Starting phenix.real_space_refine
on Sun Apr 27 18:54:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dzv_8940/04_2025/6dzv_8940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dzv_8940/04_2025/6dzv_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_8940/04_2025/6dzv_8940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dzv_8940/04_2025/6dzv_8940.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dzv_8940/04_2025/6dzv_8940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dzv_8940/04_2025/6dzv_8940.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.65, per 1000 atoms: 0.76
  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: 1.51
  Conformation dependent library (CDL) restraints added in 866.7 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: 0.62
  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: 1.56

  Time building geometry restraints manager: 1.80 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:             2.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.510
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.650
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.008   0.001   TRP A 537 
 HIS   0.002   0.001   HIS A 456 
 PHE   0.009   0.001   PHE A 474 
 TYR   0.007   0.001   TYR A 134 
 ARG   0.003   0.001   ARG A 144 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01958 (    1)
  link_NAG-ASN         : angle       2.62600 (    3)
  link_BETA1-4         : bond        0.00217 (    1)
  link_BETA1-4         : angle       3.70605 (    3)
  hydrogen bonds       : bond        0.33104 (  222)
  hydrogen bonds       : angle       9.76081 (  618)
  SS BOND              : bond        0.00205 (    3)
  SS BOND              : angle       0.56803 (    6)
  covalent geometry    : bond        0.01273 ( 6307)
  covalent geometry    : angle       0.70457 ( 8596)

*********************** 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  : 0.720 
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: 0.7156 (tm-30)
REVERT: A  414 ILE cc_start: 0.6103 (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: 0.6887 (m-80)
REVERT: A  605 LYS cc_start: 0.8264 (tttt) cc_final: 0.7654 (pttt)
REVERT: B   42 LYS cc_start: 0.8890 (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: 0.7751 (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: 0.8398 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.2039
  time to fit residues: 74.5408
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  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 GLN
A 520 GLN
B  24 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.141266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.122140 restraints weight = 20023.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.125517 restraints weight = 13438.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.128008 restraints weight = 9749.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.4762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083   6312  Z= 0.207
  Angle     :  0.746   9.400   8608  Z= 0.380
  Chirality :  0.046   0.211    953
  Planarity :  0.005   0.039   1050
  Dihedral  : 11.197  83.087    982
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.71 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.28), residues: 759
  helix: -1.27 (0.25), residues: 327
  sheet: -2.62 (0.50), residues: 74
  loop : -1.78 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  66 
 HIS   0.004   0.001   HIS A 240 
 PHE   0.039   0.002   PHE A 287 
 TYR   0.019   0.002   TYR C  73 
 ARG   0.005   0.001   ARG B 117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00248 (    1)
  link_NAG-ASN         : angle       3.63437 (    3)
  link_BETA1-4         : bond        0.00000 (    1)
  link_BETA1-4         : angle       4.22773 (    3)
  hydrogen bonds       : bond        0.05952 (  222)
  hydrogen bonds       : angle       6.21022 (  618)
  SS BOND              : bond        0.00269 (    3)
  SS BOND              : angle       1.52078 (    6)
  covalent geometry    : bond        0.00450 ( 6307)
  covalent geometry    : angle       0.73852 ( 8596)

*********************** 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
  209 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 207
  time to evaluate  : 0.688 
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: 0.8956 (m-30) cc_final: 0.8534 (m-30)
REVERT: A  142 TYR cc_start: 0.7979 (t80) cc_final: 0.7735 (t80)
REVERT: A  158 PHE cc_start: 0.8642 (m-80) cc_final: 0.8035 (m-80)
REVERT: A  260 MET cc_start: 0.7510 (mmp) cc_final: 0.6751 (ttt)
REVERT: A  262 ILE cc_start: 0.8489 (mm) cc_final: 0.8248 (mm)
REVERT: A  332 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7040 (tm-30)
REVERT: A  370 MET cc_start: 0.8282 (tmm) cc_final: 0.8069 (tmm)
REVERT: A  414 ILE cc_start: 0.6826 (mm) cc_final: 0.6304 (mm)
REVERT: A  454 PHE cc_start: 0.8643 (m-10) cc_final: 0.8303 (m-10)
REVERT: A  461 ARG cc_start: 0.8883 (mtt90) cc_final: 0.8310 (mtt180)
REVERT: A  547 LEU cc_start: 0.8660 (tp) cc_final: 0.8422 (tp)
REVERT: A  558 MET cc_start: 0.8394 (mtm) cc_final: 0.8188 (tpt)
REVERT: A  595 TYR cc_start: 0.7243 (m-10) cc_final: 0.6833 (m-80)
REVERT: A  605 LYS cc_start: 0.8485 (tttt) cc_final: 0.8233 (tttm)
REVERT: B   42 LYS cc_start: 0.8980 (tptt) cc_final: 0.8472 (tppt)
REVERT: B   83 PHE cc_start: 0.7793 (m-80) cc_final: 0.7258 (m-10)
REVERT: B   88 THR cc_start: 0.8157 (p) cc_final: 0.7904 (p)
REVERT: B  120 TYR cc_start: 0.6404 (m-80) cc_final: 0.6125 (m-10)
REVERT: B  127 MET cc_start: 0.8593 (mmm) cc_final: 0.8346 (mmp)
REVERT: C   70 LEU cc_start: 0.8371 (mt) cc_final: 0.8125 (mt)
REVERT: C  105 ASP cc_start: 0.8383 (m-30) cc_final: 0.7840 (m-30)
REVERT: C  107 THR cc_start: 0.8622 (m) cc_final: 0.8373 (p)
REVERT: C  127 LYS cc_start: 0.8605 (mppt) cc_final: 0.8050 (mppt)
  outliers start: 2
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1903
  time to fit residues: 51.2464
Evaluate side-chains
  142 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 47 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 ASN
A 177 ASN
A 316 ASN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.143179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.123980 restraints weight = 19938.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.127359 restraints weight = 13281.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.129800 restraints weight = 9659.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.5341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6312  Z= 0.131
  Angle     :  0.608   9.460   8608  Z= 0.303
  Chirality :  0.043   0.218    953
  Planarity :  0.005   0.039   1050
  Dihedral  :  9.490  72.077    982
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.29), residues: 759
  helix: -0.46 (0.27), residues: 325
  sheet: -2.30 (0.51), residues: 75
  loop : -1.67 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 120 
 HIS   0.002   0.000   HIS A 240 
 PHE   0.033   0.002   PHE A 423 
 TYR   0.012   0.001   TYR A 410 
 ARG   0.006   0.001   ARG A 462 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00343 (    1)
  link_NAG-ASN         : angle       2.77668 (    3)
  link_BETA1-4         : bond        0.00807 (    1)
  link_BETA1-4         : angle       4.36052 (    3)
  hydrogen bonds       : bond        0.04824 (  222)
  hydrogen bonds       : angle       5.51263 (  618)
  SS BOND              : bond        0.00405 (    3)
  SS BOND              : angle       0.73735 (    6)
  covalent geometry    : bond        0.00279 ( 6307)
  covalent geometry    : angle       0.60036 ( 8596)

*********************** 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
  190 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.698 
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: A   87 ASP cc_start: 0.8782 (m-30) cc_final: 0.8290 (m-30)
REVERT: A  158 PHE cc_start: 0.8700 (m-80) cc_final: 0.8134 (m-80)
REVERT: A  253 TRP cc_start: 0.8294 (p-90) cc_final: 0.7992 (p-90)
REVERT: A  260 MET cc_start: 0.7405 (mmp) cc_final: 0.6541 (ttp)
REVERT: A  332 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7133 (tm-30)
REVERT: A  461 ARG cc_start: 0.8828 (mtt90) cc_final: 0.8370 (mtt180)
REVERT: A  547 LEU cc_start: 0.8685 (tp) cc_final: 0.8471 (tp)
REVERT: A  595 TYR cc_start: 0.6984 (m-10) cc_final: 0.6646 (m-80)
REVERT: A  605 LYS cc_start: 0.8474 (tttt) cc_final: 0.8229 (tttm)
REVERT: B   42 LYS cc_start: 0.9004 (tptt) cc_final: 0.8472 (tppt)
REVERT: B   71 TYR cc_start: 0.7198 (t80) cc_final: 0.6896 (t80)
REVERT: B   83 PHE cc_start: 0.7889 (m-80) cc_final: 0.7544 (m-10)
REVERT: B   88 THR cc_start: 0.8102 (p) cc_final: 0.7832 (p)
REVERT: B  120 TYR cc_start: 0.6517 (m-80) cc_final: 0.6097 (m-10)
REVERT: C   54 ILE cc_start: 0.8668 (mm) cc_final: 0.8461 (tp)
REVERT: C  105 ASP cc_start: 0.8063 (m-30) cc_final: 0.7824 (m-30)
REVERT: C  127 LYS cc_start: 0.8546 (mppt) cc_final: 0.7984 (mppt)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1954
  time to fit residues: 47.6208
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  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 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 = 0.4204 r_free = 0.4204 target = 0.137269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.119502 restraints weight = 21676.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.122732 restraints weight = 14180.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.125072 restraints weight = 10190.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.5981

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= 0.159
  Angle     :  0.632   9.337   8608  Z= 0.314
  Chirality :  0.043   0.209    953
  Planarity :  0.005   0.050   1050
  Dihedral  :  9.139  70.945    982
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.30), residues: 759
  helix:  0.19 (0.28), residues: 315
  sheet: -1.82 (0.54), residues: 80
  loop : -1.51 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 240 
 PHE   0.021   0.002   PHE A 105 
 TYR   0.019   0.002   TYR A 410 
 ARG   0.005   0.001   ARG A 462 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00413 (    1)
  link_NAG-ASN         : angle       1.70956 (    3)
  link_BETA1-4         : bond        0.00936 (    1)
  link_BETA1-4         : angle       4.81046 (    3)
  hydrogen bonds       : bond        0.04146 (  222)
  hydrogen bonds       : angle       5.17798 (  618)
  SS BOND              : bond        0.00512 (    3)
  SS BOND              : angle       1.71391 (    6)
  covalent geometry    : bond        0.00347 ( 6307)
  covalent geometry    : angle       0.62319 ( 8596)

*********************** 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
  185 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.633 
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: 0.9007 (m110) cc_final: 0.8631 (m110)
REVERT: A  158 PHE cc_start: 0.8753 (m-80) cc_final: 0.8206 (m-10)
REVERT: A  260 MET cc_start: 0.7421 (mmp) cc_final: 0.6652 (ttp)
REVERT: A  332 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7170 (tm-30)
REVERT: A  461 ARG cc_start: 0.8909 (mtt90) cc_final: 0.8368 (mtt180)
REVERT: A  508 GLU cc_start: 0.8754 (pt0) cc_final: 0.8533 (pt0)
REVERT: A  547 LEU cc_start: 0.8715 (tp) cc_final: 0.8509 (tp)
REVERT: A  595 TYR cc_start: 0.7240 (m-10) cc_final: 0.6828 (m-80)
REVERT: A  606 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8902 (mm-30)
REVERT: B   42 LYS cc_start: 0.9005 (tptt) cc_final: 0.8500 (tppt)
REVERT: B   59 ARG cc_start: 0.8177 (ttt180) cc_final: 0.7644 (ttm170)
REVERT: B   71 TYR cc_start: 0.7382 (t80) cc_final: 0.6912 (t80)
REVERT: B   83 PHE cc_start: 0.8317 (m-80) cc_final: 0.7577 (m-10)
REVERT: B   88 THR cc_start: 0.8210 (p) cc_final: 0.7923 (p)
REVERT: B  120 TYR cc_start: 0.6785 (m-80) cc_final: 0.6238 (m-80)
REVERT: C   54 ILE cc_start: 0.8707 (mm) cc_final: 0.8464 (tp)
REVERT: C  105 ASP cc_start: 0.8108 (m-30) cc_final: 0.7861 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1971
  time to fit residues: 46.9595
Evaluate side-chains
  137 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 254 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.130834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.113035 restraints weight = 20896.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.116431 restraints weight = 13582.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.118803 restraints weight = 9610.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.6698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6312  Z= 0.188
  Angle     :  0.668   9.310   8608  Z= 0.340
  Chirality :  0.044   0.220    953
  Planarity :  0.005   0.039   1050
  Dihedral  :  9.199  72.419    982
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.30), residues: 759
  helix:  0.13 (0.27), residues: 324
  sheet: -1.36 (0.58), residues: 81
  loop : -1.51 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 197 
 HIS   0.004   0.001   HIS A 240 
 PHE   0.019   0.002   PHE A 380 
 TYR   0.020   0.002   TYR C  73 
 ARG   0.010   0.001   ARG A 464 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00411 (    1)
  link_NAG-ASN         : angle       1.75820 (    3)
  link_BETA1-4         : bond        0.00598 (    1)
  link_BETA1-4         : angle       4.96303 (    3)
  hydrogen bonds       : bond        0.04105 (  222)
  hydrogen bonds       : angle       5.26692 (  618)
  SS BOND              : bond        0.00648 (    3)
  SS BOND              : angle       1.20836 (    6)
  covalent geometry    : bond        0.00411 ( 6307)
  covalent geometry    : angle       0.66061 ( 8596)

*********************** 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
  175 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.704 
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: 0.9076 (m110) cc_final: 0.8838 (m110)
REVERT: A  158 PHE cc_start: 0.8819 (m-80) cc_final: 0.8370 (m-10)
REVERT: A  237 LEU cc_start: 0.8758 (tp) cc_final: 0.8553 (tp)
REVERT: A  260 MET cc_start: 0.7414 (mmp) cc_final: 0.6742 (ttp)
REVERT: A  370 MET cc_start: 0.8127 (tmm) cc_final: 0.7829 (tmm)
REVERT: A  461 ARG cc_start: 0.8864 (mtt90) cc_final: 0.8315 (mtt180)
REVERT: A  495 TYR cc_start: 0.6935 (m-80) cc_final: 0.6524 (m-80)
REVERT: A  508 GLU cc_start: 0.8727 (pt0) cc_final: 0.8480 (pt0)
REVERT: A  528 MET cc_start: 0.8439 (mpp) cc_final: 0.8187 (mpp)
REVERT: A  595 TYR cc_start: 0.7433 (m-10) cc_final: 0.6772 (m-80)
REVERT: A  606 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8979 (mm-30)
REVERT: B   42 LYS cc_start: 0.8891 (tptt) cc_final: 0.8433 (tppt)
REVERT: B   59 ARG cc_start: 0.8366 (ttt180) cc_final: 0.7998 (ttt180)
REVERT: B   71 TYR cc_start: 0.7333 (t80) cc_final: 0.7009 (t80)
REVERT: B   83 PHE cc_start: 0.8268 (m-80) cc_final: 0.7528 (m-10)
REVERT: B  120 TYR cc_start: 0.6860 (m-80) cc_final: 0.6362 (m-80)
REVERT: B  127 MET cc_start: 0.9018 (mmp) cc_final: 0.8565 (mmp)
REVERT: C   54 ILE cc_start: 0.8750 (mm) cc_final: 0.8518 (tp)
REVERT: C  105 ASP cc_start: 0.8131 (m-30) cc_final: 0.7890 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1981
  time to fit residues: 44.4934
Evaluate side-chains
  139 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 23 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0870
   chunk 41 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.3162

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
** B  25 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 = 0.4162 r_free = 0.4162 target = 0.135059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.116807 restraints weight = 20093.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.120253 restraints weight = 12878.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.122632 restraints weight = 9053.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.6851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6312  Z= 0.126
  Angle     :  0.607   9.542   8608  Z= 0.304
  Chirality :  0.042   0.208    953
  Planarity :  0.005   0.039   1050
  Dihedral  :  8.782  71.537    982
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.31), residues: 759
  helix:  0.53 (0.28), residues: 325
  sheet: -1.09 (0.58), residues: 81
  loop : -1.37 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A 537 
 HIS   0.002   0.001   HIS A 240 
 PHE   0.019   0.002   PHE A 380 
 TYR   0.013   0.001   TYR C  73 
 ARG   0.007   0.001   ARG A 464 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00483 (    1)
  link_NAG-ASN         : angle       1.67554 (    3)
  link_BETA1-4         : bond        0.00738 (    1)
  link_BETA1-4         : angle       4.84417 (    3)
  hydrogen bonds       : bond        0.03683 (  222)
  hydrogen bonds       : angle       4.93605 (  618)
  SS BOND              : bond        0.00405 (    3)
  SS BOND              : angle       1.11203 (    6)
  covalent geometry    : bond        0.00284 ( 6307)
  covalent geometry    : angle       0.59879 ( 8596)

*********************** 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
  178 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.636 
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  134 TYR cc_start: 0.9227 (t80) cc_final: 0.8933 (t80)
REVERT: A  158 PHE cc_start: 0.8819 (m-80) cc_final: 0.8320 (m-10)
REVERT: A  230 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8472 (mm-30)
REVERT: A  237 LEU cc_start: 0.8778 (tp) cc_final: 0.8550 (tp)
REVERT: A  251 ILE cc_start: 0.7064 (mm) cc_final: 0.6557 (tp)
REVERT: A  260 MET cc_start: 0.7375 (mmp) cc_final: 0.6607 (ttp)
REVERT: A  332 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7540 (tm-30)
REVERT: A  461 ARG cc_start: 0.8810 (mtt90) cc_final: 0.8293 (mtt180)
REVERT: A  465 PHE cc_start: 0.8727 (t80) cc_final: 0.8526 (t80)
REVERT: A  508 GLU cc_start: 0.8691 (pt0) cc_final: 0.8337 (pt0)
REVERT: A  528 MET cc_start: 0.8447 (mpp) cc_final: 0.8186 (mpp)
REVERT: A  547 LEU cc_start: 0.8732 (tp) cc_final: 0.8528 (tp)
REVERT: A  592 TYR cc_start: 0.6171 (m-80) cc_final: 0.5866 (m-80)
REVERT: A  595 TYR cc_start: 0.7171 (m-10) cc_final: 0.6714 (m-80)
REVERT: A  606 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8915 (mm-30)
REVERT: B   42 LYS cc_start: 0.8895 (tptt) cc_final: 0.8448 (tppt)
REVERT: B   59 ARG cc_start: 0.8293 (ttt180) cc_final: 0.7896 (ttt180)
REVERT: B   71 TYR cc_start: 0.7233 (t80) cc_final: 0.6955 (t80)
REVERT: B   83 PHE cc_start: 0.8173 (m-80) cc_final: 0.7399 (m-10)
REVERT: B  120 TYR cc_start: 0.6942 (m-80) cc_final: 0.6490 (m-80)
REVERT: B  127 MET cc_start: 0.9001 (mmp) cc_final: 0.8641 (mmp)
REVERT: B  130 TRP cc_start: 0.8450 (m100) cc_final: 0.7858 (m100)
REVERT: C  105 ASP cc_start: 0.8094 (m-30) cc_final: 0.7869 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1909
  time to fit residues: 43.6042
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  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0670
   chunk 23 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0370
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.4202

-------------------------------------------------------------------------------
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 ** 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 = 0.4157 r_free = 0.4157 target = 0.134814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.116570 restraints weight = 20410.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.120023 restraints weight = 13176.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.122414 restraints weight = 9307.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.7037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6312  Z= 0.128
  Angle     :  0.622   9.536   8608  Z= 0.307
  Chirality :  0.044   0.247    953
  Planarity :  0.004   0.042   1050
  Dihedral  :  8.660  71.186    982
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.31), residues: 759
  helix:  0.43 (0.28), residues: 330
  sheet: -0.78 (0.59), residues: 79
  loop : -1.34 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 537 
 HIS   0.002   0.001   HIS A 235 
 PHE   0.016   0.002   PHE A 380 
 TYR   0.014   0.001   TYR C  73 
 ARG   0.006   0.001   ARG A 464 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00489 (    1)
  link_NAG-ASN         : angle       1.48453 (    3)
  link_BETA1-4         : bond        0.00821 (    1)
  link_BETA1-4         : angle       4.80046 (    3)
  hydrogen bonds       : bond        0.03649 (  222)
  hydrogen bonds       : angle       4.89738 (  618)
  SS BOND              : bond        0.00361 (    3)
  SS BOND              : angle       1.04468 (    6)
  covalent geometry    : bond        0.00290 ( 6307)
  covalent geometry    : angle       0.61432 ( 8596)

*********************** 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
  172 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.805 
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  121 TYR cc_start: 0.7481 (t80) cc_final: 0.7253 (t80)
REVERT: A  158 PHE cc_start: 0.8775 (m-80) cc_final: 0.8302 (m-10)
REVERT: A  230 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8502 (mm-30)
REVERT: A  237 LEU cc_start: 0.8794 (tp) cc_final: 0.8560 (tp)
REVERT: A  251 ILE cc_start: 0.7048 (mm) cc_final: 0.6566 (tp)
REVERT: A  260 MET cc_start: 0.7314 (mmp) cc_final: 0.6594 (ttp)
REVERT: A  332 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7195 (tm-30)
REVERT: A  461 ARG cc_start: 0.8815 (mtt90) cc_final: 0.8229 (mtt180)
REVERT: A  528 MET cc_start: 0.8441 (mpp) cc_final: 0.8209 (mmm)
REVERT: A  595 TYR cc_start: 0.7137 (m-10) cc_final: 0.6637 (m-80)
REVERT: A  606 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8917 (mm-30)
REVERT: B   42 LYS cc_start: 0.8914 (tptt) cc_final: 0.8464 (tppt)
REVERT: B   59 ARG cc_start: 0.8313 (ttt180) cc_final: 0.8091 (ttt180)
REVERT: B   71 TYR cc_start: 0.7203 (t80) cc_final: 0.6964 (t80)
REVERT: B   83 PHE cc_start: 0.8145 (m-80) cc_final: 0.7193 (m-10)
REVERT: B  120 TYR cc_start: 0.7034 (m-80) cc_final: 0.6564 (m-80)
REVERT: B  127 MET cc_start: 0.8970 (mmp) cc_final: 0.8611 (mmp)
REVERT: B  130 TRP cc_start: 0.8369 (m100) cc_final: 0.7887 (m100)
REVERT: C  105 ASP cc_start: 0.8109 (m-30) cc_final: 0.7887 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1936
  time to fit residues: 43.1634
Evaluate side-chains
  143 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 68 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0980
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    1.8188

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
** B  25 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 = 0.4135 r_free = 0.4135 target = 0.132889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.114701 restraints weight = 20147.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.118086 restraints weight = 12937.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.120482 restraints weight = 9117.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.7259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6312  Z= 0.130
  Angle     :  0.623   9.427   8608  Z= 0.311
  Chirality :  0.044   0.247    953
  Planarity :  0.004   0.040   1050
  Dihedral  :  8.574  70.795    982
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.31), residues: 759
  helix:  0.42 (0.28), residues: 331
  sheet: -0.62 (0.60), residues: 79
  loop : -1.29 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  55 
 HIS   0.002   0.001   HIS A 235 
 PHE   0.016   0.001   PHE A 380 
 TYR   0.013   0.001   TYR A 410 
 ARG   0.005   0.001   ARG A 464 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00486 (    1)
  link_NAG-ASN         : angle       1.48985 (    3)
  link_BETA1-4         : bond        0.00726 (    1)
  link_BETA1-4         : angle       4.75613 (    3)
  hydrogen bonds       : bond        0.03628 (  222)
  hydrogen bonds       : angle       4.81461 (  618)
  SS BOND              : bond        0.00322 (    3)
  SS BOND              : angle       1.03285 (    6)
  covalent geometry    : bond        0.00294 ( 6307)
  covalent geometry    : angle       0.61548 ( 8596)

*********************** 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
  173 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.768 
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  121 TYR cc_start: 0.7522 (t80) cc_final: 0.7241 (t80)
REVERT: A  158 PHE cc_start: 0.8799 (m-80) cc_final: 0.8374 (m-10)
REVERT: A  237 LEU cc_start: 0.8736 (tp) cc_final: 0.8496 (tp)
REVERT: A  251 ILE cc_start: 0.7136 (mm) cc_final: 0.6677 (tp)
REVERT: A  260 MET cc_start: 0.7313 (mmp) cc_final: 0.6551 (ttp)
REVERT: A  332 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: A  392 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6539 (tm-30)
REVERT: A  396 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7819 (mp0)
REVERT: A  461 ARG cc_start: 0.8829 (mtt90) cc_final: 0.8180 (mtt180)
REVERT: A  528 MET cc_start: 0.8347 (mpp) cc_final: 0.8013 (mmm)
REVERT: A  548 PHE cc_start: 0.7403 (m-10) cc_final: 0.7183 (m-10)
REVERT: A  606 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8939 (mm-30)
REVERT: B   42 LYS cc_start: 0.8923 (tptt) cc_final: 0.8493 (tppt)
REVERT: B   59 ARG cc_start: 0.8423 (ttt180) cc_final: 0.8176 (ttt180)
REVERT: B   65 GLU cc_start: 0.8875 (tp30) cc_final: 0.8629 (tp30)
REVERT: B   83 PHE cc_start: 0.8136 (m-80) cc_final: 0.7328 (m-10)
REVERT: B   84 LYS cc_start: 0.8655 (mppt) cc_final: 0.8270 (mmtm)
REVERT: B  120 TYR cc_start: 0.7056 (m-80) cc_final: 0.6587 (m-80)
REVERT: B  130 TRP cc_start: 0.8471 (m100) cc_final: 0.7861 (m100)
REVERT: C  105 ASP cc_start: 0.8135 (m-30) cc_final: 0.7882 (m-30)
REVERT: C  107 THR cc_start: 0.8264 (p) cc_final: 0.7954 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1985
  time to fit residues: 44.9344
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  : 0.616 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0670
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 66 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.6126

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
B  25 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.129869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.111935 restraints weight = 20645.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.115293 restraints weight = 13221.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.117678 restraints weight = 9267.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.7685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6312  Z= 0.154
  Angle     :  0.648   9.305   8608  Z= 0.325
  Chirality :  0.045   0.237    953
  Planarity :  0.005   0.036   1050
  Dihedral  :  8.628  70.361    982
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.31), residues: 759
  helix:  0.47 (0.28), residues: 336
  sheet: -0.33 (0.61), residues: 79
  loop : -1.38 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 537 
 HIS   0.003   0.001   HIS A 456 
 PHE   0.027   0.002   PHE A 263 
 TYR   0.015   0.001   TYR A 410 
 ARG   0.007   0.001   ARG A 464 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00458 (    1)
  link_NAG-ASN         : angle       1.61434 (    3)
  link_BETA1-4         : bond        0.00827 (    1)
  link_BETA1-4         : angle       4.67384 (    3)
  hydrogen bonds       : bond        0.03800 (  222)
  hydrogen bonds       : angle       4.87661 (  618)
  SS BOND              : bond        0.00446 (    3)
  SS BOND              : angle       1.08358 (    6)
  covalent geometry    : bond        0.00342 ( 6307)
  covalent geometry    : angle       0.64132 ( 8596)

*********************** 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
  170 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.745 
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  112 ASN cc_start: 0.9117 (m110) cc_final: 0.8870 (m110)
REVERT: A  121 TYR cc_start: 0.7556 (t80) cc_final: 0.7298 (t80)
REVERT: A  158 PHE cc_start: 0.8791 (m-80) cc_final: 0.8488 (m-10)
REVERT: A  237 LEU cc_start: 0.8804 (tp) cc_final: 0.8542 (tp)
REVERT: A  260 MET cc_start: 0.7104 (mmp) cc_final: 0.6277 (ttp)
REVERT: A  289 TYR cc_start: 0.8409 (t80) cc_final: 0.8069 (t80)
REVERT: A  332 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7188 (tm-30)
REVERT: A  392 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6704 (tm-30)
REVERT: A  461 ARG cc_start: 0.8849 (mtt90) cc_final: 0.8227 (mtt180)
REVERT: A  495 TYR cc_start: 0.6922 (m-80) cc_final: 0.6456 (m-80)
REVERT: A  528 MET cc_start: 0.8312 (mpp) cc_final: 0.8008 (mmm)
REVERT: A  548 PHE cc_start: 0.7419 (m-10) cc_final: 0.7170 (m-10)
REVERT: A  595 TYR cc_start: 0.7282 (m-10) cc_final: 0.6762 (m-80)
REVERT: A  606 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8948 (mm-30)
REVERT: B   42 LYS cc_start: 0.8892 (tptt) cc_final: 0.8437 (tppt)
REVERT: B   59 ARG cc_start: 0.8455 (ttt180) cc_final: 0.8203 (ttt180)
REVERT: B   65 GLU cc_start: 0.8910 (tp30) cc_final: 0.8631 (tp30)
REVERT: B   83 PHE cc_start: 0.8185 (m-80) cc_final: 0.7327 (m-10)
REVERT: B  120 TYR cc_start: 0.7073 (m-80) cc_final: 0.6565 (m-80)
REVERT: B  127 MET cc_start: 0.8991 (mmp) cc_final: 0.8459 (mmp)
REVERT: B  130 TRP cc_start: 0.8630 (m100) cc_final: 0.7928 (m100)
REVERT: C  107 THR cc_start: 0.8432 (p) cc_final: 0.8119 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2411
  time to fit residues: 53.1376
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  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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**
B  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.133877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.115881 restraints weight = 20777.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.119295 restraints weight = 13364.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.121680 restraints weight = 9394.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.7710

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= 0.118
  Angle     :  0.630  11.715   8608  Z= 0.313
  Chirality :  0.043   0.204    953
  Planarity :  0.004   0.040   1050
  Dihedral  :  8.401  68.462    982
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.31), residues: 759
  helix:  0.68 (0.28), residues: 328
  sheet: -0.24 (0.64), residues: 73
  loop : -1.27 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 235 
 PHE   0.017   0.001   PHE C  95 
 TYR   0.012   0.001   TYR C  94 
 ARG   0.005   0.001   ARG C  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00492 (    1)
  link_NAG-ASN         : angle       1.66692 (    3)
  link_BETA1-4         : bond        0.00701 (    1)
  link_BETA1-4         : angle       4.78150 (    3)
  hydrogen bonds       : bond        0.03435 (  222)
  hydrogen bonds       : angle       4.73748 (  618)
  SS BOND              : bond        0.00552 (    3)
  SS BOND              : angle       1.33487 (    6)
  covalent geometry    : bond        0.00263 ( 6307)
  covalent geometry    : angle       0.62237 ( 8596)

********************** 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
  167 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.738 
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  112 ASN cc_start: 0.9071 (m110) cc_final: 0.8853 (m110)
REVERT: A  121 TYR cc_start: 0.7573 (t80) cc_final: 0.7281 (t80)
REVERT: A  158 PHE cc_start: 0.8708 (m-80) cc_final: 0.8415 (m-10)
REVERT: A  237 LEU cc_start: 0.8852 (tp) cc_final: 0.8572 (tp)
REVERT: A  260 MET cc_start: 0.7118 (mmp) cc_final: 0.6314 (ttp)
REVERT: A  332 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: A  370 MET cc_start: 0.8840 (tpp) cc_final: 0.8361 (mtt)
REVERT: A  430 MET cc_start: 0.8012 (ttm) cc_final: 0.7739 (mtm)
REVERT: A  461 ARG cc_start: 0.8727 (mtt90) cc_final: 0.8170 (mtt180)
REVERT: A  528 MET cc_start: 0.8266 (mpp) cc_final: 0.7970 (mmm)
REVERT: A  595 TYR cc_start: 0.7034 (m-10) cc_final: 0.6602 (m-80)
REVERT: B   42 LYS cc_start: 0.8902 (tptt) cc_final: 0.8462 (tppt)
REVERT: B   53 MET cc_start: 0.7644 (tpp) cc_final: 0.7211 (mmm)
REVERT: B   59 ARG cc_start: 0.8410 (ttt180) cc_final: 0.8160 (ttt180)
REVERT: B   65 GLU cc_start: 0.8929 (tp30) cc_final: 0.8611 (tp30)
REVERT: B   83 PHE cc_start: 0.8093 (m-80) cc_final: 0.7272 (m-10)
REVERT: B   84 LYS cc_start: 0.8682 (mppt) cc_final: 0.8454 (mmtm)
REVERT: B  120 TYR cc_start: 0.7086 (m-80) cc_final: 0.6683 (m-80)
REVERT: B  127 MET cc_start: 0.9040 (mmp) cc_final: 0.8816 (mmp)
REVERT: B  130 TRP cc_start: 0.8486 (m100) cc_final: 0.7965 (m100)
REVERT: C  107 THR cc_start: 0.8331 (p) cc_final: 0.8002 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2603
  time to fit residues: 56.7060
Evaluate side-chains
  140 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 72 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0020
   chunk 59 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 61 optimal weight:    8.9990
   overall best weight:    3.7994

-------------------------------------------------------------------------------
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**
B  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.125258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.108857 restraints weight = 22569.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.111899 restraints weight = 14605.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.114082 restraints weight = 10334.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.8219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6312  Z= 0.201
  Angle     :  0.737  11.188   8608  Z= 0.372
  Chirality :  0.046   0.204    953
  Planarity :  0.005   0.057   1050
  Dihedral  :  8.807  68.568    982
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.31), residues: 759
  helix:  0.43 (0.28), residues: 346
  sheet: -0.10 (0.65), residues: 72
  loop : -1.68 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 541 
 HIS   0.003   0.001   HIS A 456 
 PHE   0.019   0.002   PHE A 380 
 TYR   0.016   0.002   TYR A 410 
 ARG   0.014   0.001   ARG A 464 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00445 (    1)
  link_NAG-ASN         : angle       1.67236 (    3)
  link_BETA1-4         : bond        0.00621 (    1)
  link_BETA1-4         : angle       4.68207 (    3)
  hydrogen bonds       : bond        0.03825 (  222)
  hydrogen bonds       : angle       5.04325 (  618)
  SS BOND              : bond        0.00672 (    3)
  SS BOND              : angle       1.60334 (    6)
  covalent geometry    : bond        0.00434 ( 6307)
  covalent geometry    : angle       0.72996 ( 8596)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3148.99 seconds
wall clock time: 57 minutes 2.23 seconds (3422.23 seconds total)