Starting phenix.real_space_refine (version: dev)
on Sun Feb 19 22:00:10 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/02_2023/6hrb_0258_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/02_2023/6hrb_0258.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/02_2023/6hrb_0258.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/02_2023/6hrb_0258.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/02_2023/6hrb_0258_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/02_2023/6hrb_0258_updated.pdb"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  381": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   32": "NH1" <-> "NH2"
    Residue "B ARG  461": "NH1" <-> "NH2"
    Residue "B ARG  572": "NH1" <-> "NH2"
    Residue "C ARG  106": "NH1" <-> "NH2"
    Residue "C ARG  148": "NH1" <-> "NH2"
    Residue "C TYR  170": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 10787
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4155
          Classifications: {'peptide': 557}
          Link IDs: {'PTRANS': 25, 'TRANS': 531}
    Chain: "B"
      Number of atoms: 5008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5008
          Classifications: {'peptide': 674}
          Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 646}
    Chain: "C"
      Number of atoms: 1423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1423
          Classifications: {'peptide': 189}
          Link IDs: {'PTRANS': 13, 'TRANS': 175}
    Chain: "D"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 200
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'  K': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.60, per 1000 atoms: 0.61
  Number of scatterers: 10787
  At special positions: 0
  Unit cell: (88.044, 114.356, 161.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       1     19.00
     S      61     16.00
     P       1     15.00
     O    1959      8.00
     N    1818      7.00
     C    6947      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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
  Time building additional restraints: 4.50
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2632

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      63 helices and 7 sheets defined
      52.7% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 31
      removed outlier: 3.548A  pdb=" N   ILE A   9 " --> pdb=" O   GLY A   5 " (cutoff:3.500A)
      Proline residue:  A  22  - end of helix
      removed outlier: 4.116A  pdb=" N   ARG A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU A  30 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 50
      removed outlier: 3.734A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG A  48 " --> pdb=" O   ARG A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 80
      removed outlier: 3.597A  pdb=" N   CYS A  64 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 86
    Processing helix  chain 'A' and resid 99 through 110
      removed outlier: 3.853A  pdb=" N   VAL A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 123
      No H-bonds generated for 'chain 'A' and resid 120 through 123'
    Processing helix  chain 'A' and resid 134 through 156
      removed outlier: 3.866A  pdb=" N   PHE A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A 142 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL A 147 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 176
    Processing helix  chain 'A' and resid 178 through 191
      removed outlier: 3.529A  pdb=" N   ALA A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 228
      removed outlier: 3.603A  pdb=" N   ALA A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ILE A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   MET A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 259
    Processing helix  chain 'A' and resid 261 through 273
      removed outlier: 3.755A  pdb=" N   ALA A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   CYS A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 4.021A  pdb=" N   MET A 282 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 304
      removed outlier: 3.613A  pdb=" N   VAL A 289 " --> pdb=" O   TRP A 285 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   ILE A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   VAL A 298 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 329 through 341
      removed outlier: 3.556A  pdb=" N   VAL A 337 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   THR A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 353
      No H-bonds generated for 'chain 'A' and resid 351 through 353'
    Processing helix  chain 'A' and resid 356 through 367
      Proline residue:  A 362  - end of helix
      removed outlier: 3.546A  pdb=" N   GLN A 367 " --> pdb=" O   MET A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 398
      removed outlier: 3.893A  pdb=" N   PHE A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   PHE A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 429
      removed outlier: 4.027A  pdb=" N   LEU A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   THR A 417 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU A 422 " --> pdb=" O   ALA A 418 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      Proline residue:  A 425  - end of helix
      removed outlier: 4.009A  pdb=" N   VAL A 428 " --> pdb=" O   THR A 424 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU A 429 " --> pdb=" O   PRO A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 437
    Processing helix  chain 'A' and resid 442 through 444
      No H-bonds generated for 'chain 'A' and resid 442 through 444'
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 3.528A  pdb=" N   SER A 454 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL A 456 " --> pdb=" O   GLY A 452 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ALA A 459 " --> pdb=" O   GLU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 494
      removed outlier: 3.856A  pdb=" N   ALA A 486 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 506
    Processing helix  chain 'A' and resid 525 through 548
      removed outlier: 3.729A  pdb=" N   GLY A 529 " --> pdb=" O   PRO A 525 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU A 530 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY A 533 " --> pdb=" O   GLY A 529 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   LEU A 537 " --> pdb=" O   GLY A 533 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLY A 539 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      Proline residue:  A 545  - end of helix
    Processing helix  chain 'A' and resid 551 through 556
    Processing helix  chain 'B' and resid 12 through 23
      removed outlier: 3.558A  pdb=" N   ALA B  17 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS B  19 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   GLU B  20 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ALA B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 55
      removed outlier: 3.843A  pdb=" N   ILE B  38 " --> pdb=" O   PRO B  34 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR B  47 " --> pdb=" O   SER B  43 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 86
      removed outlier: 3.604A  pdb=" N   ALA B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TRP B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU B  72 " --> pdb=" O   ILE B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 102
      removed outlier: 3.618A  pdb=" N   VAL B 100 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   LYS B 101 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 207
      removed outlier: 4.033A  pdb=" N   MET B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 237
      removed outlier: 3.578A  pdb=" N   LEU B 221 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR B 222 " --> pdb=" O   GLU B 218 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE B 223 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU B 224 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   THR B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   VAL B 231 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 236 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 243
    Processing helix  chain 'B' and resid 252 through 262
      removed outlier: 3.672A  pdb=" N   ALA B 257 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 273
      No H-bonds generated for 'chain 'B' and resid 270 through 273'
    Processing helix  chain 'B' and resid 275 through 285
      removed outlier: 4.070A  pdb=" N   LEU B 283 " --> pdb=" O   MET B 279 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   GLY B 284 " --> pdb=" O   SER B 280 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA B 285 " --> pdb=" O   ARG B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 299
      removed outlier: 3.707A  pdb=" N   GLU B 296 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA B 298 " --> pdb=" O   ALA B 294 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   GLY B 299 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 341
    Processing helix  chain 'B' and resid 347 through 356
      removed outlier: 4.023A  pdb=" N   ILE B 352 " --> pdb=" O   GLU B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 408
      removed outlier: 3.590A  pdb=" N   HIS B 404 " --> pdb=" O   ALA B 400 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU B 406 " --> pdb=" O   ARG B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 423
    Processing helix  chain 'B' and resid 454 through 462
      removed outlier: 3.600A  pdb=" N   GLN B 459 " --> pdb=" O   GLU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 483
      removed outlier: 4.472A  pdb=" N   ALA B 480 " --> pdb=" O   LEU B 476 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE B 481 " --> pdb=" O   THR B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 508
      removed outlier: 3.665A  pdb=" N   LEU B 500 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 525
      No H-bonds generated for 'chain 'B' and resid 522 through 525'
    Processing helix  chain 'B' and resid 540 through 545
      removed outlier: 3.726A  pdb=" N   GLU B 544 " --> pdb=" O   GLN B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 590
      removed outlier: 3.791A  pdb=" N   GLN B 567 " --> pdb=" O   HIS B 563 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   SER B 574 " --> pdb=" O   MET B 570 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA B 581 " --> pdb=" O   THR B 577 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   VAL B 584 " --> pdb=" O   ILE B 580 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE B 588 " --> pdb=" O   VAL B 584 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA B 589 " --> pdb=" O   ALA B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 595
      removed outlier: 3.677A  pdb=" N   PHE B 595 " --> pdb=" O   PRO B 592 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 592 through 595'
    Processing helix  chain 'B' and resid 600 through 605
      removed outlier: 3.917A  pdb=" N   ALA B 604 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 613 through 636
      removed outlier: 3.706A  pdb=" N   ILE B 617 " --> pdb=" O   PRO B 613 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU B 618 " --> pdb=" O   ASP B 614 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL B 629 " --> pdb=" O   ALA B 625 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ILE B 632 " --> pdb=" O   ILE B 628 " (cutoff:3.500A)
      Proline residue:  B 633  - end of helix
    Processing helix  chain 'B' and resid 647 through 656
      removed outlier: 3.581A  pdb=" N   TRP B 655 " --> pdb=" O   ARG B 651 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B 656 " --> pdb=" O   ARG B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 658 through 678
      removed outlier: 3.546A  pdb=" N   LEU B 662 " --> pdb=" O   GLY B 658 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL B 664 " --> pdb=" O   GLY B 660 " (cutoff:3.500A)
      Proline residue:  B 665  - end of helix
      removed outlier: 3.868A  pdb=" N   LYS B 670 " --> pdb=" O   PHE B 666 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU B 674 " --> pdb=" O   LYS B 670 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 18
      removed outlier: 3.789A  pdb=" N   THR C  10 " --> pdb=" O   PRO C   6 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   PHE C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 33
    Processing helix  chain 'C' and resid 35 through 39
      removed outlier: 3.549A  pdb=" N   ASN C  39 " --> pdb=" O   PRO C  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 35 through 39'
    Processing helix  chain 'C' and resid 92 through 108
      removed outlier: 3.507A  pdb=" N   ALA C 103 " --> pdb=" O   ALA C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 121
      No H-bonds generated for 'chain 'C' and resid 118 through 121'
    Processing helix  chain 'C' and resid 134 through 139
    Processing helix  chain 'C' and resid 141 through 147
    Processing helix  chain 'C' and resid 152 through 162
    Processing helix  chain 'C' and resid 179 through 189
    Processing helix  chain 'D' and resid 7 through 24
      removed outlier: 4.126A  pdb=" N   TYR D  21 " --> pdb=" O   GLY D  17 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 203 through 205
      removed outlier: 3.527A  pdb=" N   GLN A 212 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 106 through 109
    Processing sheet with id=  C, first strand: chain 'B' and resid 131 through 134
      removed outlier: 6.735A  pdb=" N   GLU B 190 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   VAL B 146 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 150 through 154
    Processing sheet with id=  E, first strand: chain 'B' and resid 287 through 289
    Processing sheet with id=  F, first strand: chain 'B' and resid 513 through 516
      removed outlier: 7.286A  pdb=" N   VAL B 303 " --> pdb=" O   ALA B 514 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   THR B 516 " --> pdb=" O   VAL B 303 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   LEU B 305 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS B 466 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 8.225A  pdb=" N   LEU B 306 " --> pdb=" O   LYS B 466 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   VAL B 468 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ASP B 489 " --> pdb=" O   MET B 469 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  F
    Processing sheet with id=  G, first strand: chain 'B' and resid 373 through 375
      removed outlier: 3.810A  pdb=" N   GLY B 441 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLU B 435 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   VAL B 439 " --> pdb=" O   GLU B 435 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1239 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.27

  Time building geometry restraints manager: 4.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3441
        1.34 -     1.46: 1833
        1.46 -     1.57: 5598
        1.57 -     1.69: 4
        1.69 -     1.81: 110
  Bond restraints: 10986
  Sorted by residual:
  bond pdb=" N   ARG B  89 "
       pdb=" CA  ARG B  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.502 -0.044 1.90e-02 2.77e+03 5.25e+00
  bond pdb=" CB  VAL A 428 "
       pdb=" CG2 VAL A 428 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.70e+00
  bond pdb=" C   LEU A 213 "
       pdb=" N   LEU A 214 "
    ideal  model  delta    sigma   weight residual
    1.331  1.368 -0.037 2.07e-02 2.33e+03 3.19e+00
  bond pdb=" CA  ARG B  89 "
       pdb=" CB  ARG B  89 "
    ideal  model  delta    sigma   weight residual
    1.530  1.565 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C   GLN C 164 "
       pdb=" N   GLN C 165 "
    ideal  model  delta    sigma   weight residual
    1.331  1.283  0.048 2.83e-02 1.25e+03 2.92e+00
  ... (remaining 10981 not shown)

  Histogram of bond angle deviations from ideal:
       97.31 -   105.00: 243
      105.00 -   112.69: 5982
      112.69 -   120.39: 4756
      120.39 -   128.08: 3883
      128.08 -   135.78: 90
  Bond angle restraints: 14954
  Sorted by residual:
  angle pdb=" C   MET A 360 "
        pdb=" N   VAL A 361 "
        pdb=" CA  VAL A 361 "
      ideal   model   delta    sigma   weight residual
     120.24  124.03   -3.79 6.30e-01 2.52e+00 3.61e+01
  angle pdb=" N   ASN B  26 "
        pdb=" CA  ASN B  26 "
        pdb=" C   ASN B  26 "
      ideal   model   delta    sigma   weight residual
     109.81  119.59   -9.78 2.21e+00 2.05e-01 1.96e+01
  angle pdb=" C   GLY B  88 "
        pdb=" N   ARG B  89 "
        pdb=" CA  ARG B  89 "
      ideal   model   delta    sigma   weight residual
     123.00  135.78  -12.78 3.00e+00 1.11e-01 1.81e+01
  angle pdb=" C   ALA B 319 "
        pdb=" N   SER B 320 "
        pdb=" CA  SER B 320 "
      ideal   model   delta    sigma   weight residual
     121.54  129.41   -7.87 1.91e+00 2.74e-01 1.70e+01
  angle pdb=" CB  LEU A 133 "
        pdb=" CG  LEU A 133 "
        pdb=" CD2 LEU A 133 "
      ideal   model   delta    sigma   weight residual
     110.70   98.39   12.31 3.00e+00 1.11e-01 1.68e+01
  ... (remaining 14949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.50: 6245
       15.50 -    31.01: 244
       31.01 -    46.51: 36
       46.51 -    62.01: 5
       62.01 -    77.51: 3
  Dihedral angle restraints: 6533
    sinusoidal: 2436
      harmonic: 4097
  Sorted by residual:
  dihedral pdb=" CA  ASN A 239 "
           pdb=" C   ASN A 239 "
           pdb=" N   SER A 240 "
           pdb=" CA  SER A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.70   31.30     0      5.00e+00 4.00e-02 3.92e+01
  dihedral pdb=" CA  ALA B 319 "
           pdb=" C   ALA B 319 "
           pdb=" N   SER B 320 "
           pdb=" CA  SER B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.18   29.82     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  ALA A 238 "
           pdb=" C   ALA A 238 "
           pdb=" N   ASN A 239 "
           pdb=" CA  ASN A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.31  -28.69     0      5.00e+00 4.00e-02 3.29e+01
  ... (remaining 6530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1144
       0.046 -    0.092: 499
       0.092 -    0.138: 138
       0.138 -    0.185: 16
       0.185 -    0.231: 6
  Chirality restraints: 1803
  Sorted by residual:
  chirality pdb=" CA  ARG B  89 "
            pdb=" N   ARG B  89 "
            pdb=" C   ARG B  89 "
            pdb=" CB  ARG B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  ILE B 388 "
            pdb=" CA  ILE B 388 "
            pdb=" CG1 ILE B 388 "
            pdb=" CG2 ILE B 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  VAL B 449 "
            pdb=" CA  VAL B 449 "
            pdb=" CG1 VAL B 449 "
            pdb=" CG2 VAL B 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1800 not shown)

  Planarity restraints: 1898
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 424 "   -0.058 5.00e-02 4.00e+02   8.67e-02 1.20e+01
        pdb=" N   PRO A 425 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 425 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 425 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 240 "   -0.041 5.00e-02 4.00e+02   6.09e-02 5.93e+00
        pdb=" N   PRO B 241 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 241 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 241 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 523 "   -0.040 5.00e-02 4.00e+02   6.02e-02 5.81e+00
        pdb=" N   PRO B 524 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 524 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 524 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1895 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.78: 2681
        2.78 -     3.37: 12233
        3.37 -     3.96: 20841
        3.96 -     4.55: 29259
        4.55 -     5.14: 41926
  Nonbonded interactions: 106940
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 307 "
            pdb=" OG1 THR B 311 "
     model   vdw
     2.186 2.440
  nonbonded pdb=" OG1 THR C  72 "
            pdb=" O   MET C  75 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   VAL A 107 "
            pdb=" OG1 THR A 111 "
     model   vdw
     2.248 2.440
  nonbonded pdb=" OG  SER A 343 "
            pdb=" O   ASN A 466 "
     model   vdw
     2.262 2.440
  nonbonded pdb=" O   MET A 130 "
            pdb=" OG1 THR A 134 "
     model   vdw
     2.264 2.440
  ... (remaining 106935 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     K       1      8.98       5
     P       1      5.49       5
     S      61      5.16       5
     C    6947      2.51       5
     N    1818      2.21       5
     O    1959      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  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:          3.940
  Check model and map are aligned:         0.150
  Process input model:                     31.480
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    0.110
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
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      :  0.008   0.085  10986  Z= 0.513
  Angle     :  0.962  12.778  14954  Z= 0.496
  Chirality :  0.054   0.231   1803
  Planarity :  0.007   0.087   1898
  Dihedral  :  9.280  77.514   3901
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer Outliers :  0.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.97 (0.16), residues: 1436
  helix: -3.80 (0.10), residues: 765
  sheet: -2.20 (0.46), residues: 91
  loop : -2.48 (0.22), residues: 580

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 240
  time to evaluate  : 1.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 242
  average time/residue: 0.2342
  time to fit residues: 80.3069
Evaluate side-chains
  121 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 1.259 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0962
  time to fit residues: 1.8697
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0670
   chunk 72 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 111 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   chunk 128 optimal weight:    9.9990
   overall best weight:    3.6126

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 ASN
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 ASN
B 326 GLN
B 338 GLN
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 554 ASN
B 567 GLN
** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
C 154 GLN
** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.086  10986  Z= 0.355
  Angle     :  0.750  14.986  14954  Z= 0.375
  Chirality :  0.044   0.149   1803
  Planarity :  0.005   0.051   1898
  Dihedral  :  5.740  24.056   1524
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer Outliers :  2.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -3.21 (0.19), residues: 1436
  helix: -1.96 (0.15), residues: 821
  sheet: -1.97 (0.45), residues: 104
  loop : -2.14 (0.26), residues: 511

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 14
  residues processed: 161
  average time/residue: 0.1918
  time to fit residues: 47.1856
Evaluate side-chains
  124 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 1.263 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.1047
  time to fit residues: 4.4962
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 40 optimal weight:   20.0000
   chunk 107 optimal weight:    0.9990
   chunk 87 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 129 optimal weight:    0.0060
   chunk 139 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 128 optimal weight:    0.1980
   chunk 44 optimal weight:    6.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    1.0402

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 HIS
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 GLN
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 404 HIS
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10986  Z= 0.191
  Angle     :  0.639  15.245  14954  Z= 0.311
  Chirality :  0.041   0.249   1803
  Planarity :  0.003   0.043   1898
  Dihedral  :  5.164  22.206   1524
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer Outliers :  0.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -2.20 (0.21), residues: 1436
  helix: -1.04 (0.17), residues: 812
  sheet: -1.62 (0.46), residues: 105
  loop : -1.89 (0.26), residues: 519

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 3
  residues processed: 156
  average time/residue: 0.2060
  time to fit residues: 48.9967
Evaluate side-chains
  124 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 1.236 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1056
  time to fit residues: 2.2400
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 127 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 129 optimal weight:    3.9990
   chunk 137 optimal weight:    7.9990
   chunk 122 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 114 optimal weight:    4.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 ASN
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10986  Z= 0.331
  Angle     :  0.703  14.551  14954  Z= 0.342
  Chirality :  0.042   0.129   1803
  Planarity :  0.003   0.043   1898
  Dihedral  :  5.040  22.195   1524
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer Outliers :  1.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -1.65 (0.21), residues: 1436
  helix: -0.49 (0.17), residues: 825
  sheet: -1.57 (0.46), residues: 107
  loop : -1.83 (0.27), residues: 504

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 10
  residues processed: 125
  average time/residue: 0.1942
  time to fit residues: 38.3122
Evaluate side-chains
  109 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 1.427 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1104
  time to fit residues: 3.7576
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0050
   chunk 56 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0170
   chunk 123 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.0036

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 231 ASN
** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  86 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10986  Z= 0.181
  Angle     :  0.615  15.207  14954  Z= 0.294
  Chirality :  0.041   0.186   1803
  Planarity :  0.003   0.044   1898
  Dihedral  :  4.730  22.517   1524
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer Outliers :  1.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -1.12 (0.22), residues: 1436
  helix:  0.02 (0.18), residues: 821
  sheet: -1.17 (0.50), residues: 101
  loop : -1.80 (0.27), residues: 514

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 3
  residues processed: 132
  average time/residue: 0.1826
  time to fit residues: 37.7245
Evaluate side-chains
  112 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 1.138 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1018
  time to fit residues: 2.1745
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 80 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 137 optimal weight:    7.9990
   chunk 114 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 11 optimal weight:    0.1980
   chunk 45 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 132 optimal weight:    6.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 ASN
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10986  Z= 0.180
  Angle     :  0.598  15.083  14954  Z= 0.288
  Chirality :  0.040   0.144   1803
  Planarity :  0.003   0.043   1898
  Dihedral  :  4.528  22.942   1524
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer Outliers :  1.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.81 (0.22), residues: 1436
  helix:  0.30 (0.18), residues: 822
  sheet: -1.17 (0.49), residues: 106
  loop : -1.70 (0.27), residues: 508

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 4
  residues processed: 139
  average time/residue: 0.1995
  time to fit residues: 42.7316
Evaluate side-chains
  113 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 1.310 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1116
  time to fit residues: 2.4395
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 115 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 136 optimal weight:    8.9990
   chunk 85 optimal weight:    0.7980
   chunk 83 optimal weight:    9.9990
   chunk 63 optimal weight:    0.0020
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10986  Z= 0.162
  Angle     :  0.606  15.201  14954  Z= 0.287
  Chirality :  0.040   0.156   1803
  Planarity :  0.003   0.042   1898
  Dihedral  :  4.393  23.434   1524
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer Outliers :  0.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.52 (0.23), residues: 1436
  helix:  0.51 (0.19), residues: 826
  sheet: -1.00 (0.50), residues: 106
  loop : -1.54 (0.27), residues: 504

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 144
  average time/residue: 0.2019
  time to fit residues: 44.5579
Evaluate side-chains
  125 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 1.290 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1159
  time to fit residues: 2.7122
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 93 optimal weight:   10.0000
   chunk 67 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 107 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
A 279 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 ASN
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  86 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.4285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10986  Z= 0.179
  Angle     :  0.621  15.144  14954  Z= 0.292
  Chirality :  0.040   0.211   1803
  Planarity :  0.003   0.038   1898
  Dihedral  :  4.325  23.588   1524
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer Outliers :  0.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.22), residues: 1436
  helix:  0.52 (0.18), residues: 833
  sheet: -0.92 (0.50), residues: 106
  loop : -1.55 (0.27), residues: 497

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 125
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 127
  average time/residue: 0.2002
  time to fit residues: 40.0821
Evaluate side-chains
  120 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 1.330 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1315
  time to fit residues: 2.1110
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    0.9990
   chunk 127 optimal weight:    0.8980
   chunk 131 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0370
   chunk 100 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 115 optimal weight:    3.9990
   chunk 120 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 134 optimal weight:    5.9990
   overall best weight:    0.9862

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10986  Z= 0.179
  Angle     :  0.646  15.267  14954  Z= 0.303
  Chirality :  0.041   0.137   1803
  Planarity :  0.003   0.037   1898
  Dihedral  :  4.289  23.740   1524
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer Outliers :  0.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.32 (0.23), residues: 1436
  helix:  0.67 (0.19), residues: 826
  sheet: -0.93 (0.50), residues: 106
  loop : -1.45 (0.28), residues: 504

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 1.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 127
  average time/residue: 0.1909
  time to fit residues: 37.8656
Evaluate side-chains
  112 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 1.298 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0997
  time to fit residues: 1.7421
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 141 optimal weight:    8.9990
   chunk 130 optimal weight:    8.9990
   chunk 112 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0670
   chunk 87 optimal weight:    6.9990
   chunk 69 optimal weight:   20.0000
   chunk 89 optimal weight:    5.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    1.9924

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 547 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.4467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10986  Z= 0.233
  Angle     :  0.670  15.118  14954  Z= 0.317
  Chirality :  0.042   0.303   1803
  Planarity :  0.003   0.036   1898
  Dihedral  :  4.367  23.933   1524
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer Outliers :  0.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.30 (0.23), residues: 1436
  helix:  0.65 (0.19), residues: 832
  sheet: -0.96 (0.50), residues: 106
  loop : -1.40 (0.28), residues: 498

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 1.379 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 113
  average time/residue: 0.2449
  time to fit residues: 43.8466
Evaluate side-chains
  108 residues out of total 1133 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 1.116 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1094
  time to fit residues: 2.3078
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 103 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 115 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 465 ASN
** B  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 536 ASN ** 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 = 0.3116 r_free = 0.3116 target = 0.058464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.048025 restraints weight = 50321.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.049416 restraints weight = 24883.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.050336 restraints weight = 14973.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10986  Z= 0.219
  Angle     :  0.664  15.383  14954  Z= 0.313
  Chirality :  0.041   0.167   1803
  Planarity :  0.003   0.036   1898
  Dihedral  :  4.375  24.522   1524
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer Outliers :  0.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    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: -0.25 (0.23), residues: 1436
  helix:  0.70 (0.18), residues: 829
  sheet: -0.95 (0.50), residues: 106
  loop : -1.38 (0.28), residues: 501

===============================================================================
Job complete
usr+sys time: 1918.91 seconds
wall clock time: 36 minutes 21.76 seconds (2181.76 seconds total)