Starting phenix.real_space_refine
on Wed Jun  3 14:10:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dzv_8940/06_2026/6dzv_8940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dzv_8940/06_2026/6dzv_8940.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dzv_8940/06_2026/6dzv_8940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dzv_8940/06_2026/6dzv_8940.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dzv_8940/06_2026/6dzv_8940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dzv_8940/06_2026/6dzv_8940.cif"
  }
  resolution = 4.2
  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=   0.003 sd=   0.522
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      34      5.16       5
     C    4039      2.51       5
     N     962      2.21       5
     O    1086      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6121
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4292
          Classifications: {'peptide': 537}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 514}
    Chain: "B"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 913
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 830
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    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: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 58
          Unusual residues: {'HJM': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.66, per 1000 atoms: 0.27
  Number of scatterers: 6121
  At special positions: 0
  Unit cell: (83.123, 76.539, 117.689, 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      34     16.00
     O    1086      8.00
     N     962      7.00
     C    4039      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " 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 D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 321.5 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 7 sheets defined
      56.1% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.601A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER A  91 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 110
      removed outlier: 3.724A  pdb=" N   PHE A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
      removed outlier: 3.810A  pdb=" N   TYR A 110 " --> pdb=" O   PRO A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 113
      No H-bonds generated for 'chain 'A' and resid 111 through 113'
    Processing helix  chain 'A' and resid 114 through 128
      removed outlier: 3.826A  pdb=" N   LEU A 118 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      Proline residue:  A 120  - end of helix
    Processing helix  chain 'A' and resid 128 through 144
      removed outlier: 4.360A  pdb=" N   LEU A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   HIS A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 4.103A  pdb=" N   ILE A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 159
      removed outlier: 3.550A  pdb=" N   LYS A 159 " --> pdb=" O   PRO A 156 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 156 through 159'
    Processing helix  chain 'A' and resid 160 through 190
      removed outlier: 3.720A  pdb=" N   TYR A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA A 181 " --> pdb=" O   ASN A 177 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   TRP A 182 " --> pdb=" O   THR A 178 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA A 183 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A 189 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 209
    Processing helix  chain 'A' and resid 226 through 234
    Processing helix  chain 'A' and resid 252 through 273
      removed outlier: 3.667A  pdb=" N   ALA A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   CYS A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   MET A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER A 269 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A 272 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 280
      removed outlier: 3.588A  pdb=" N   VAL A 280 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 300
      removed outlier: 4.574A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER A 293 " --> pdb=" O   TYR A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 304
      No H-bonds generated for 'chain 'A' and resid 302 through 304'
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 3.846A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A 310 " --> pdb=" O   TRP A 306 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   PHE A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 320
      removed outlier: 4.169A  pdb=" N   LYS A 319 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 338
      removed outlier: 3.785A  pdb=" N   ALA A 330 " --> pdb=" O   TRP A 326 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE A 333 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 348
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 356 through 391
      removed outlier: 3.525A  pdb=" N   ASP A 360 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   PHE A 373 " --> pdb=" O   CYS A 369 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR A 381 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   TYR A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   MET A 389 " --> pdb=" O   TYR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 417
      removed outlier: 4.074A  pdb=" N   PHE A 407 " --> pdb=" O   PRO A 403 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU A 412 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA A 413 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 414 " --> pdb=" O   TYR A 410 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN A 416 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 454
      removed outlier: 3.661A  pdb=" N   ILE A 426 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 429 " --> pdb=" O   ILE A 425 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   MET A 430 " --> pdb=" O   ILE A 426 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LEU A 431 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLY A 445 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   VAL A 450 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 451 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 460
      removed outlier: 4.254A  pdb=" N   LYS A 460 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 482
      removed outlier: 3.717A  pdb=" N   LEU A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   PHE A 474 " --> pdb=" O   VAL A 470 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   PHE A 475 " --> pdb=" O   ILE A 471 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   THR A 480 " --> pdb=" O   GLY A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 495
      removed outlier: 4.569A  pdb=" N   GLU A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR A 495 " --> pdb=" O   LEU A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
      removed outlier: 3.507A  pdb=" N   ALA A 509 " --> pdb=" O   ALA A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 530
      removed outlier: 3.809A  pdb=" N   ARG A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ASP A 524 " --> pdb=" O   GLN A 520 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   GLU A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   MET A 528 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 541
      removed outlier: 4.132A  pdb=" N   CYS A 540 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TRP A 541 " --> pdb=" O   TRP A 537 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 536 through 541'
    Processing helix  chain 'A' and resid 543 through 559
      removed outlier: 3.806A  pdb=" N   LEU A 549 " --> pdb=" O   SER A 545 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LEU A 550 " --> pdb=" O   PRO A 546 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE A 551 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ILE A 552 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ILE A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 557 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 585
      removed outlier: 3.575A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 572 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A 577 " --> pdb=" O   TRP A 573 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY A 578 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY A 582 " --> pdb=" O   GLY A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 3.717A  pdb=" N   ILE A 593 " --> pdb=" O   ILE A 589 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ALA A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR A 595 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 612
    Processing helix  chain 'B' and resid 106 through 110
    Processing helix  chain 'C' and resid 103 through 107
      removed outlier: 3.702A  pdb=" N   THR C 107 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 30
      removed outlier: 3.882A  pdb=" N   GLU B  29 " --> pdb=" O   SER B 135 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TYR B 113 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE B 114 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL B  56 " --> pdb=" O   PHE B 114 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   TRP B  55 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   GLY B  68 " --> pdb=" O   TRP B  55 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LYS B  57 " --> pdb=" O   TRP B  66 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   TRP B  66 " --> pdb=" O   LYS B  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 39
      removed outlier: 3.662A  pdb=" N   VAL B  37 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU B 102 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   THR B  97 " --> pdb=" O   ASP B  92 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASP B  92 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 25
    Processing sheet with id=AA4, first strand: chain 'C' and resid 30 through 32
      removed outlier: 5.852A  pdb=" N   LEU C  31 " --> pdb=" O   GLU C 129 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 50 through 51
      removed outlier: 4.314A  pdb=" N   ASN C  51 " --> pdb=" O   ILE C  54 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78
      removed outlier: 7.290A  pdb=" N   TRP C  59 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASN C  58 " --> pdb=" O   GLN C 113 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 90
      removed outlier: 3.661A  pdb=" N   SER C  89 " --> pdb=" O   SER C  96 " (cutoff:3.500A)

    222 hydrogen bonds defined for protein.
    618 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: 0.89

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.00 -     1.16: 1
        1.16 -     1.33: 955
        1.33 -     1.49: 2754
        1.49 -     1.65: 2541
        1.65 -     1.81: 56
  Bond restraints: 6307
  Sorted by residual:
  bond pdb=" CBD Y01 A 704 "
       pdb=" CBG Y01 A 704 "
    ideal  model  delta    sigma   weight residual
    1.520  1.001  0.519 2.00e-02 2.50e+03 6.73e+02
  bond pdb=" CAS Y01 A 704 "
       pdb=" CAU Y01 A 704 "
    ideal  model  delta    sigma   weight residual
    1.530  1.191  0.339 2.00e-02 2.50e+03 2.88e+02
  bond pdb=" CAU Y01 A 704 "
       pdb=" CBI Y01 A 704 "
    ideal  model  delta    sigma   weight residual
    1.530  1.254  0.276 2.00e-02 2.50e+03 1.90e+02
  bond pdb=" CAP Y01 A 704 "
       pdb=" CAQ Y01 A 704 "
    ideal  model  delta    sigma   weight residual
    1.541  1.803 -0.262 2.00e-02 2.50e+03 1.72e+02
  bond pdb=" CAK Y01 A 704 "
       pdb=" CBD Y01 A 704 "
    ideal  model  delta    sigma   weight residual
    1.525  1.264  0.261 2.00e-02 2.50e+03 1.70e+02
  ... (remaining 6302 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 8482
        2.35 -     4.70: 81
        4.70 -     7.05: 22
        7.05 -     9.40: 9
        9.40 -    11.75: 2
  Bond angle restraints: 8596
  Sorted by residual:
  angle pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
        pdb=" CA  SER C  48 "
      ideal   model   delta    sigma   weight residual
     121.70  133.45  -11.75 1.80e+00 3.09e-01 4.26e+01
  angle pdb=" CAK Y01 A 704 "
        pdb=" CAI Y01 A 704 "
        pdb=" CAZ Y01 A 704 "
      ideal   model   delta    sigma   weight residual
     124.96  113.98   10.98 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" CA  GLU C  47 "
        pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
      ideal   model   delta    sigma   weight residual
     115.51  119.43   -3.92 1.27e+00 6.20e-01 9.51e+00
  angle pdb=" CAM Y01 A 704 "
        pdb=" CAY Y01 A 704 "
        pdb=" OAW Y01 A 704 "
      ideal   model   delta    sigma   weight residual
     111.19  120.17   -8.98 3.00e+00 1.11e-01 8.96e+00
  angle pdb=" CAQ Y01 A 704 "
        pdb=" CBG Y01 A 704 "
        pdb=" CBD Y01 A 704 "
      ideal   model   delta    sigma   weight residual
     118.56  127.14   -8.58 3.00e+00 1.11e-01 8.18e+00
  ... (remaining 8591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.71: 3594
       22.71 -    45.42: 73
       45.42 -    68.13: 12
       68.13 -    90.84: 12
       90.84 -   113.55: 6
  Dihedral angle restraints: 3697
    sinusoidal: 1497
      harmonic: 2200
  Sorted by residual:
  dihedral pdb=" CA  GLU C  47 "
           pdb=" C   GLU C  47 "
           pdb=" N   SER C  48 "
           pdb=" CA  SER C  48 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   27.72  -27.72     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" C1  NAG D   2 "
           pdb=" C2  NAG D   2 "
           pdb=" C3  NAG D   2 "
           pdb=" O3  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -61.54 -113.55     1      3.00e+01 1.11e-03 1.49e+01
  dihedral pdb=" N2  NAG D   2 "
           pdb=" C2  NAG D   2 "
           pdb=" C3  NAG D   2 "
           pdb=" O3  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.25  174.86 -112.61     1      3.00e+01 1.11e-03 1.48e+01
  ... (remaining 3694 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.317: 949
       0.317 -    0.633: 1
       0.633 -    0.950: 2
       0.950 -    1.267: 0
       1.267 -    1.584: 1
  Chirality restraints: 953
  Sorted by residual:
  chirality pdb=" CBD Y01 A 704 "
            pdb=" CAK Y01 A 704 "
            pdb=" CBF Y01 A 704 "
            pdb=" CBG Y01 A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70    1.11    1.58 2.00e-01 2.50e+01 6.27e+01
  chirality pdb=" CBG Y01 A 704 "
            pdb=" CAQ Y01 A 704 "
            pdb=" CBD Y01 A 704 "
            pdb=" CBI Y01 A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -1.63   -0.71 2.00e-01 2.50e+01 1.25e+01
  chirality pdb=" CBI Y01 A 704 "
            pdb=" CAU Y01 A 704 "
            pdb=" CBE Y01 A 704 "
            pdb=" CBG Y01 A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94    2.27    0.66 2.00e-01 2.50e+01 1.10e+01
  ... (remaining 950 not shown)

  Planarity restraints: 1051
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" O   HJM A 703 "   -0.163 2.00e-02 2.50e+03   1.03e-01 3.16e+02
        pdb=" C11 HJM A 703 "    0.031 2.00e-02 2.50e+03
        pdb=" C12 HJM A 703 "    0.149 2.00e-02 2.50e+03
        pdb=" C13 HJM A 703 "    0.070 2.00e-02 2.50e+03
        pdb=" C15 HJM A 703 "    0.075 2.00e-02 2.50e+03
        pdb=" C16 HJM A 703 "   -0.004 2.00e-02 2.50e+03
        pdb=" C17 HJM A 703 "    0.065 2.00e-02 2.50e+03
        pdb=" C18 HJM A 703 "   -0.011 2.00e-02 2.50e+03
        pdb=" C19 HJM A 703 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2  HJM A 703 "   -0.229 2.00e-02 2.50e+03
        pdb=" C8  HJM A 703 "   -0.057 2.00e-02 2.50e+03
        pdb=" N2  HJM A 703 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 417 "   -0.033 5.00e-02 4.00e+02   5.07e-02 4.12e+00
        pdb=" N   PRO A 418 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 418 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 418 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 155 "   -0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO A 156 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 156 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 156 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1048 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 66
        2.65 -     3.21: 5806
        3.21 -     3.78: 8553
        3.78 -     4.34: 12529
        4.34 -     4.90: 19883
  Nonbonded interactions: 46837
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 145 "
            pdb=" OG  SER A 149 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" O   MET A 260 "
            pdb=" OG1 THR A 264 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" O   SER B  49 "
            pdb=" OH  TYR B  71 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" OG1 THR A 221 "
            pdb=" OG  SER A 224 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" O   LEU A 478 "
            pdb=" OG1 THR A 482 "
     model   vdw
     2.140 3.040
  ... (remaining 46832 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             4.070
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.630
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6501
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      :  0.013   0.519   6312  Z= 0.634
  Angle     :  0.709  11.748   8608  Z= 0.335
  Chirality :  0.075   1.584    953
  Planarity :  0.005   0.103   1050
  Dihedral  : 12.108 113.546   2292
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -4.08 (0.25), residues: 759
  helix: -3.53 (0.16), residues: 283
  sheet: -3.51 (0.51), residues: 73
  loop : -1.83 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 144 
 TYR   0.007   0.001   TYR A 134 
 PHE   0.009   0.001   PHE A 474 
 TRP   0.008   0.001   TRP A 537 
 HIS   0.002   0.001   HIS A 456 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01273 /  0.63 ( 6307)
  covalent geometry    : angle       0.70457 /  0.33 ( 8596)
  SS BOND              : bond        0.00205 /  0.10 (    3)
  SS BOND              : angle       0.56803 /  0.29 (    6)
  hydrogen bonds       : bond        0.33104 / 22.22 (  222)
  hydrogen bonds       : angle       9.76081 /  6.97 (  618)
  link_BETA1-4         : bond        0.00217 /  0.11 (    1)
  link_BETA1-4         : angle       3.70605 /  2.01 (    3)
  link_NAG-ASN         : bond        0.01958 /  1.03 (    1)
  link_NAG-ASN         : angle       2.62600 /  1.34 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 TYR cc_start: 0.8800 (t80) cc_final: 0.8580 (t80)
REVERT: A  157 ILE cc_start: 0.8426 (tt) cc_final: 0.8217 (mt)
REVERT: A  186 TYR cc_start: 0.6988 (m-10) cc_final: 0.6758 (m-10)
REVERT: A  253 TRP cc_start: 0.8190 (p-90) cc_final: 0.6784 (m100)
REVERT: A  260 MET cc_start: 0.7397 (mmp) cc_final: 0.6648 (ttt)
REVERT: A  332 GLN cc_start: 0.7369 (tm-30) cc_final: 0.7157 (tm-30)
REVERT: A  414 ILE cc_start: 0.6104 (mm) cc_final: 0.5796 (mt)
REVERT: A  495 TYR cc_start: 0.6069 (m-80) cc_final: 0.5795 (m-80)
REVERT: A  558 MET cc_start: 0.8408 (mtm) cc_final: 0.8103 (tpt)
REVERT: A  595 TYR cc_start: 0.7234 (m-10) cc_final: 0.6888 (m-80)
REVERT: A  605 LYS cc_start: 0.8264 (tttt) cc_final: 0.7654 (pttt)
REVERT: B   42 LYS cc_start: 0.8891 (tptt) cc_final: 0.8023 (tppt)
REVERT: B   47 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7840 (ttp-110)
REVERT: B   83 PHE cc_start: 0.7752 (m-80) cc_final: 0.7186 (m-10)
REVERT: B  101 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8038 (tp40)
REVERT: B  120 TYR cc_start: 0.5376 (m-80) cc_final: 0.4344 (m-80)
REVERT: C   71 LEU cc_start: 0.8342 (mt) cc_final: 0.8064 (mm)
REVERT: C   78 GLN cc_start: 0.7165 (mt0) cc_final: 0.6911 (mm-40)
REVERT: C  118 VAL cc_start: 0.8148 (t) cc_final: 0.7820 (p)
REVERT: C  130 ILE cc_start: 0.8802 (mt) cc_final: 0.8399 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.0931
  time to fit residues: 34.1731
Evaluate side-chains
  150 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.145800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.126576 restraints weight = 20426.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.130186 restraints weight = 13515.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.132753 restraints weight = 9710.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.134613 restraints weight = 7392.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.136021 restraints weight = 5895.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   6312  Z= 0.178
  Angle     :  0.703   9.549   8608  Z= 0.356
  Chirality :  0.046   0.226    953
  Planarity :  0.005   0.034   1050
  Dihedral  : 11.414  85.501    982
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.56 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -2.63 (0.28), residues: 759
  helix: -1.35 (0.26), residues: 324
  sheet: -2.66 (0.54), residues: 69
  loop : -1.84 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 117 
 TYR   0.016   0.002   TYR A 410 
 PHE   0.039   0.002   PHE A 287 
 TRP   0.024   0.002   TRP C 120 
 HIS   0.004   0.001   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.18 ( 6307)
  covalent geometry    : angle       0.69481 /  0.35 ( 8596)
  SS BOND              : bond        0.00253 /  0.13 (    3)
  SS BOND              : angle       0.99054 /  0.53 (    6)
  hydrogen bonds       : bond        0.06179 /  3.98 (  222)
  hydrogen bonds       : angle       6.21072 /  4.58 (  618)
  link_BETA1-4         : bond        0.00182 /  0.10 (    1)
  link_BETA1-4         : angle       4.10047 /  2.30 (    3)
  link_NAG-ASN         : bond        0.00329 /  0.17 (    1)
  link_NAG-ASN         : angle       3.85644 /  2.24 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8954 (m-30) cc_final: 0.8601 (m-30)
REVERT: A  142 TYR cc_start: 0.7690 (t80) cc_final: 0.7484 (t80)
REVERT: A  158 PHE cc_start: 0.8594 (m-80) cc_final: 0.8014 (m-80)
REVERT: A  260 MET cc_start: 0.7482 (mmp) cc_final: 0.6700 (ttt)
REVERT: A  262 ILE cc_start: 0.8476 (mm) cc_final: 0.8228 (mm)
REVERT: A  332 GLN cc_start: 0.7634 (tm-30) cc_final: 0.6791 (tm-30)
REVERT: A  336 SER cc_start: 0.8816 (t) cc_final: 0.8579 (p)
REVERT: A  454 PHE cc_start: 0.8596 (m-10) cc_final: 0.8292 (m-10)
REVERT: A  461 ARG cc_start: 0.8857 (mtt90) cc_final: 0.8269 (mtt180)
REVERT: A  471 ILE cc_start: 0.8656 (mt) cc_final: 0.8451 (mt)
REVERT: A  547 LEU cc_start: 0.8626 (tp) cc_final: 0.8388 (tp)
REVERT: A  558 MET cc_start: 0.8471 (mtm) cc_final: 0.8248 (tpt)
REVERT: A  595 TYR cc_start: 0.7247 (m-10) cc_final: 0.6842 (m-80)
REVERT: A  605 LYS cc_start: 0.8489 (tttt) cc_final: 0.8216 (tttm)
REVERT: B   42 LYS cc_start: 0.8931 (tptt) cc_final: 0.8415 (tppt)
REVERT: B   59 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7368 (ttt180)
REVERT: B   83 PHE cc_start: 0.7659 (m-80) cc_final: 0.7405 (m-10)
REVERT: B   88 THR cc_start: 0.8099 (p) cc_final: 0.7293 (p)
REVERT: B  114 PHE cc_start: 0.7657 (m-80) cc_final: 0.7320 (m-80)
REVERT: B  120 TYR cc_start: 0.6213 (m-80) cc_final: 0.5916 (m-10)
REVERT: B  127 MET cc_start: 0.8644 (mmm) cc_final: 0.8349 (mmp)
REVERT: B  130 TRP cc_start: 0.8115 (m100) cc_final: 0.7612 (m100)
REVERT: C  105 ASP cc_start: 0.8391 (m-30) cc_final: 0.8119 (m-30)
REVERT: C  127 LYS cc_start: 0.8438 (mppt) cc_final: 0.7956 (mppt)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0820
  time to fit residues: 21.3874
Evaluate side-chains
  145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0870
   chunk 14 optimal weight:   10.0000
   overall best weight:    1.9162

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 177 ASN
A 316 ASN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.142153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.123337 restraints weight = 20319.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.126696 restraints weight = 13608.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.129056 restraints weight = 9833.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.130784 restraints weight = 7611.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.132090 restraints weight = 6105.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.5372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6312  Z= 0.147
  Angle     :  0.620   9.434   8608  Z= 0.310
  Chirality :  0.043   0.220    953
  Planarity :  0.005   0.040   1050
  Dihedral  :  9.532  72.158    982
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.84 (0.29), residues: 759
  helix: -0.47 (0.27), residues: 330
  sheet: -2.12 (0.53), residues: 74
  loop : -1.69 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 462 
 TYR   0.016   0.001   TYR A 110 
 PHE   0.033   0.002   PHE A 423 
 TRP   0.017   0.001   TRP C 120 
 HIS   0.003   0.001   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 ( 6307)
  covalent geometry    : angle       0.61315 /  0.31 ( 8596)
  SS BOND              : bond        0.00344 /  0.17 (    3)
  SS BOND              : angle       0.88385 /  0.41 (    6)
  hydrogen bonds       : bond        0.04813 /  3.16 (  222)
  hydrogen bonds       : angle       5.50939 /  4.16 (  618)
  link_BETA1-4         : bond        0.00769 /  0.40 (    1)
  link_BETA1-4         : angle       4.25049 /  2.34 (    3)
  link_NAG-ASN         : bond        0.00410 /  0.22 (    1)
  link_NAG-ASN         : angle       2.76445 /  1.50 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8837 (m-30) cc_final: 0.8362 (m-30)
REVERT: A  112 ASN cc_start: 0.8945 (m-40) cc_final: 0.8738 (m110)
REVERT: A  126 ILE cc_start: 0.6805 (tp) cc_final: 0.6586 (tp)
REVERT: A  158 PHE cc_start: 0.8671 (m-80) cc_final: 0.8132 (m-80)
REVERT: A  253 TRP cc_start: 0.8269 (p-90) cc_final: 0.7965 (p-90)
REVERT: A  260 MET cc_start: 0.7361 (mmp) cc_final: 0.6473 (ttp)
REVERT: A  290 ILE cc_start: 0.8432 (mm) cc_final: 0.8126 (mt)
REVERT: A  332 GLN cc_start: 0.7690 (tm-30) cc_final: 0.6951 (tm-30)
REVERT: A  461 ARG cc_start: 0.8848 (mtt90) cc_final: 0.8387 (mtt180)
REVERT: A  547 LEU cc_start: 0.8645 (tp) cc_final: 0.8417 (tp)
REVERT: A  558 MET cc_start: 0.8377 (mtm) cc_final: 0.8177 (tpt)
REVERT: A  595 TYR cc_start: 0.7083 (m-10) cc_final: 0.6716 (m-80)
REVERT: A  605 LYS cc_start: 0.8481 (tttt) cc_final: 0.8225 (tttm)
REVERT: B   71 TYR cc_start: 0.7082 (t80) cc_final: 0.6802 (t80)
REVERT: B   83 PHE cc_start: 0.8183 (m-80) cc_final: 0.7482 (m-10)
REVERT: B   88 THR cc_start: 0.8111 (p) cc_final: 0.7598 (p)
REVERT: B  114 PHE cc_start: 0.7675 (m-80) cc_final: 0.7360 (m-80)
REVERT: B  120 TYR cc_start: 0.6536 (m-80) cc_final: 0.6051 (m-80)
REVERT: B  130 TRP cc_start: 0.8066 (m100) cc_final: 0.7687 (m100)
REVERT: C  105 ASP cc_start: 0.8309 (m-30) cc_final: 0.7768 (m-30)
REVERT: C  127 LYS cc_start: 0.8523 (mppt) cc_final: 0.7967 (mppt)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0756
  time to fit residues: 19.0988
Evaluate side-chains
  145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 100 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 = 0.4284 r_free = 0.4284 target = 0.143616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.124899 restraints weight = 20408.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.128260 restraints weight = 13743.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.130666 restraints weight = 9949.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.132488 restraints weight = 7614.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.133808 restraints weight = 6067.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.5630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6312  Z= 0.124
  Angle     :  0.598   9.525   8608  Z= 0.297
  Chirality :  0.043   0.204    953
  Planarity :  0.004   0.044   1050
  Dihedral  :  8.958  70.027    982
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.34 (0.30), residues: 759
  helix:  0.03 (0.28), residues: 328
  sheet: -1.74 (0.55), residues: 74
  loop : -1.54 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 462 
 TYR   0.014   0.001   TYR A 410 
 PHE   0.022   0.002   PHE A 423 
 TRP   0.020   0.001   TRP B  55 
 HIS   0.002   0.000   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 6307)
  covalent geometry    : angle       0.59036 /  0.30 ( 8596)
  SS BOND              : bond        0.00143 /  0.07 (    3)
  SS BOND              : angle       0.89597 /  0.43 (    6)
  hydrogen bonds       : bond        0.04154 /  2.72 (  222)
  hydrogen bonds       : angle       5.17730 /  3.90 (  618)
  link_BETA1-4         : bond        0.00877 /  0.46 (    1)
  link_BETA1-4         : angle       4.64186 /  2.56 (    3)
  link_NAG-ASN         : bond        0.00338 /  0.18 (    1)
  link_NAG-ASN         : angle       1.94638 /  1.01 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8759 (m-30) cc_final: 0.8240 (m-30)
REVERT: A  112 ASN cc_start: 0.9023 (m-40) cc_final: 0.8707 (m110)
REVERT: A  158 PHE cc_start: 0.8639 (m-80) cc_final: 0.8114 (m-80)
REVERT: A  253 TRP cc_start: 0.8217 (p-90) cc_final: 0.7917 (p-90)
REVERT: A  260 MET cc_start: 0.7116 (mmp) cc_final: 0.6210 (ttp)
REVERT: A  290 ILE cc_start: 0.8479 (mm) cc_final: 0.8190 (mt)
REVERT: A  291 ILE cc_start: 0.8869 (mp) cc_final: 0.8606 (mp)
REVERT: A  332 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7246 (tm-30)
REVERT: A  461 ARG cc_start: 0.8845 (mtt90) cc_final: 0.8288 (mtt180)
REVERT: A  544 ILE cc_start: 0.8305 (mm) cc_final: 0.7027 (mm)
REVERT: A  547 LEU cc_start: 0.8594 (tp) cc_final: 0.8374 (tp)
REVERT: A  595 TYR cc_start: 0.7072 (m-10) cc_final: 0.6630 (m-80)
REVERT: A  605 LYS cc_start: 0.8406 (tttt) cc_final: 0.8157 (tttm)
REVERT: B   42 LYS cc_start: 0.8902 (tptt) cc_final: 0.8379 (tppt)
REVERT: B   59 ARG cc_start: 0.7911 (ttt180) cc_final: 0.7425 (ttm170)
REVERT: B   83 PHE cc_start: 0.7947 (m-80) cc_final: 0.7216 (m-10)
REVERT: B   88 THR cc_start: 0.7878 (p) cc_final: 0.7573 (p)
REVERT: B  114 PHE cc_start: 0.7475 (m-80) cc_final: 0.7200 (m-80)
REVERT: B  120 TYR cc_start: 0.6644 (m-80) cc_final: 0.6034 (m-80)
REVERT: B  130 TRP cc_start: 0.8098 (m100) cc_final: 0.7767 (m100)
REVERT: C   54 ILE cc_start: 0.8662 (mm) cc_final: 0.8412 (tp)
REVERT: C  105 ASP cc_start: 0.8063 (m-30) cc_final: 0.7841 (m-30)
REVERT: C  127 LYS cc_start: 0.8523 (mppt) cc_final: 0.7945 (mppt)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0875
  time to fit residues: 20.5216
Evaluate side-chains
  150 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0670
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 55 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    3.4124

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

Flipped N/Q/H residues before XYZ refinement:
A 254 GLN
B  25 GLN
** C 100 HIS ** 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 = 0.4150 r_free = 0.4150 target = 0.132919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.115286 restraints weight = 21765.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.118440 restraints weight = 14400.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.120682 restraints weight = 10394.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.122296 restraints weight = 7966.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.123532 restraints weight = 6426.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.6482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6312  Z= 0.184
  Angle     :  0.685   9.465   8608  Z= 0.344
  Chirality :  0.045   0.219    953
  Planarity :  0.005   0.046   1050
  Dihedral  :  9.171  71.173    982
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.24 (0.30), residues: 759
  helix:  0.16 (0.28), residues: 324
  sheet: -1.20 (0.60), residues: 80
  loop : -1.64 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 464 
 TYR   0.021   0.002   TYR C  73 
 PHE   0.017   0.002   PHE A 423 
 TRP   0.015   0.002   TRP B  55 
 HIS   0.002   0.001   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.18 ( 6307)
  covalent geometry    : angle       0.67734 /  0.34 ( 8596)
  SS BOND              : bond        0.00335 /  0.17 (    3)
  SS BOND              : angle       1.27770 /  0.63 (    6)
  hydrogen bonds       : bond        0.04128 /  2.72 (  222)
  hydrogen bonds       : angle       5.26143 /  3.99 (  618)
  link_BETA1-4         : bond        0.00423 /  0.22 (    1)
  link_BETA1-4         : angle       5.12288 /  2.84 (    3)
  link_NAG-ASN         : bond        0.00375 /  0.20 (    1)
  link_NAG-ASN         : angle       1.48041 /  0.76 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 TRP cc_start: 0.7095 (m-10) cc_final: 0.6831 (m-10)
REVERT: A  112 ASN cc_start: 0.9137 (m-40) cc_final: 0.8857 (m110)
REVERT: A  134 TYR cc_start: 0.9144 (t80) cc_final: 0.8755 (t80)
REVERT: A  158 PHE cc_start: 0.8746 (m-80) cc_final: 0.8230 (m-10)
REVERT: A  230 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8453 (mm-30)
REVERT: A  260 MET cc_start: 0.7181 (mmp) cc_final: 0.6253 (ttp)
REVERT: A  332 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7126 (tm-30)
REVERT: A  461 ARG cc_start: 0.8842 (mtt90) cc_final: 0.8283 (mtt180)
REVERT: A  508 GLU cc_start: 0.8692 (pt0) cc_final: 0.8462 (pt0)
REVERT: A  595 TYR cc_start: 0.7305 (m-10) cc_final: 0.6804 (m-80)
REVERT: A  605 LYS cc_start: 0.8575 (tttt) cc_final: 0.8361 (tttm)
REVERT: A  606 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8941 (mm-30)
REVERT: B   42 LYS cc_start: 0.8823 (tptt) cc_final: 0.8217 (tppt)
REVERT: B   59 ARG cc_start: 0.8229 (ttt180) cc_final: 0.8014 (ttt180)
REVERT: B   83 PHE cc_start: 0.8217 (m-80) cc_final: 0.7386 (m-10)
REVERT: B  120 TYR cc_start: 0.6559 (m-80) cc_final: 0.5925 (m-80)
REVERT: C   54 ILE cc_start: 0.8721 (mm) cc_final: 0.8477 (tp)
REVERT: C  105 ASP cc_start: 0.8079 (m-30) cc_final: 0.7839 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0763
  time to fit residues: 18.1014
Evaluate side-chains
  134 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0870
   chunk 70 optimal weight:   20.0000
   chunk 73 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8164

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

Flipped N/Q/H residues before XYZ refinement:
B  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.137993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.119262 restraints weight = 19704.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.122659 restraints weight = 12718.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.125075 restraints weight = 9073.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.126890 restraints weight = 6908.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.128205 restraints weight = 5471.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.6672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6312  Z= 0.120
  Angle     :  0.606   9.521   8608  Z= 0.304
  Chirality :  0.043   0.213    953
  Planarity :  0.004   0.036   1050
  Dihedral  :  8.746  69.831    982
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -0.86 (0.30), residues: 759
  helix:  0.41 (0.28), residues: 327
  sheet: -0.88 (0.59), residues: 81
  loop : -1.41 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 523 
 TYR   0.013   0.001   TYR C  73 
 PHE   0.021   0.002   PHE A 380 
 TRP   0.014   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 6307)
  covalent geometry    : angle       0.59778 /  0.30 ( 8596)
  SS BOND              : bond        0.00292 /  0.15 (    3)
  SS BOND              : angle       1.03897 /  0.53 (    6)
  hydrogen bonds       : bond        0.03607 /  2.39 (  222)
  hydrogen bonds       : angle       4.96298 /  3.77 (  618)
  link_BETA1-4         : bond        0.00710 /  0.37 (    1)
  link_BETA1-4         : angle       4.95435 /  2.74 (    3)
  link_NAG-ASN         : bond        0.00421 /  0.22 (    1)
  link_NAG-ASN         : angle       1.59704 /  0.80 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 ASN cc_start: 0.9033 (m-40) cc_final: 0.8743 (m110)
REVERT: A  134 TYR cc_start: 0.9162 (t80) cc_final: 0.8703 (t80)
REVERT: A  158 PHE cc_start: 0.8755 (m-80) cc_final: 0.8284 (m-10)
REVERT: A  230 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8435 (mm-30)
REVERT: A  237 LEU cc_start: 0.8736 (tp) cc_final: 0.8527 (tp)
REVERT: A  260 MET cc_start: 0.7067 (mmp) cc_final: 0.6260 (ttp)
REVERT: A  332 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7252 (tm-30)
REVERT: A  461 ARG cc_start: 0.8759 (mtt90) cc_final: 0.8243 (mtt180)
REVERT: A  544 ILE cc_start: 0.8238 (mm) cc_final: 0.7005 (mm)
REVERT: A  595 TYR cc_start: 0.7150 (m-10) cc_final: 0.6672 (m-80)
REVERT: A  605 LYS cc_start: 0.8504 (tttt) cc_final: 0.8285 (tttm)
REVERT: A  606 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8865 (mm-30)
REVERT: B   42 LYS cc_start: 0.8781 (tptt) cc_final: 0.8251 (tppt)
REVERT: B   53 MET cc_start: 0.7681 (tpp) cc_final: 0.7219 (tpp)
REVERT: B   59 ARG cc_start: 0.8189 (ttt180) cc_final: 0.7612 (ttm170)
REVERT: B   83 PHE cc_start: 0.8065 (m-80) cc_final: 0.7270 (m-10)
REVERT: B  120 TYR cc_start: 0.6616 (m-80) cc_final: 0.6106 (m-80)
REVERT: C   54 ILE cc_start: 0.8677 (mm) cc_final: 0.8439 (tp)
REVERT: C  105 ASP cc_start: 0.8081 (m-30) cc_final: 0.7854 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0765
  time to fit residues: 17.6664
Evaluate side-chains
  150 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0270
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    4.0046

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 205 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.128081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.109493 restraints weight = 20191.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.112798 restraints weight = 13038.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.115173 restraints weight = 9243.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.116948 restraints weight = 6994.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.118220 restraints weight = 5559.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.7455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6312  Z= 0.218
  Angle     :  0.735   9.481   8608  Z= 0.371
  Chirality :  0.046   0.215    953
  Planarity :  0.005   0.038   1050
  Dihedral  :  9.007  71.247    982
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.40 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.11 (0.30), residues: 759
  helix:  0.16 (0.28), residues: 325
  sheet: -0.69 (0.59), residues: 79
  loop : -1.60 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 464 
 TYR   0.023   0.002   TYR C  73 
 PHE   0.022   0.002   PHE A 263 
 TRP   0.024   0.002   TRP B  55 
 HIS   0.003   0.001   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00471 /  0.22 ( 6307)
  covalent geometry    : angle       0.72820 /  0.37 ( 8596)
  SS BOND              : bond        0.00581 /  0.29 (    3)
  SS BOND              : angle       1.65002 /  0.86 (    6)
  hydrogen bonds       : bond        0.04147 /  2.78 (  222)
  hydrogen bonds       : angle       5.36630 /  4.00 (  618)
  link_BETA1-4         : bond        0.00881 /  0.46 (    1)
  link_BETA1-4         : angle       4.82010 /  2.71 (    3)
  link_NAG-ASN         : bond        0.00509 /  0.27 (    1)
  link_NAG-ASN         : angle       1.57781 /  0.79 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 ASN cc_start: 0.9209 (m-40) cc_final: 0.8959 (m110)
REVERT: A  134 TYR cc_start: 0.9257 (t80) cc_final: 0.9046 (t80)
REVERT: A  158 PHE cc_start: 0.8823 (m-80) cc_final: 0.8439 (m-10)
REVERT: A  230 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8528 (mm-30)
REVERT: A  237 LEU cc_start: 0.8780 (tp) cc_final: 0.8536 (tp)
REVERT: A  260 MET cc_start: 0.6998 (mmp) cc_final: 0.6094 (ttp)
REVERT: A  392 GLU cc_start: 0.8594 (tp30) cc_final: 0.8056 (tp30)
REVERT: A  396 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7847 (mp0)
REVERT: A  429 LEU cc_start: 0.8693 (mt) cc_final: 0.8479 (mt)
REVERT: A  461 ARG cc_start: 0.8902 (mtt90) cc_final: 0.8357 (mtt180)
REVERT: A  465 PHE cc_start: 0.8774 (t80) cc_final: 0.8551 (t80)
REVERT: A  528 MET cc_start: 0.8470 (mpp) cc_final: 0.8261 (mpp)
REVERT: A  547 LEU cc_start: 0.8719 (tp) cc_final: 0.8488 (tp)
REVERT: A  548 PHE cc_start: 0.7460 (m-10) cc_final: 0.7243 (m-10)
REVERT: A  595 TYR cc_start: 0.7441 (m-10) cc_final: 0.6801 (m-80)
REVERT: A  606 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9017 (mm-30)
REVERT: B   42 LYS cc_start: 0.8784 (tptt) cc_final: 0.8213 (tppt)
REVERT: B   59 ARG cc_start: 0.8435 (ttt180) cc_final: 0.8197 (ttt180)
REVERT: B   65 GLU cc_start: 0.8868 (tp30) cc_final: 0.8660 (tp30)
REVERT: B   83 PHE cc_start: 0.8279 (m-80) cc_final: 0.7427 (m-10)
REVERT: B  120 TYR cc_start: 0.6745 (m-80) cc_final: 0.6071 (m-80)
REVERT: C   44 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7974 (tpp-160)
REVERT: C   54 ILE cc_start: 0.8730 (mm) cc_final: 0.8492 (tp)
REVERT: C  105 ASP cc_start: 0.8052 (m-30) cc_final: 0.7779 (m-30)
REVERT: C  107 THR cc_start: 0.8421 (p) cc_final: 0.8059 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0875
  time to fit residues: 19.7843
Evaluate side-chains
  138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    0.4980
   chunk 60 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 520 GLN
B  25 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.132183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.114015 restraints weight = 20069.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.117380 restraints weight = 12738.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.119740 restraints weight = 8965.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.121463 restraints weight = 6766.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.122693 restraints weight = 5370.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.7475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6312  Z= 0.126
  Angle     :  0.626   9.635   8608  Z= 0.313
  Chirality :  0.043   0.203    953
  Planarity :  0.004   0.038   1050
  Dihedral  :  8.695  70.947    982
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -0.83 (0.30), residues: 759
  helix:  0.31 (0.28), residues: 340
  sheet: -0.24 (0.62), residues: 78
  loop : -1.50 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 464 
 TYR   0.013   0.001   TYR A 385 
 PHE   0.018   0.002   PHE A 380 
 TRP   0.009   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 6307)
  covalent geometry    : angle       0.61782 /  0.31 ( 8596)
  SS BOND              : bond        0.00419 /  0.21 (    3)
  SS BOND              : angle       1.36270 /  0.70 (    6)
  hydrogen bonds       : bond        0.03701 /  2.45 (  222)
  hydrogen bonds       : angle       5.03908 /  3.77 (  618)
  link_BETA1-4         : bond        0.00694 /  0.37 (    1)
  link_BETA1-4         : angle       4.75399 /  2.65 (    3)
  link_NAG-ASN         : bond        0.00363 /  0.19 (    1)
  link_NAG-ASN         : angle       1.62887 /  0.82 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 TRP cc_start: 0.7073 (m-10) cc_final: 0.6666 (m-10)
REVERT: A  112 ASN cc_start: 0.9118 (m110) cc_final: 0.8911 (m110)
REVERT: A  134 TYR cc_start: 0.9221 (t80) cc_final: 0.8935 (t80)
REVERT: A  158 PHE cc_start: 0.8782 (m-80) cc_final: 0.8416 (m-10)
REVERT: A  237 LEU cc_start: 0.8761 (tp) cc_final: 0.8506 (tp)
REVERT: A  253 TRP cc_start: 0.8060 (p-90) cc_final: 0.7838 (p-90)
REVERT: A  260 MET cc_start: 0.6920 (mmp) cc_final: 0.6132 (ttp)
REVERT: A  429 LEU cc_start: 0.8672 (mt) cc_final: 0.8375 (mt)
REVERT: A  595 TYR cc_start: 0.7195 (m-10) cc_final: 0.6676 (m-80)
REVERT: A  606 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8935 (mm-30)
REVERT: B   42 LYS cc_start: 0.8755 (tptt) cc_final: 0.8213 (tppt)
REVERT: B   53 MET cc_start: 0.7867 (tpp) cc_final: 0.7485 (tpp)
REVERT: B   59 ARG cc_start: 0.8393 (ttt180) cc_final: 0.8113 (ttt180)
REVERT: B   65 GLU cc_start: 0.8831 (tp30) cc_final: 0.8587 (tp30)
REVERT: B   83 PHE cc_start: 0.8158 (m-80) cc_final: 0.7298 (m-10)
REVERT: B  114 PHE cc_start: 0.7426 (m-80) cc_final: 0.7019 (m-80)
REVERT: B  120 TYR cc_start: 0.6752 (m-80) cc_final: 0.6110 (m-80)
REVERT: B  130 TRP cc_start: 0.8577 (m100) cc_final: 0.7912 (m100)
REVERT: C   44 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.7752 (tpp-160)
REVERT: C   54 ILE cc_start: 0.8702 (mm) cc_final: 0.8492 (tp)
REVERT: C  105 ASP cc_start: 0.8090 (m-30) cc_final: 0.7814 (m-30)
REVERT: C  107 THR cc_start: 0.8275 (p) cc_final: 0.7849 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0792
  time to fit residues: 18.0418
Evaluate side-chains
  145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 45 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   overall best weight:    3.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN
** C 114 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 = 0.4084 r_free = 0.4084 target = 0.127059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.109384 restraints weight = 20569.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.112642 restraints weight = 12949.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.114927 restraints weight = 9102.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.116596 restraints weight = 6909.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.117782 restraints weight = 5479.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.7883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   6312  Z= 0.195
  Angle     :  0.744  17.013   8608  Z= 0.366
  Chirality :  0.046   0.207    953
  Planarity :  0.005   0.071   1050
  Dihedral  :  8.883  71.276    982
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -1.00 (0.31), residues: 759
  helix:  0.12 (0.28), residues: 335
  sheet: -0.01 (0.64), residues: 78
  loop : -1.60 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  85 
 TYR   0.017   0.002   TYR C  73 
 PHE   0.019   0.002   PHE A 380 
 TRP   0.017   0.002   TRP B  55 
 HIS   0.004   0.001   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.19 ( 6307)
  covalent geometry    : angle       0.73831 /  0.36 ( 8596)
  SS BOND              : bond        0.00436 /  0.22 (    3)
  SS BOND              : angle       1.23911 /  0.64 (    6)
  hydrogen bonds       : bond        0.04071 /  2.67 (  222)
  hydrogen bonds       : angle       5.30327 /  3.89 (  618)
  link_BETA1-4         : bond        0.00531 /  0.28 (    1)
  link_BETA1-4         : angle       4.69242 /  2.63 (    3)
  link_NAG-ASN         : bond        0.00443 /  0.23 (    1)
  link_NAG-ASN         : angle       1.69274 /  0.85 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 TRP cc_start: 0.7137 (m-10) cc_final: 0.6728 (m-10)
REVERT: A  112 ASN cc_start: 0.9177 (m110) cc_final: 0.8950 (m110)
REVERT: A  134 TYR cc_start: 0.9185 (t80) cc_final: 0.8765 (t80)
REVERT: A  158 PHE cc_start: 0.8776 (m-80) cc_final: 0.8576 (m-10)
REVERT: A  237 LEU cc_start: 0.8824 (tp) cc_final: 0.8555 (tp)
REVERT: A  253 TRP cc_start: 0.8114 (p-90) cc_final: 0.7884 (p-90)
REVERT: A  260 MET cc_start: 0.7111 (mmp) cc_final: 0.6260 (ttp)
REVERT: A  429 LEU cc_start: 0.8666 (mt) cc_final: 0.8415 (mt)
REVERT: A  461 ARG cc_start: 0.8832 (mtt90) cc_final: 0.8285 (mtt180)
REVERT: A  528 MET cc_start: 0.8453 (mpp) cc_final: 0.8175 (mpp)
REVERT: A  537 TRP cc_start: 0.7834 (m-90) cc_final: 0.7625 (m-90)
REVERT: A  548 PHE cc_start: 0.7373 (m-10) cc_final: 0.7114 (m-10)
REVERT: A  606 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8955 (mm-30)
REVERT: B   42 LYS cc_start: 0.8825 (tptt) cc_final: 0.8275 (tppt)
REVERT: B   59 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8210 (ttt180)
REVERT: B   83 PHE cc_start: 0.8296 (m-80) cc_final: 0.7384 (m-10)
REVERT: B  114 PHE cc_start: 0.7425 (m-80) cc_final: 0.6936 (m-80)
REVERT: B  120 TYR cc_start: 0.6697 (m-80) cc_final: 0.6025 (m-80)
REVERT: B  130 TRP cc_start: 0.8675 (m100) cc_final: 0.7849 (m100)
REVERT: C   54 ILE cc_start: 0.8725 (mm) cc_final: 0.8505 (tp)
REVERT: C  107 THR cc_start: 0.8366 (p) cc_final: 0.8025 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0767
  time to fit residues: 16.8269
Evaluate side-chains
  136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 ASN
B  25 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.127898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.110553 restraints weight = 21245.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.113758 restraints weight = 13751.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.115936 restraints weight = 9816.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.117589 restraints weight = 7482.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.118759 restraints weight = 5953.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.8103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6312  Z= 0.154
  Angle     :  0.708  15.780   8608  Z= 0.346
  Chirality :  0.045   0.203    953
  Planarity :  0.005   0.067   1050
  Dihedral  :  8.765  70.032    982
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -0.88 (0.31), residues: 759
  helix:  0.19 (0.28), residues: 337
  sheet:  0.17 (0.68), residues: 71
  loop : -1.51 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  85 
 TYR   0.014   0.001   TYR A 410 
 PHE   0.018   0.002   PHE A 380 
 TRP   0.017   0.002   TRP B  55 
 HIS   0.003   0.001   HIS A 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 ( 6307)
  covalent geometry    : angle       0.70052 /  0.34 ( 8596)
  SS BOND              : bond        0.00484 /  0.24 (    3)
  SS BOND              : angle       1.41853 /  0.75 (    6)
  hydrogen bonds       : bond        0.03845 /  2.51 (  222)
  hydrogen bonds       : angle       5.10112 /  3.78 (  618)
  link_BETA1-4         : bond        0.00732 /  0.39 (    1)
  link_BETA1-4         : angle       4.69462 /  2.63 (    3)
  link_NAG-ASN         : bond        0.00422 /  0.22 (    1)
  link_NAG-ASN         : angle       2.05521 /  1.04 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 TRP cc_start: 0.7105 (m-10) cc_final: 0.6709 (m-10)
REVERT: A  112 ASN cc_start: 0.9199 (m110) cc_final: 0.8984 (m110)
REVERT: A  134 TYR cc_start: 0.9194 (t80) cc_final: 0.8659 (t80)
REVERT: A  237 LEU cc_start: 0.8831 (tp) cc_final: 0.8547 (tp)
REVERT: A  253 TRP cc_start: 0.8083 (p-90) cc_final: 0.7852 (p-90)
REVERT: A  260 MET cc_start: 0.7120 (mmp) cc_final: 0.6228 (ttp)
REVERT: A  289 TYR cc_start: 0.8275 (t80) cc_final: 0.8024 (t80)
REVERT: A  396 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7622 (mp0)
REVERT: A  429 LEU cc_start: 0.8685 (mt) cc_final: 0.8451 (mt)
REVERT: A  461 ARG cc_start: 0.8767 (mtt90) cc_final: 0.8146 (mtt180)
REVERT: A  528 MET cc_start: 0.8420 (mpp) cc_final: 0.8131 (mpp)
REVERT: A  537 TRP cc_start: 0.7901 (m-90) cc_final: 0.7524 (m-90)
REVERT: A  547 LEU cc_start: 0.8692 (tp) cc_final: 0.8487 (tp)
REVERT: A  548 PHE cc_start: 0.7360 (m-10) cc_final: 0.7130 (m-10)
REVERT: A  595 TYR cc_start: 0.7214 (m-10) cc_final: 0.6710 (m-80)
REVERT: A  606 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8963 (mm-30)
REVERT: B   42 LYS cc_start: 0.8785 (tptt) cc_final: 0.8249 (tppt)
REVERT: B   53 MET cc_start: 0.7944 (tpp) cc_final: 0.7327 (tmm)
REVERT: B   59 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8146 (ttt180)
REVERT: B   65 GLU cc_start: 0.8750 (tp30) cc_final: 0.8335 (tt0)
REVERT: B   83 PHE cc_start: 0.8229 (m-80) cc_final: 0.7608 (m-80)
REVERT: B  114 PHE cc_start: 0.7589 (m-80) cc_final: 0.7067 (m-80)
REVERT: B  120 TYR cc_start: 0.6870 (m-80) cc_final: 0.6247 (m-80)
REVERT: B  127 MET cc_start: 0.8443 (tpt) cc_final: 0.7993 (tpp)
REVERT: B  130 TRP cc_start: 0.8805 (m100) cc_final: 0.8090 (m100)
REVERT: C   54 ILE cc_start: 0.8685 (mm) cc_final: 0.8479 (tp)
REVERT: C  107 THR cc_start: 0.8439 (p) cc_final: 0.8126 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0843
  time to fit residues: 19.3762
Evaluate side-chains
  141 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0970
   chunk 27 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 46 optimal weight:    3.9990
   chunk 62 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.131131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.113773 restraints weight = 20941.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.117063 restraints weight = 13627.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.119384 restraints weight = 9681.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.121038 restraints weight = 7320.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.122239 restraints weight = 5832.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.8206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6312  Z= 0.123
  Angle     :  0.654  11.052   8608  Z= 0.324
  Chirality :  0.043   0.202    953
  Planarity :  0.005   0.061   1050
  Dihedral  :  8.530  68.260    982
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    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: -0.70 (0.31), residues: 759
  helix:  0.41 (0.28), residues: 336
  sheet:  0.13 (0.67), residues: 71
  loop : -1.44 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  85 
 TYR   0.022   0.001   TYR B  46 
 PHE   0.016   0.002   PHE A 380 
 TRP   0.021   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 6307)
  covalent geometry    : angle       0.64664 /  0.32 ( 8596)
  SS BOND              : bond        0.00184 /  0.09 (    3)
  SS BOND              : angle       0.88420 /  0.43 (    6)
  hydrogen bonds       : bond        0.03660 /  2.40 (  222)
  hydrogen bonds       : angle       5.00215 /  3.65 (  618)
  link_BETA1-4         : bond        0.00573 /  0.30 (    1)
  link_BETA1-4         : angle       4.81521 /  2.68 (    3)
  link_NAG-ASN         : bond        0.00444 /  0.23 (    1)
  link_NAG-ASN         : angle       1.80836 /  0.91 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1340.77 seconds
wall clock time: 23 minutes 49.70 seconds (1429.70 seconds total)