Starting phenix.real_space_refine
on Tue Mar 11 17:19:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dzv_8940/03_2025/6dzv_8940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dzv_8940/03_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_8940/03_2025/6dzv_8940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dzv_8940/03_2025/6dzv_8940.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dzv_8940/03_2025/6dzv_8940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dzv_8940/03_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-5624/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: 5.53, per 1000 atoms: 0.90
  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: 1.81
  Conformation dependent library (CDL) restraints added in 939.6 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: 0.67
  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: 1.80

  Time building geometry restraints manager: 2.15 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:             3.420
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     21.030
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.640
-------------------------------------------------------------------------------
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   6307  Z= 0.844
  Angle     :  0.705  11.748   8596  Z= 0.334
  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 

*********************** 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  : 0.724 
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: 0.2162
  time to fit residues: 78.6742
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  : 0.662 
-------------------------------------------------------------------------------
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   6307  Z= 0.286
  Angle     :  0.739   9.400   8596  Z= 0.378
  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 

*********************** 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  : 0.677 
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: 0.1913
  time to fit residues: 51.3490
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  : 0.637 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.4279 r_free = 0.4279 target = 0.144430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.126326 restraints weight = 20860.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.129659 restraints weight = 13885.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.131888 restraints weight = 10071.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.5287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6307  Z= 0.184
  Angle     :  0.607   9.467   8596  Z= 0.303
  Chirality :  0.043   0.218    953
  Planarity :  0.005   0.039   1050
  Dihedral  :  9.562  72.112    982
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  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: -1.88 (0.29), residues: 759
  helix: -0.54 (0.27), residues: 332
  sheet: -2.31 (0.51), residues: 75
  loop : -1.63 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 120 
 HIS   0.002   0.000   HIS A 240 
 PHE   0.029   0.002   PHE A 423 
 TYR   0.012   0.001   TYR A 410 
 ARG   0.005   0.001   ARG A 462 

*********************** 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  : 1.167 
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: symmetry clash
REVERT: A   87 ASP cc_start: 0.8792 (m-30) cc_final: 0.8300 (m-30)
REVERT: A  158 PHE cc_start: 0.8673 (m-80) cc_final: 0.8110 (m-80)
REVERT: A  253 TRP cc_start: 0.8290 (p-90) cc_final: 0.7998 (p-90)
REVERT: A  260 MET cc_start: 0.7356 (mmp) cc_final: 0.6521 (ttt)
REVERT: A  332 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7092 (tm-30)
REVERT: A  461 ARG cc_start: 0.8837 (mtt90) cc_final: 0.8334 (mtt180)
REVERT: A  547 LEU cc_start: 0.8666 (tp) cc_final: 0.8453 (tp)
REVERT: A  595 TYR cc_start: 0.6994 (m-10) cc_final: 0.6644 (m-80)
REVERT: A  605 LYS cc_start: 0.8477 (tttt) cc_final: 0.8226 (tttm)
REVERT: B   71 TYR cc_start: 0.7177 (t80) cc_final: 0.6890 (t80)
REVERT: B   83 PHE cc_start: 0.7842 (m-80) cc_final: 0.7580 (m-10)
REVERT: B   88 THR cc_start: 0.8103 (p) cc_final: 0.7822 (p)
REVERT: B  120 TYR cc_start: 0.6499 (m-80) cc_final: 0.6053 (m-10)
REVERT: C   54 ILE cc_start: 0.8659 (mm) cc_final: 0.8457 (tp)
REVERT: C  105 ASP cc_start: 0.8042 (m-30) cc_final: 0.7810 (m-30)
REVERT: C  127 LYS cc_start: 0.8533 (mppt) cc_final: 0.7982 (mppt)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2045
  time to fit residues: 50.1269
Evaluate side-chains
  147 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0980
   chunk 10 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    3.0186

-------------------------------------------------------------------------------
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 = 0.4161 r_free = 0.4161 target = 0.134666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.116724 restraints weight = 21180.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.119958 restraints weight = 13929.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.122205 restraints weight = 9949.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.6131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6307  Z= 0.255
  Angle     :  0.655   9.330   8596  Z= 0.330
  Chirality :  0.044   0.215    953
  Planarity :  0.005   0.051   1050
  Dihedral  :  9.288  72.082    982
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  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: -1.34 (0.30), residues: 759
  helix:  0.16 (0.28), residues: 312
  sheet: -1.86 (0.53), residues: 80
  loop : -1.57 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  55 
 HIS   0.003   0.001   HIS A 240 
 PHE   0.025   0.002   PHE A 105 
 TYR   0.021   0.002   TYR A 410 
 ARG   0.005   0.001   ARG A 462 

*********************** 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
  188 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.617 
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: symmetry clash
REVERT: A  112 ASN cc_start: 0.8985 (m110) cc_final: 0.8628 (m110)
REVERT: A  158 PHE cc_start: 0.8748 (m-80) cc_final: 0.8214 (m-10)
REVERT: A  260 MET cc_start: 0.7262 (mmp) cc_final: 0.6449 (ttp)
REVERT: A  332 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: A  461 ARG cc_start: 0.8921 (mtt90) cc_final: 0.8401 (mtt180)
REVERT: A  547 LEU cc_start: 0.8708 (tp) cc_final: 0.8504 (tp)
REVERT: A  595 TYR cc_start: 0.7281 (m-10) cc_final: 0.6870 (m-80)
REVERT: A  606 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8877 (mm-30)
REVERT: B   42 LYS cc_start: 0.8806 (tptt) cc_final: 0.8336 (tppt)
REVERT: B   59 ARG cc_start: 0.8226 (ttt180) cc_final: 0.7664 (ttm170)
REVERT: B   71 TYR cc_start: 0.7345 (t80) cc_final: 0.6976 (t80)
REVERT: B   83 PHE cc_start: 0.8412 (m-80) cc_final: 0.7580 (m-10)
REVERT: B   88 THR cc_start: 0.8167 (p) cc_final: 0.7821 (p)
REVERT: B  120 TYR cc_start: 0.6816 (m-80) cc_final: 0.6312 (m-80)
REVERT: C   54 ILE cc_start: 0.8732 (mm) cc_final: 0.8500 (tp)
REVERT: C  105 ASP cc_start: 0.8099 (m-30) cc_final: 0.7896 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1970
  time to fit residues: 47.3166
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  : 0.692 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 72 optimal weight:    0.3980
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.1784

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.138880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.120339 restraints weight = 20203.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.123774 restraints weight = 13206.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.126185 restraints weight = 9370.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.6360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6307  Z= 0.168
  Angle     :  0.581   9.498   8596  Z= 0.293
  Chirality :  0.042   0.211    953
  Planarity :  0.004   0.038   1050
  Dihedral  :  8.860  70.629    982
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  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: -0.97 (0.30), residues: 759
  helix:  0.38 (0.28), residues: 326
  sheet: -1.50 (0.57), residues: 81
  loop : -1.37 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 240 
 PHE   0.021   0.001   PHE A 380 
 TYR   0.014   0.001   TYR C  73 
 ARG   0.007   0.001   ARG A 464 

*********************** 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
  176 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.637 
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  112 ASN cc_start: 0.8946 (m110) cc_final: 0.8667 (m110)
REVERT: A  158 PHE cc_start: 0.8730 (m-80) cc_final: 0.8243 (m-10)
REVERT: A  230 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8481 (mm-30)
REVERT: A  237 LEU cc_start: 0.8690 (tp) cc_final: 0.8486 (tp)
REVERT: A  260 MET cc_start: 0.7148 (mmp) cc_final: 0.6276 (ttp)
REVERT: A  332 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7190 (tm-30)
REVERT: A  461 ARG cc_start: 0.8763 (mtt90) cc_final: 0.8212 (mtt180)
REVERT: A  508 GLU cc_start: 0.8700 (pt0) cc_final: 0.8416 (pt0)
REVERT: A  528 MET cc_start: 0.8365 (mpp) cc_final: 0.8156 (mpp)
REVERT: A  595 TYR cc_start: 0.7328 (m-10) cc_final: 0.6824 (m-80)
REVERT: A  606 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8933 (mm-30)
REVERT: B   42 LYS cc_start: 0.8672 (tptt) cc_final: 0.8179 (tppt)
REVERT: B   59 ARG cc_start: 0.8256 (ttt180) cc_final: 0.7850 (ttm170)
REVERT: B   71 TYR cc_start: 0.7280 (t80) cc_final: 0.6860 (t80)
REVERT: B   83 PHE cc_start: 0.8103 (m-80) cc_final: 0.7381 (m-10)
REVERT: B   88 THR cc_start: 0.8016 (p) cc_final: 0.7788 (p)
REVERT: B  114 PHE cc_start: 0.7150 (m-80) cc_final: 0.6731 (m-10)
REVERT: B  120 TYR cc_start: 0.6820 (m-80) cc_final: 0.6280 (m-80)
REVERT: B  127 MET cc_start: 0.8936 (mmp) cc_final: 0.8554 (mmp)
REVERT: B  130 TRP cc_start: 0.8264 (m100) cc_final: 0.7684 (m100)
REVERT: C  105 ASP cc_start: 0.8182 (m-30) cc_final: 0.7946 (m-30)
REVERT: C  107 THR cc_start: 0.8266 (p) cc_final: 0.7938 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1946
  time to fit residues: 43.9973
Evaluate side-chains
  149 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 52 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 41 optimal weight:    0.4980
   chunk 4 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
A 254 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.135640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.117509 restraints weight = 20326.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.121002 restraints weight = 13057.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.123459 restraints weight = 9130.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.6709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6307  Z= 0.183
  Angle     :  0.593   9.392   8596  Z= 0.298
  Chirality :  0.043   0.209    953
  Planarity :  0.004   0.038   1050
  Dihedral  :  8.699  70.740    982
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  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: -0.80 (0.31), residues: 759
  helix:  0.49 (0.28), residues: 326
  sheet: -1.18 (0.58), residues: 81
  loop : -1.32 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 240 
 PHE   0.017   0.001   PHE A 380 
 TYR   0.015   0.001   TYR A 410 
 ARG   0.004   0.001   ARG A 464 

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

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.702 
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: 0.8969 (m110) cc_final: 0.8695 (m110)
REVERT: A  134 TYR cc_start: 0.9113 (t80) cc_final: 0.8664 (t80)
REVERT: A  158 PHE cc_start: 0.8746 (m-80) cc_final: 0.8244 (m-10)
REVERT: A  230 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8466 (mm-30)
REVERT: A  237 LEU cc_start: 0.8735 (tp) cc_final: 0.8518 (tp)
REVERT: A  260 MET cc_start: 0.7114 (mmp) cc_final: 0.6268 (ttp)
REVERT: A  461 ARG cc_start: 0.8842 (mtt90) cc_final: 0.8192 (mtt180)
REVERT: A  508 GLU cc_start: 0.8702 (pt0) cc_final: 0.8390 (pt0)
REVERT: A  528 MET cc_start: 0.8378 (mpp) cc_final: 0.8163 (mpp)
REVERT: A  592 TYR cc_start: 0.6278 (m-80) cc_final: 0.5745 (m-80)
REVERT: A  595 TYR cc_start: 0.7139 (m-10) cc_final: 0.6682 (m-80)
REVERT: B   42 LYS cc_start: 0.8675 (tptt) cc_final: 0.8114 (tppt)
REVERT: B   59 ARG cc_start: 0.8321 (ttt180) cc_final: 0.7897 (ttm170)
REVERT: B   71 TYR cc_start: 0.7172 (t80) cc_final: 0.6873 (t80)
REVERT: B   83 PHE cc_start: 0.8237 (m-80) cc_final: 0.7483 (m-10)
REVERT: B  114 PHE cc_start: 0.7245 (m-80) cc_final: 0.6673 (m-10)
REVERT: B  120 TYR cc_start: 0.7008 (m-80) cc_final: 0.6530 (m-80)
REVERT: B  130 TRP cc_start: 0.8324 (m100) cc_final: 0.7749 (m100)
REVERT: C  105 ASP cc_start: 0.8112 (m-30) cc_final: 0.7859 (m-30)
REVERT: C  107 THR cc_start: 0.8303 (p) cc_final: 0.8028 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1914
  time to fit residues: 43.4422
Evaluate side-chains
  146 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 59 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
A 177 ASN
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.127650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.110586 restraints weight = 20998.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.113846 restraints weight = 13471.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.116156 restraints weight = 9461.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.7352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6307  Z= 0.273
  Angle     :  0.695   9.628   8596  Z= 0.349
  Chirality :  0.045   0.204    953
  Planarity :  0.005   0.043   1050
  Dihedral  :  8.974  72.389    982
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  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: -0.95 (0.31), residues: 759
  helix:  0.32 (0.28), residues: 331
  sheet: -0.78 (0.60), residues: 80
  loop : -1.50 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  55 
 HIS   0.003   0.001   HIS A 240 
 PHE   0.017   0.002   PHE A 380 
 TYR   0.023   0.002   TYR C  73 
 ARG   0.007   0.001   ARG A 464 

*********************** 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
  176 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.681 
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  112 ASN cc_start: 0.9081 (m110) cc_final: 0.8828 (m110)
REVERT: A  134 TYR cc_start: 0.9236 (t80) cc_final: 0.8993 (t80)
REVERT: A  158 PHE cc_start: 0.8805 (m-80) cc_final: 0.8436 (m-10)
REVERT: A  230 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8533 (mm-30)
REVERT: A  237 LEU cc_start: 0.8773 (tp) cc_final: 0.8525 (tp)
REVERT: A  260 MET cc_start: 0.7270 (mmp) cc_final: 0.6567 (ttp)
REVERT: A  289 TYR cc_start: 0.8349 (t80) cc_final: 0.8019 (t80)
REVERT: A  332 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7186 (tm-30)
REVERT: A  461 ARG cc_start: 0.8895 (mtt90) cc_final: 0.8277 (mtt180)
REVERT: A  495 TYR cc_start: 0.6908 (m-80) cc_final: 0.6487 (m-80)
REVERT: A  508 GLU cc_start: 0.8724 (pt0) cc_final: 0.8476 (pt0)
REVERT: A  528 MET cc_start: 0.8447 (mpp) cc_final: 0.8110 (mmm)
REVERT: A  537 TRP cc_start: 0.7727 (m-90) cc_final: 0.7497 (m-90)
REVERT: A  547 LEU cc_start: 0.8769 (tp) cc_final: 0.8559 (tp)
REVERT: A  548 PHE cc_start: 0.7447 (m-10) cc_final: 0.7176 (m-10)
REVERT: A  595 TYR cc_start: 0.7313 (m-10) cc_final: 0.6636 (m-80)
REVERT: B   42 LYS cc_start: 0.8659 (tptt) cc_final: 0.8184 (tppt)
REVERT: B   59 ARG cc_start: 0.8494 (ttt180) cc_final: 0.7888 (ttm170)
REVERT: B   83 PHE cc_start: 0.8287 (m-80) cc_final: 0.7532 (m-10)
REVERT: B  120 TYR cc_start: 0.6947 (m-80) cc_final: 0.6427 (m-80)
REVERT: C  105 ASP cc_start: 0.8156 (m-30) cc_final: 0.7871 (m-30)
REVERT: C  107 THR cc_start: 0.8544 (p) cc_final: 0.8261 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.2034
  time to fit residues: 46.2203
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  : 0.674 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.7786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.131380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.113579 restraints weight = 20131.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.116930 restraints weight = 12803.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.119292 restraints weight = 8987.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.7485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6307  Z= 0.185
  Angle     :  0.634   9.477   8596  Z= 0.318
  Chirality :  0.044   0.202    953
  Planarity :  0.005   0.038   1050
  Dihedral  :  8.659  71.075    982
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.30), residues: 759
  helix:  0.44 (0.28), residues: 338
  sheet: -0.62 (0.60), residues: 80
  loop : -1.47 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 235 
 PHE   0.016   0.002   PHE A 380 
 TYR   0.013   0.001   TYR C  73 
 ARG   0.006   0.001   ARG A 607 

*********************** 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
  168 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.606 
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  112 ASN cc_start: 0.9037 (m110) cc_final: 0.8796 (m110)
REVERT: A  134 TYR cc_start: 0.9192 (t80) cc_final: 0.8588 (t80)
REVERT: A  158 PHE cc_start: 0.8744 (m-80) cc_final: 0.8400 (m-10)
REVERT: A  237 LEU cc_start: 0.8816 (tp) cc_final: 0.8555 (tp)
REVERT: A  260 MET cc_start: 0.7045 (mmp) cc_final: 0.6158 (ttp)
REVERT: A  332 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7278 (tm-30)
REVERT: A  370 MET cc_start: 0.8940 (tpt) cc_final: 0.8429 (tpp)
REVERT: A  495 TYR cc_start: 0.6951 (m-80) cc_final: 0.6471 (m-80)
REVERT: A  508 GLU cc_start: 0.8728 (pt0) cc_final: 0.8274 (pt0)
REVERT: A  528 MET cc_start: 0.8326 (mpp) cc_final: 0.8000 (mmm)
REVERT: A  592 TYR cc_start: 0.6386 (m-80) cc_final: 0.5817 (m-80)
REVERT: A  595 TYR cc_start: 0.7212 (m-10) cc_final: 0.6687 (m-80)
REVERT: B   42 LYS cc_start: 0.8654 (tptt) cc_final: 0.8154 (tppt)
REVERT: B   59 ARG cc_start: 0.8503 (ttt180) cc_final: 0.8242 (ttt180)
REVERT: B   65 GLU cc_start: 0.8858 (tp30) cc_final: 0.8615 (tp30)
REVERT: B   83 PHE cc_start: 0.8219 (m-80) cc_final: 0.7229 (m-10)
REVERT: B  120 TYR cc_start: 0.6995 (m-80) cc_final: 0.6608 (m-80)
REVERT: B  127 MET cc_start: 0.8779 (mmp) cc_final: 0.8531 (mmp)
REVERT: B  130 TRP cc_start: 0.8602 (m100) cc_final: 0.7979 (m100)
REVERT: C  105 ASP cc_start: 0.8159 (m-30) cc_final: 0.7875 (m-30)
REVERT: C  107 THR cc_start: 0.8337 (p) cc_final: 0.8003 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1857
  time to fit residues: 40.9215
Evaluate side-chains
  147 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 52 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    8.9990
   chunk 66 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    2.1388

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.129696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.111862 restraints weight = 20564.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.115171 restraints weight = 12977.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.117551 restraints weight = 9185.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.7702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6307  Z= 0.201
  Angle     :  0.637   9.324   8596  Z= 0.318
  Chirality :  0.043   0.203    953
  Planarity :  0.005   0.039   1050
  Dihedral  :  8.629  70.228    982
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -0.67 (0.31), residues: 759
  helix:  0.54 (0.29), residues: 335
  sheet: -0.35 (0.61), residues: 79
  loop : -1.45 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 235 
 PHE   0.017   0.002   PHE A 380 
 TYR   0.015   0.001   TYR A 410 
 ARG   0.007   0.001   ARG A 464 

*********************** 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
  168 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 ASN cc_start: 0.9075 (m110) cc_final: 0.8838 (m110)
REVERT: A  134 TYR cc_start: 0.9150 (t80) cc_final: 0.8579 (t80)
REVERT: A  135 MET cc_start: 0.9313 (ttt) cc_final: 0.9060 (ttt)
REVERT: A  158 PHE cc_start: 0.8738 (m-80) cc_final: 0.8469 (m-10)
REVERT: A  237 LEU cc_start: 0.8831 (tp) cc_final: 0.8549 (tp)
REVERT: A  260 MET cc_start: 0.6925 (mmp) cc_final: 0.6021 (ttp)
REVERT: A  332 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7287 (tm-30)
REVERT: A  370 MET cc_start: 0.8944 (tpt) cc_final: 0.8430 (tpp)
REVERT: A  495 TYR cc_start: 0.7004 (m-80) cc_final: 0.6475 (m-80)
REVERT: A  528 MET cc_start: 0.8389 (mpp) cc_final: 0.8075 (mmm)
REVERT: A  548 PHE cc_start: 0.7453 (m-10) cc_final: 0.7221 (m-10)
REVERT: A  595 TYR cc_start: 0.7246 (m-10) cc_final: 0.6674 (m-80)
REVERT: A  605 LYS cc_start: 0.8509 (tttm) cc_final: 0.8087 (pttt)
REVERT: B   42 LYS cc_start: 0.8659 (tptt) cc_final: 0.8142 (tppt)
REVERT: B   59 ARG cc_start: 0.8534 (ttt180) cc_final: 0.8278 (ttt180)
REVERT: B   83 PHE cc_start: 0.8259 (m-80) cc_final: 0.7480 (m-10)
REVERT: B  120 TYR cc_start: 0.7139 (m-80) cc_final: 0.6623 (m-80)
REVERT: B  127 MET cc_start: 0.8849 (mmp) cc_final: 0.8582 (mmp)
REVERT: B  130 TRP cc_start: 0.8575 (m100) cc_final: 0.7854 (m100)
REVERT: C  107 THR cc_start: 0.8392 (p) cc_final: 0.8053 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1924
  time to fit residues: 42.5740
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  : 0.733 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 67 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.131584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.114334 restraints weight = 21605.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.117527 restraints weight = 14056.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.119725 restraints weight = 9994.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.7849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6307  Z= 0.178
  Angle     :  0.641   9.588   8596  Z= 0.318
  Chirality :  0.043   0.203    953
  Planarity :  0.005   0.040   1050
  Dihedral  :  8.473  68.518    982
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  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: -0.61 (0.31), residues: 759
  helix:  0.60 (0.29), residues: 335
  sheet: -0.34 (0.61), residues: 79
  loop : -1.41 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 235 
 PHE   0.017   0.002   PHE A 380 
 TYR   0.012   0.001   TYR A 410 
 ARG   0.011   0.001   ARG A 464 

********************** 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
  164 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 ASN cc_start: 0.9093 (m110) cc_final: 0.8847 (m110)
REVERT: A  134 TYR cc_start: 0.9249 (t80) cc_final: 0.8494 (t80)
REVERT: A  158 PHE cc_start: 0.8698 (m-80) cc_final: 0.8473 (m-10)
REVERT: A  230 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8546 (mm-30)
REVERT: A  237 LEU cc_start: 0.8870 (tp) cc_final: 0.8577 (tp)
REVERT: A  260 MET cc_start: 0.6612 (mmp) cc_final: 0.5678 (ttp)
REVERT: A  332 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7395 (tm-30)
REVERT: A  370 MET cc_start: 0.8985 (tpt) cc_final: 0.8468 (tpp)
REVERT: A  396 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7751 (mp0)
REVERT: A  461 ARG cc_start: 0.8768 (mtt90) cc_final: 0.8551 (mmm-85)
REVERT: A  528 MET cc_start: 0.8349 (mpp) cc_final: 0.8045 (mmm)
REVERT: A  595 TYR cc_start: 0.7112 (m-10) cc_final: 0.6620 (m-80)
REVERT: A  605 LYS cc_start: 0.8471 (tttm) cc_final: 0.8081 (pttt)
REVERT: B   42 LYS cc_start: 0.8700 (tptt) cc_final: 0.8180 (tppt)
REVERT: B   59 ARG cc_start: 0.8509 (ttt180) cc_final: 0.8255 (ttt180)
REVERT: B   65 GLU cc_start: 0.8817 (tp30) cc_final: 0.8488 (tp30)
REVERT: B   83 PHE cc_start: 0.8144 (m-80) cc_final: 0.7228 (m-10)
REVERT: B   84 LYS cc_start: 0.8706 (mppt) cc_final: 0.8506 (mmtm)
REVERT: B  120 TYR cc_start: 0.7178 (m-80) cc_final: 0.6715 (m-80)
REVERT: B  127 MET cc_start: 0.8880 (mmp) cc_final: 0.8247 (mmp)
REVERT: B  130 TRP cc_start: 0.8505 (m100) cc_final: 0.7815 (m100)
REVERT: C  107 THR cc_start: 0.8314 (p) cc_final: 0.8017 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1937
  time to fit residues: 41.0393
Evaluate side-chains
  135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 50 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.4107 r_free = 0.4107 target = 0.130285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.112840 restraints weight = 21636.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.116048 restraints weight = 14002.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.118306 restraints weight = 9987.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.8055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6307  Z= 0.175
  Angle     :  0.634   9.461   8596  Z= 0.312
  Chirality :  0.043   0.204    953
  Planarity :  0.005   0.058   1050
  Dihedral  :  8.336  65.697    982
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.45 (0.31), residues: 759
  helix:  0.77 (0.28), residues: 337
  sheet: -0.32 (0.61), residues: 80
  loop : -1.37 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 103 
 HIS   0.003   0.001   HIS C 100 
 PHE   0.016   0.001   PHE A 380 
 TYR   0.034   0.001   TYR A 107 
 ARG   0.011   0.001   ARG C  85 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2375.26 seconds
wall clock time: 41 minutes 47.85 seconds (2507.85 seconds total)