Starting phenix.real_space_refine
on Wed Feb  4 05:36:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n65_49049/02_2026/9n65_49049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n65_49049/02_2026/9n65_49049.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n65_49049/02_2026/9n65_49049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n65_49049/02_2026/9n65_49049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n65_49049/02_2026/9n65_49049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n65_49049/02_2026/9n65_49049.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.015
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S      40      5.16       5
     C    5568      2.51       5
     N    1516      2.21       5
     O    1645      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8776
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4405
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 21, 'TRANS': 548}
    Chain: "B"
      Number of atoms: 4311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4311
          Classifications: {'peptide': 551}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 530}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.75, per 1000 atoms: 0.20
  Number of scatterers: 8776
  At special positions: 0
  Unit cell: (73.96, 123.84, 146.2, 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)
     S      40     16.00
     P       5     15.00
     Mg      2     11.99
     O    1645      8.00
     N    1516      7.00
     C    5568      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  - 3.00
        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
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 331.9 milliseconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2066

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 4 sheets defined
      66.6% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 173 through 180
      removed outlier: 3.573A  pdb=" N   LEU A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 202
      removed outlier: 3.563A  pdb=" N   MET A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 217
      removed outlier: 3.585A  pdb=" N   GLY A 209 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ARG A 210 " --> pdb=" O   PHE A 206 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 211 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 269
      removed outlier: 3.703A  pdb=" N   LEU A 228 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   THR A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   THR A 235 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.767A  pdb=" N   MET A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 324
      removed outlier: 3.687A  pdb=" N   SER A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   SER A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TRP A 322 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 334
      removed outlier: 3.529A  pdb=" N   LEU A 332 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
    Processing helix  chain 'A' and resid 340 through 372
      removed outlier: 3.620A  pdb=" N   GLN A 350 " --> pdb=" O   GLY A 346 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A 351 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU A 352 " --> pdb=" O   TRP A 348 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLN A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 382 through 436
      removed outlier: 3.868A  pdb=" N   LYS A 393 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN A 402 " --> pdb=" O   LYS A 398 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LYS A 403 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   SER A 416 " --> pdb=" O   SER A 412 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   SER A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLY A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET A 420 " --> pdb=" O   SER A 416 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LYS A 423 " --> pdb=" O   GLY A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 483
      removed outlier: 3.736A  pdb=" N   LEU A 444 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   MET A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      Proline residue:  A 466  - end of helix
      removed outlier: 3.726A  pdb=" N   GLY A 473 " --> pdb=" O   GLN A 469 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASP A 483 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 552
      removed outlier: 3.533A  pdb=" N   ALA A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLN A 552 " --> pdb=" O   ALA A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 572
    Processing helix  chain 'A' and resid 573 through 580
      removed outlier: 3.589A  pdb=" N   HIS A 578 " --> pdb=" O   HIS A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 600
    Processing helix  chain 'A' and resid 608 through 620
      removed outlier: 3.657A  pdb=" N   ILE A 612 " --> pdb=" O   THR A 608 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A 613 " --> pdb=" O   MET A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 626
      removed outlier: 3.670A  pdb=" N   SER A 626 " --> pdb=" O   HIS A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 659
      removed outlier: 4.683A  pdb=" N   ARG A 659 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 681
    Processing helix  chain 'A' and resid 681 through 687
    Processing helix  chain 'A' and resid 688 through 694
      removed outlier: 3.606A  pdb=" N   ARG A 691 " --> pdb=" O   SER A 688 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER A 693 " --> pdb=" O   GLU A 690 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG A 694 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 733
      removed outlier: 3.652A  pdb=" N   LYS A 733 " --> pdb=" O   LEU A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 742
      removed outlier: 3.976A  pdb=" N   ALA A 738 " --> pdb=" O   GLY A 734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 144
      removed outlier: 4.049A  pdb=" N   VAL B 136 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   LEU B 137 " --> pdb=" O   ASN B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 167
    Processing helix  chain 'B' and resid 168 through 181
      removed outlier: 3.538A  pdb=" N   ILE B 177 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 234
      removed outlier: 3.509A  pdb=" N   SER B 219 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 4.010A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 255
      removed outlier: 3.527A  pdb=" N   LEU B 249 " --> pdb=" O   LYS B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 262
      removed outlier: 3.585A  pdb=" N   LEU B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN B 262 " --> pdb=" O   THR B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 289
      removed outlier: 3.643A  pdb=" N   LEU B 266 " --> pdb=" O   ASN B 262 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER B 287 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 298
      removed outlier: 3.690A  pdb=" N   LEU B 294 " --> pdb=" O   PRO B 290 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU B 295 " --> pdb=" O   ARG B 291 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 338
      removed outlier: 3.683A  pdb=" N   THR B 312 " --> pdb=" O   LYS B 308 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ARG B 313 " --> pdb=" O   VAL B 309 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B 319 " --> pdb=" O   GLN B 315 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLU B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B 331 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY B 337 " --> pdb=" O   ARG B 333 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 344
    Processing helix  chain 'B' and resid 347 through 402
      removed outlier: 3.567A  pdb=" N   GLU B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU B 357 " --> pdb=" O   CYS B 353 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA B 358 " --> pdb=" O   ARG B 354 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL B 387 " --> pdb=" O   LEU B 383 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP B 401 " --> pdb=" O   GLN B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 428
      removed outlier: 3.725A  pdb=" N   SER B 418 " --> pdb=" O   ILE B 414 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL B 419 " --> pdb=" O   TYR B 415 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLY B 420 " --> pdb=" O   GLN B 416 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR B 422 " --> pdb=" O   SER B 418 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLN B 424 " --> pdb=" O   GLY B 420 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR B 428 " --> pdb=" O   GLN B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 437
    Processing helix  chain 'B' and resid 440 through 449
    Processing helix  chain 'B' and resid 510 through 517
      removed outlier: 3.516A  pdb=" N   LEU B 515 " --> pdb=" O   THR B 511 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLN B 517 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 545
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 575 through 580
    Processing helix  chain 'B' and resid 613 through 621
    Processing helix  chain 'B' and resid 634 through 640
      removed outlier: 4.394A  pdb=" N   VAL B 639 " --> pdb=" O   ALA B 636 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 528
      removed outlier: 6.305A  pdb=" N   GLN A 522 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   SER A 509 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   LEU A 524 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   PHE A 526 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL A 503 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 583
      removed outlier: 6.670A  pdb=" N   LEU A 664 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   ILE A 699 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   LEU A 666 " --> pdb=" O   ILE A 699 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 698 " --> pdb=" O   THR A 534 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   VAL A 533 " --> pdb=" O   HIS A 711 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   LEU A 713 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ALA A 535 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 491 through 493
      removed outlier: 3.642A  pdb=" N   PHE B 491 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL B 468 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLN B 471 " --> pdb=" O   GLN B 526 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLN B 526 " --> pdb=" O   GLN B 471 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 546 through 549
      removed outlier: 3.693A  pdb=" N   VAL B 547 " --> pdb=" O   VAL B 627 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU B 628 " --> pdb=" O   LEU B 657 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ILE B 659 " --> pdb=" O   LEU B 628 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LEU B 630 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR B 499 " --> pdb=" O   VAL B 658 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   ALA B 660 " --> pdb=" O   THR B 499 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   LEU B 501 " --> pdb=" O   ALA B 660 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL B 498 " --> pdb=" O   GLN B 671 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LEU B 673 " --> pdb=" O   VAL B 498 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   ALA B 500 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LEU B 675 " --> pdb=" O   ALA B 500 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   VAL B 502 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)

    505 hydrogen bonds defined for protein.
    1491 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.83

  Time building geometry restraints manager: 0.91 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: 2890
        1.34 -     1.46: 1895
        1.46 -     1.58: 4080
        1.58 -     1.70: 7
        1.70 -     1.82: 66
  Bond restraints: 8938
  Sorted by residual:
  bond pdb=" CA  ASP B 624 "
       pdb=" CB  ASP B 624 "
    ideal  model  delta    sigma   weight residual
    1.525  1.538 -0.013 8.30e-03 1.45e+04 2.64e+00
  bond pdb=" CA  ILE B 169 "
       pdb=" C   ILE B 169 "
    ideal  model  delta    sigma   weight residual
    1.520  1.534 -0.014 8.80e-03 1.29e+04 2.49e+00
  bond pdb=" C   ILE B 169 "
       pdb=" N   PRO B 170 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.23e-02 6.61e+03 2.46e+00
  bond pdb=" CB  PHE A 526 "
       pdb=" CG  PHE A 526 "
    ideal  model  delta    sigma   weight residual
    1.502  1.537 -0.035 2.30e-02 1.89e+03 2.38e+00
  bond pdb=" CB  TRP A 322 "
       pdb=" CG  TRP A 322 "
    ideal  model  delta    sigma   weight residual
    1.498  1.544 -0.046 3.10e-02 1.04e+03 2.21e+00
  ... (remaining 8933 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 11805
        2.01 -     4.01: 234
        4.01 -     6.02: 63
        6.02 -     8.03: 20
        8.03 -    10.03: 12
  Bond angle restraints: 12134
  Sorted by residual:
  angle pdb=" C   SER B 635 "
        pdb=" CA  SER B 635 "
        pdb=" CB  SER B 635 "
      ideal   model   delta    sigma   weight residual
     116.63  110.44    6.19 1.16e+00 7.43e-01 2.85e+01
  angle pdb=" CA  GLN A 350 "
        pdb=" CB  GLN A 350 "
        pdb=" CG  GLN A 350 "
      ideal   model   delta    sigma   weight residual
     114.10  123.32   -9.22 2.00e+00 2.50e-01 2.13e+01
  angle pdb=" C   ARG B 623 "
        pdb=" N   ASP B 624 "
        pdb=" CA  ASP B 624 "
      ideal   model   delta    sigma   weight residual
     124.21  129.67   -5.46 1.21e+00 6.83e-01 2.03e+01
  angle pdb=" CA  TRP A 322 "
        pdb=" CB  TRP A 322 "
        pdb=" CG  TRP A 322 "
      ideal   model   delta    sigma   weight residual
     113.60  121.49   -7.89 1.90e+00 2.77e-01 1.72e+01
  angle pdb=" CA  GLN B 646 "
        pdb=" CB  GLN B 646 "
        pdb=" CG  GLN B 646 "
      ideal   model   delta    sigma   weight residual
     114.10  122.38   -8.28 2.00e+00 2.50e-01 1.71e+01
  ... (remaining 12129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4580
       17.89 -    35.77: 578
       35.77 -    53.66: 174
       53.66 -    71.54: 28
       71.54 -    89.43: 16
  Dihedral angle restraints: 5376
    sinusoidal: 2156
      harmonic: 3220
  Sorted by residual:
  dihedral pdb=" CA  ALA A 639 "
           pdb=" C   ALA A 639 "
           pdb=" N   GLY A 640 "
           pdb=" CA  GLY A 640 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.13   20.87     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" C   ILE B 169 "
           pdb=" N   ILE B 169 "
           pdb=" CA  ILE B 169 "
           pdb=" CB  ILE B 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.70    8.70     0      2.50e+00 1.60e-01 1.21e+01
  dihedral pdb=" CA  ASP B 256 "
           pdb=" CB  ASP B 256 "
           pdb=" CG  ASP B 256 "
           pdb=" OD1 ASP B 256 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.26   58.26     1      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 5373 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1299
       0.078 -    0.156: 103
       0.156 -    0.234: 2
       0.234 -    0.311: 0
       0.311 -    0.389: 1
  Chirality restraints: 1405
  Sorted by residual:
  chirality pdb=" CB  ILE B 169 "
            pdb=" CA  ILE B 169 "
            pdb=" CG1 ILE B 169 "
            pdb=" CG2 ILE B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CA  ILE B 169 "
            pdb=" N   ILE B 169 "
            pdb=" C   ILE B 169 "
            pdb=" CB  ILE B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.25    0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CB  THR A 527 "
            pdb=" CA  THR A 527 "
            pdb=" OG1 THR A 527 "
            pdb=" CG2 THR A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.38e-01
  ... (remaining 1402 not shown)

  Planarity restraints: 1551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 300 "   -0.040 5.00e-02 4.00e+02   5.95e-02 5.66e+00
        pdb=" N   PRO B 301 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 301 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 301 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 202 "    0.011 2.00e-02 2.50e+03   2.25e-02 5.08e+00
        pdb=" C   MET A 202 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   MET A 202 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA A 203 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 526 "   -0.012 2.00e-02 2.50e+03   1.66e-02 4.82e+00
        pdb=" CG  PHE A 526 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 526 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 526 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 526 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 526 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 526 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1548 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 61
        2.59 -     3.17: 6697
        3.17 -     3.74: 13491
        3.74 -     4.32: 16699
        4.32 -     4.90: 28176
  Nonbonded interactions: 65124
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 586 "
            pdb="MG    MG A 802 "
     model   vdw
     2.010 2.170
  nonbonded pdb=" O2G ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.060 2.170
  nonbonded pdb=" O2B ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.080 2.170
  nonbonded pdb=" O   ASP B 448 "
            pdb=" OD1 ASP B 448 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" OH  TYR A 686 "
            pdb=" O   LEU A 705 "
     model   vdw
     2.273 3.040
  ... (remaining 65119 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:                  0.010
  Normalize map: mean=0, sd=1:             3.860
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     7.820
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
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      :  0.003   0.063   8938  Z= 0.159
  Angle     :  0.798  10.034  12134  Z= 0.407
  Chirality :  0.043   0.389   1405
  Planarity :  0.005   0.059   1551
  Dihedral  : 17.846  89.426   3310
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 24.08 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.43 (0.19), residues: 1117
  helix: -2.61 (0.12), residues: 703
  sheet:  1.85 (0.68), residues: 62
  loop : -1.88 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 210 
 TYR   0.018   0.001   TYR B 566 
 PHE   0.038   0.002   PHE A 526 
 TRP   0.005   0.001   TRP B 648 
 HIS   0.004   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8938)
  covalent geometry    : angle       0.79812 (12134)
  hydrogen bonds       : bond        0.28272 (  505)
  hydrogen bonds       : angle       8.13257 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 219
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0867
  time to fit residues: 25.8863
Evaluate side-chains
  146 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 255 HIS
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 GLN
A 578 HIS
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 702 HIS
A 711 HIS
B 242 GLN
B 479 ASN
B 517 GLN
B 539 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.115215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.095176 restraints weight = 21111.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.097896 restraints weight = 11048.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.099748 restraints weight = 7108.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.101004 restraints weight = 5224.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.101793 restraints weight = 4196.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8938  Z= 0.247
  Angle     :  0.775   9.086  12134  Z= 0.387
  Chirality :  0.043   0.183   1405
  Planarity :  0.005   0.045   1551
  Dihedral  :  7.475  71.990   1261
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 23.13 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.24), residues: 1117
  helix:  0.64 (0.19), residues: 701
  sheet:  1.59 (0.68), residues: 62
  loop : -1.55 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 381 
 TYR   0.023   0.002   TYR B 541 
 PHE   0.019   0.002   PHE A 206 
 TRP   0.013   0.002   TRP A 308 
 HIS   0.005   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 8938)
  covalent geometry    : angle       0.77547 (12134)
  hydrogen bonds       : bond        0.07399 (  505)
  hydrogen bonds       : angle       4.65662 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 146
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.7829 (tp30) cc_final: 0.7486 (tp30)
  outliers start: 62
  outliers final: 37
  residues processed: 190
  average time/residue: 0.0691
  time to fit residues: 19.0472
Evaluate side-chains
  168 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  668 ASP
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ASP
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  540 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 35 optimal weight:   10.0000
   chunk 74 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 80 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 HIS
B 242 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.118238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.098619 restraints weight = 20633.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.101348 restraints weight = 10584.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.103201 restraints weight = 6724.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.104478 restraints weight = 4894.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.105290 restraints weight = 3911.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8938  Z= 0.149
  Angle     :  0.637   8.421  12134  Z= 0.312
  Chirality :  0.040   0.183   1405
  Planarity :  0.003   0.032   1551
  Dihedral  :  7.273  68.311   1261
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 25.76 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.25), residues: 1117
  helix:  1.50 (0.20), residues: 700
  sheet:  1.86 (0.66), residues: 61
  loop : -1.49 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 333 
 TYR   0.020   0.001   TYR A 686 
 PHE   0.016   0.001   PHE B 157 
 TRP   0.008   0.001   TRP B 263 
 HIS   0.003   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8938)
  covalent geometry    : angle       0.63705 (12134)
  hydrogen bonds       : bond        0.06253 (  505)
  hydrogen bonds       : angle       4.22292 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 156
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.7951 (tp30) cc_final: 0.7520 (tp30)
REVERT: A  447 PHE cc_start: 0.8540 (t80) cc_final: 0.8337 (t80)
REVERT: B  282 TYR cc_start: 0.8235 (m-80) cc_final: 0.8017 (m-80)
REVERT: B  308 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8176 (ttmm)
  outliers start: 41
  outliers final: 26
  residues processed: 188
  average time/residue: 0.0667
  time to fit residues: 18.2328
Evaluate side-chains
  165 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  448 ASP
Chi-restraints excluded: chain B residue  470 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0030
   chunk 97 optimal weight:    5.9990
   chunk 43 optimal weight:    0.1980
   chunk 61 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 GLN
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 HIS
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.119732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.100228 restraints weight = 20625.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.102938 restraints weight = 10613.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.104796 restraints weight = 6777.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.106024 restraints weight = 4936.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.106811 restraints weight = 3963.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8938  Z= 0.126
  Angle     :  0.619   7.949  12134  Z= 0.298
  Chirality :  0.039   0.179   1405
  Planarity :  0.003   0.027   1551
  Dihedral  :  7.158  65.935   1261
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 26.39 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.26), residues: 1117
  helix:  1.96 (0.20), residues: 693
  sheet:  1.84 (0.66), residues: 61
  loop : -1.49 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 333 
 TYR   0.019   0.001   TYR B 422 
 PHE   0.016   0.001   PHE B 240 
 TRP   0.008   0.001   TRP B 648 
 HIS   0.004   0.001   HIS A 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8938)
  covalent geometry    : angle       0.61938 (12134)
  hydrogen bonds       : bond        0.05498 (  505)
  hydrogen bonds       : angle       3.90868 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 SER cc_start: 0.8386 (m) cc_final: 0.8077 (p)
REVERT: A  392 GLU cc_start: 0.7893 (tp30) cc_final: 0.7514 (tp30)
REVERT: B  308 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8173 (ttmm)
  outliers start: 40
  outliers final: 28
  residues processed: 184
  average time/residue: 0.0690
  time to fit residues: 18.5191
Evaluate side-chains
  170 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ASP
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  527 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 110 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 90 optimal weight:    0.0870
   chunk 64 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.8762

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 HIS
A 642 GLN
B 242 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.116838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.096929 restraints weight = 20952.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.099602 restraints weight = 11100.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.101457 restraints weight = 7187.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.102720 restraints weight = 5295.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.103464 restraints weight = 4267.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8938  Z= 0.137
  Angle     :  0.642  14.030  12134  Z= 0.306
  Chirality :  0.040   0.202   1405
  Planarity :  0.003   0.024   1551
  Dihedral  :  7.079  65.031   1261
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.97 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.26), residues: 1117
  helix:  2.01 (0.20), residues: 701
  sheet:  1.77 (0.66), residues: 61
  loop : -1.42 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 319 
 TYR   0.013   0.001   TYR A 736 
 PHE   0.018   0.001   PHE A 447 
 TRP   0.012   0.001   TRP B 263 
 HIS   0.004   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8938)
  covalent geometry    : angle       0.64190 (12134)
  hydrogen bonds       : bond        0.05386 (  505)
  hydrogen bonds       : angle       3.82826 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7644 (mtm-85)
REVERT: A  296 SER cc_start: 0.8391 (m) cc_final: 0.8083 (p)
REVERT: A  392 GLU cc_start: 0.7939 (tp30) cc_final: 0.7559 (tp30)
REVERT: B  308 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8206 (ttmm)
  outliers start: 43
  outliers final: 30
  residues processed: 181
  average time/residue: 0.0665
  time to fit residues: 17.5011
Evaluate side-chains
  177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ASP
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  607 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0370
   chunk 44 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.9262

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 HIS
B 479 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.116049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.096211 restraints weight = 21089.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.098877 restraints weight = 11119.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.100724 restraints weight = 7209.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.101928 restraints weight = 5300.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.102786 restraints weight = 4293.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8938  Z= 0.140
  Angle     :  0.650  10.928  12134  Z= 0.308
  Chirality :  0.040   0.194   1405
  Planarity :  0.003   0.024   1551
  Dihedral  :  7.011  65.558   1261
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 26.60 %
    Favored  : 68.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.26), residues: 1117
  helix:  2.11 (0.20), residues: 701
  sheet:  1.74 (0.66), residues: 61
  loop : -1.42 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 319 
 TYR   0.020   0.001   TYR B 422 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B 263 
 HIS   0.004   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8938)
  covalent geometry    : angle       0.65039 (12134)
  hydrogen bonds       : bond        0.05301 (  505)
  hydrogen bonds       : angle       3.78015 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 150
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7671 (mtm-85)
REVERT: A  296 SER cc_start: 0.8375 (m) cc_final: 0.8077 (p)
REVERT: A  392 GLU cc_start: 0.7979 (tp30) cc_final: 0.7614 (tp30)
  outliers start: 46
  outliers final: 36
  residues processed: 183
  average time/residue: 0.0636
  time to fit residues: 17.2179
Evaluate side-chains
  179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 142
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain B residue  607 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0770
   chunk 79 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0170
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
A 259 HIS
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.117677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.097902 restraints weight = 20972.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.100674 restraints weight = 10856.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.102568 restraints weight = 6922.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.103838 restraints weight = 5049.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.104577 restraints weight = 4051.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8938  Z= 0.121
  Angle     :  0.633  10.281  12134  Z= 0.299
  Chirality :  0.039   0.190   1405
  Planarity :  0.003   0.041   1551
  Dihedral  :  6.912  67.436   1261
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 27.66 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.26), residues: 1117
  helix:  2.28 (0.20), residues: 696
  sheet:  1.73 (0.66), residues: 61
  loop : -1.39 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 319 
 TYR   0.018   0.001   TYR B 310 
 PHE   0.013   0.001   PHE B 157 
 TRP   0.014   0.001   TRP B 263 
 HIS   0.005   0.001   HIS A 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8938)
  covalent geometry    : angle       0.63326 (12134)
  hydrogen bonds       : bond        0.04978 (  505)
  hydrogen bonds       : angle       3.63995 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 154
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7586 (mtm-85)
REVERT: A  296 SER cc_start: 0.8349 (m) cc_final: 0.8071 (p)
REVERT: A  392 GLU cc_start: 0.7863 (tp30) cc_final: 0.7560 (tp30)
REVERT: A  404 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7652 (tt0)
REVERT: A  609 MET cc_start: 0.6279 (tpt) cc_final: 0.5884 (mmm)
  outliers start: 40
  outliers final: 31
  residues processed: 186
  average time/residue: 0.0740
  time to fit residues: 19.9682
Evaluate side-chains
  177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ASP
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  607 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 44 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 105 optimal weight:    0.3980
   chunk 60 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.117911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.098280 restraints weight = 20611.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.100976 restraints weight = 10896.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.102826 restraints weight = 7028.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.104082 restraints weight = 5157.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.104883 restraints weight = 4146.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8938  Z= 0.122
  Angle     :  0.643  10.798  12134  Z= 0.304
  Chirality :  0.039   0.191   1405
  Planarity :  0.003   0.024   1551
  Dihedral  :  6.813  69.183   1261
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 27.97 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.26), residues: 1117
  helix:  2.33 (0.20), residues: 696
  sheet:  1.73 (0.66), residues: 61
  loop : -1.41 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 319 
 TYR   0.019   0.001   TYR B 310 
 PHE   0.017   0.001   PHE A 447 
 TRP   0.013   0.001   TRP B 263 
 HIS   0.004   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8938)
  covalent geometry    : angle       0.64277 (12134)
  hydrogen bonds       : bond        0.04872 (  505)
  hydrogen bonds       : angle       3.59046 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7597 (mtm-85)
REVERT: A  296 SER cc_start: 0.8374 (m) cc_final: 0.8068 (p)
REVERT: A  392 GLU cc_start: 0.7941 (tp30) cc_final: 0.7595 (tp30)
REVERT: A  609 MET cc_start: 0.6297 (tpt) cc_final: 0.5911 (mmm)
REVERT: A  730 MET cc_start: 0.7558 (mmm) cc_final: 0.7267 (mmm)
  outliers start: 40
  outliers final: 34
  residues processed: 181
  average time/residue: 0.0616
  time to fit residues: 16.4649
Evaluate side-chains
  177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 142
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ASP
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  607 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 93 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 95 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 702 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.125030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.104225 restraints weight = 22116.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.107365 restraints weight = 10700.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.109425 restraints weight = 6625.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.110782 restraints weight = 4794.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.111604 restraints weight = 3837.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8938  Z= 0.127
  Angle     :  0.668  13.177  12134  Z= 0.315
  Chirality :  0.039   0.183   1405
  Planarity :  0.003   0.025   1551
  Dihedral  :  6.737  70.784   1261
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 29.13 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.26), residues: 1117
  helix:  2.33 (0.20), residues: 697
  sheet:  1.74 (0.65), residues: 61
  loop : -1.40 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 319 
 TYR   0.020   0.001   TYR B 310 
 PHE   0.015   0.001   PHE A 447 
 TRP   0.010   0.001   TRP B 263 
 HIS   0.006   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8938)
  covalent geometry    : angle       0.66775 (12134)
  hydrogen bonds       : bond        0.04866 (  505)
  hydrogen bonds       : angle       3.59203 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A  186 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7631 (mtm-85)
REVERT: A  296 SER cc_start: 0.8382 (m) cc_final: 0.8057 (p)
REVERT: A  392 GLU cc_start: 0.8000 (tp30) cc_final: 0.7648 (tp30)
REVERT: A  609 MET cc_start: 0.6322 (tpt) cc_final: 0.6023 (mmm)
REVERT: A  674 ASP cc_start: 0.8192 (t0) cc_final: 0.7785 (t0)
  outliers start: 38
  outliers final: 33
  residues processed: 176
  average time/residue: 0.0723
  time to fit residues: 18.4142
Evaluate side-chains
  175 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  607 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 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 = 0.3915 r_free = 0.3915 target = 0.120320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.100420 restraints weight = 22589.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.103463 restraints weight = 11189.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.105458 restraints weight = 7015.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.106800 restraints weight = 5099.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.107661 restraints weight = 4086.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8938  Z= 0.132
  Angle     :  0.692  12.796  12134  Z= 0.324
  Chirality :  0.040   0.179   1405
  Planarity :  0.003   0.024   1551
  Dihedral  :  6.675  72.015   1261
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 29.55 %
    Favored  : 66.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.26), residues: 1117
  helix:  2.33 (0.20), residues: 696
  sheet:  1.77 (0.65), residues: 61
  loop : -1.43 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 319 
 TYR   0.020   0.001   TYR B 310 
 PHE   0.019   0.001   PHE B 241 
 TRP   0.021   0.002   TRP B 263 
 HIS   0.003   0.001   HIS B 594 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8938)
  covalent geometry    : angle       0.69226 (12134)
  hydrogen bonds       : bond        0.04920 (  505)
  hydrogen bonds       : angle       3.58206 ( 1491)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7597 (mtm-85)
REVERT: A  296 SER cc_start: 0.8397 (m) cc_final: 0.8064 (p)
REVERT: A  392 GLU cc_start: 0.8013 (tp30) cc_final: 0.7658 (tp30)
REVERT: A  404 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7805 (tt0)
REVERT: A  609 MET cc_start: 0.6348 (tpt) cc_final: 0.6046 (mmm)
REVERT: A  674 ASP cc_start: 0.8222 (t0) cc_final: 0.7805 (t0)
REVERT: B  654 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7514 (mtt90)
  outliers start: 37
  outliers final: 33
  residues processed: 171
  average time/residue: 0.0753
  time to fit residues: 18.5835
Evaluate side-chains
  177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 141
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 CYS
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  619 SER
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain B residue  607 LEU
Chi-restraints excluded: chain B residue  654 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 102 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 702 HIS
A 726 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.118343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.098884 restraints weight = 22263.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.101654 restraints weight = 11499.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.103546 restraints weight = 7436.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.104818 restraints weight = 5483.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.105663 restraints weight = 4430.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8938  Z= 0.168
  Angle     :  0.716  12.957  12134  Z= 0.338
  Chirality :  0.042   0.179   1405
  Planarity :  0.003   0.025   1551
  Dihedral  :  6.700  72.072   1261
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 29.76 %
    Favored  : 66.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.26), residues: 1117
  helix:  2.09 (0.20), residues: 702
  sheet:  1.58 (0.65), residues: 63
  loop : -1.49 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 319 
 TYR   0.018   0.002   TYR B 310 
 PHE   0.019   0.002   PHE B 241 
 TRP   0.018   0.002   TRP B 263 
 HIS   0.006   0.001   HIS A 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8938)
  covalent geometry    : angle       0.71623 (12134)
  hydrogen bonds       : bond        0.05459 (  505)
  hydrogen bonds       : angle       3.77390 ( 1491)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1351.94 seconds
wall clock time: 24 minutes 5.31 seconds (1445.31 seconds total)