892  Z= 0.121
  Angle     :  0.750  13.294  14837  Z= 0.352
  Chirality :  0.048   0.342   1713
  Planarity :  0.004   0.048   1860
  Dihedral  :  5.909  49.870   1692
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.09 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.23), residues: 1357
  helix:  0.52 (0.20), residues: 675
  sheet: -1.71 (0.35), residues: 199
  loop : -2.75 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 304 
 TYR   0.024   0.001   TYR A 776 
 PHE   0.026   0.001   PHE A 645 
 TRP   0.013   0.001   TRP A 536 
 HIS   0.006   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10874)
  covalent geometry    : angle       0.72641 (14790)
  SS BOND              : bond        0.00221 (    7)
  SS BOND              : angle       1.38059 (   14)
  hydrogen bonds       : bond        0.03710 (  531)
  hydrogen bonds       : angle       4.61554 ( 1569)
  link_BETA1-4         : bond        0.00447 (    4)
  link_BETA1-4         : angle       3.00101 (   12)
  link_BETA1-6         : bond        0.00412 (    1)
  link_BETA1-6         : angle       1.90139 (    3)
  link_NAG-ASN         : bond        0.00893 (    6)
  link_NAG-ASN         : angle       4.73247 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1562.09 seconds
wall clock time: 27 minutes 50.17 seconds (1670.17 seconds total)