Starting phenix.real_space_refine
on Wed Feb  4 05:53:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n62_49046/02_2026/9n62_49046.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n62_49046/02_2026/9n62_49046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n62_49046/02_2026/9n62_49046.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n62_49046/02_2026/9n62_49046.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n62_49046/02_2026/9n62_49046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n62_49046/02_2026/9n62_49046.map"
  }
  resolution = 3.4
  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=   0.001 sd=   0.039
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      40      5.16       5
     C    5567      2.51       5
     N    1516      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 4309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4309
          Classifications: {'peptide': 551}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 20, 'TRANS': 530}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.13, per 1000 atoms: 0.24
  Number of scatterers: 8776
  At special positions: 0
  Unit cell: (73.385, 119.674, 137.738, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P       6     15.00
     O    1647      8.00
     N    1516      7.00
     C    5567      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: 0.74
  Conformation dependent library (CDL) restraints added in 337.4 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:
      51 helices and 5 sheets defined
      72.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 173 through 181
      removed outlier: 3.924A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 201
      removed outlier: 3.640A  pdb=" N   LEU A 189 " --> pdb=" O   ARG A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 217
      removed outlier: 4.148A  pdb=" N   PHE A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 269
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.691A  pdb=" N   PHE A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 280
      No H-bonds generated for 'chain 'A' and resid 278 through 280'
    Processing helix  chain 'A' and resid 281 through 286
      removed outlier: 3.966A  pdb=" N   MET A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 324
      removed outlier: 3.691A  pdb=" N   SER A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ASN A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   VAL A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ARG A 312 " --> pdb=" O   TRP A 308 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE A 319 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 321 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   TRP A 322 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 340
      removed outlier: 3.684A  pdb=" N   THR A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
    Processing helix  chain 'A' and resid 340 through 372
      removed outlier: 4.036A  pdb=" N   LYS A 347 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   TRP A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   TYR A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 379
    Processing helix  chain 'A' and resid 382 through 437
      removed outlier: 3.658A  pdb=" N   LYS A 393 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 394 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU A 396 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   THR A 399 " --> pdb=" O   GLN A 395 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LEU A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LEU A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   LYS A 423 " --> pdb=" O   GLY A 419 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL A 424 " --> pdb=" O   MET A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 475
      removed outlier: 3.893A  pdb=" N   MET A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   GLN A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      Proline residue:  A 466  - end of helix
    Processing helix  chain 'A' and resid 475 through 483
      removed outlier: 3.930A  pdb=" N   PHE A 479 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU A 480 " --> pdb=" O   GLU A 476 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR A 481 " --> pdb=" O   LYS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 552
      removed outlier: 3.812A  pdb=" N   VAL A 547 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ALA A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 572
      No H-bonds generated for 'chain 'A' and resid 570 through 572'
    Processing helix  chain 'A' and resid 573 through 580
    Processing helix  chain 'A' and resid 594 through 600
      removed outlier: 3.597A  pdb=" N   ALA A 600 " --> pdb=" O   GLN A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 619
    Processing helix  chain 'A' and resid 621 through 626
      removed outlier: 3.905A  pdb=" N   SER A 626 " --> pdb=" O   HIS A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 637 through 641
      removed outlier: 3.659A  pdb=" N   GLY A 640 " --> pdb=" O   ASP A 637 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER A 641 " --> pdb=" O   GLU A 638 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 637 through 641'
    Processing helix  chain 'A' and resid 644 through 658
    Processing helix  chain 'A' and resid 674 through 687
    Processing helix  chain 'A' and resid 688 through 694
      removed outlier: 3.510A  pdb=" N   ARG A 691 " --> pdb=" O   SER A 688 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   TYR A 692 " --> pdb=" O   PRO A 689 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A 693 " --> pdb=" O   GLU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 708
      removed outlier: 3.866A  pdb=" N   GLN A 708 " --> pdb=" O   SER A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 733
    Processing helix  chain 'A' and resid 734 through 742
    Processing helix  chain 'B' and resid 132 through 146
    Processing helix  chain 'B' and resid 148 through 168
      removed outlier: 3.657A  pdb=" N   LEU B 168 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 181
    Processing helix  chain 'B' and resid 185 through 234
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.642A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 289
      removed outlier: 3.565A  pdb=" N   ASP B 256 " --> pdb=" O   ARG B 252 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   THR B 257 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   THR B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU B 264 " --> pdb=" O   MET B 260 " (cutoff:3.500A)
      Proline residue:  B 265  - end of helix
    Processing helix  chain 'B' and resid 289 through 298
      removed outlier: 3.569A  pdb=" N   THR B 293 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 338
      removed outlier: 3.762A  pdb=" N   THR B 303 " --> pdb=" O   HIS B 299 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU B 316 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL B 331 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   VAL B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 346
    Processing helix  chain 'B' and resid 347 through 402
      removed outlier: 4.102A  pdb=" N   GLU B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL B 352 " --> pdb=" O   GLU B 348 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN B 361 " --> pdb=" O   GLU B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 436
      removed outlier: 4.374A  pdb=" N   GLY B 420 " --> pdb=" O   GLN B 416 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   TYR B 422 " --> pdb=" O   SER B 418 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL B 423 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   TYR B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   GLY B 431 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASN B 436 " --> pdb=" O   ASP B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 439
      No H-bonds generated for 'chain 'B' and resid 437 through 439'
    Processing helix  chain 'B' and resid 440 through 449
    Processing helix  chain 'B' and resid 508 through 517
    Processing helix  chain 'B' and resid 533 through 537
      removed outlier: 3.544A  pdb=" N   TYR B 537 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 543
      removed outlier: 3.735A  pdb=" N   HIS B 543 " --> pdb=" O   HIS B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 572 through 583
      removed outlier: 3.514A  pdb=" N   VAL B 576 " --> pdb=" O   GLU B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 598
    Processing helix  chain 'B' and resid 601 through 605
    Processing helix  chain 'B' and resid 608 through 623
      removed outlier: 4.431A  pdb=" N   ARG B 623 " --> pdb=" O   ARG B 619 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 647
      removed outlier: 4.010A  pdb=" N   GLU B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLN B 646 " --> pdb=" O   GLU B 642 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 666
      removed outlier: 3.571A  pdb=" N   VAL B 666 " --> pdb=" O   LEU B 663 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 519 through 524
      removed outlier: 3.537A  pdb=" N   GLY A 523 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   VAL A 508 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 519 through 524
      removed outlier: 3.537A  pdb=" N   GLY A 523 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   VAL A 508 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   PHE A 505 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   LEU A 563 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ASP A 507 " --> pdb=" O   GLN A 561 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   GLN A 561 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 581 through 584
      removed outlier: 6.689A  pdb=" N   ALA A 582 " --> pdb=" O   ILE A 665 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   ASP A 667 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   VAL A 584 " --> pdb=" O   ASP A 667 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU A 664 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ILE A 699 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LEU A 666 " --> pdb=" O   ILE A 699 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLU A 722 " --> pdb=" O   PHE A 714 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   GLU A 716 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 5.388A  pdb=" N   ILE A 720 " --> pdb=" O   GLU A 716 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 489 through 492
      removed outlier: 7.621A  pdb=" N   PHE B 491 " --> pdb=" O   GLN B 471 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   GLN B 471 " --> pdb=" O   PHE B 491 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   VAL B 473 " --> pdb=" O   GLY B 524 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLY B 524 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 546 through 549
      removed outlier: 6.543A  pdb=" N   VAL B 547 " --> pdb=" O   ILE B 629 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   ASP B 631 " --> pdb=" O   VAL B 547 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   VAL B 549 " --> pdb=" O   ASP B 631 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU B 628 " --> pdb=" O   LEU B 657 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   ILE B 659 " --> pdb=" O   LEU B 628 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LEU B 630 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   THR B 499 " --> pdb=" O   VAL B 658 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   ALA B 660 " --> pdb=" O   THR B 499 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   LEU B 501 " --> pdb=" O   ALA B 660 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   VAL B 498 " --> pdb=" O   GLN B 671 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   LEU B 673 " --> pdb=" O   VAL B 498 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ALA B 500 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   LEU B 675 " --> pdb=" O   ALA B 500 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   VAL B 502 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)

    566 hydrogen bonds defined for protein.
    1653 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1443
        1.31 -     1.43: 2310
        1.43 -     1.56: 5110
        1.56 -     1.69: 11
        1.69 -     1.82: 66
  Bond restraints: 8940
  Sorted by residual:
  bond pdb=" CA  THR A 184 "
       pdb=" CB  THR A 184 "
    ideal  model  delta    sigma   weight residual
    1.533  1.431  0.102 1.63e-02 3.76e+03 3.91e+01
  bond pdb=" CA  THR A 184 "
       pdb=" C   THR A 184 "
    ideal  model  delta    sigma   weight residual
    1.524  1.449  0.075 1.25e-02 6.40e+03 3.58e+01
  bond pdb=" N   THR A 184 "
       pdb=" CA  THR A 184 "
    ideal  model  delta    sigma   weight residual
    1.457  1.392  0.065 1.19e-02 7.06e+03 2.98e+01
  bond pdb=" CA  GLU A 183 "
       pdb=" C   GLU A 183 "
    ideal  model  delta    sigma   weight residual
    1.528  1.473  0.055 1.18e-02 7.18e+03 2.21e+01
  bond pdb=" C   GLU A 183 "
       pdb=" O   GLU A 183 "
    ideal  model  delta    sigma   weight residual
    1.234  1.177  0.057 1.22e-02 6.72e+03 2.19e+01
  ... (remaining 8935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 11954
        2.13 -     4.25: 142
        4.25 -     6.38: 27
        6.38 -     8.51: 10
        8.51 -    10.64: 5
  Bond angle restraints: 12138
  Sorted by residual:
  angle pdb=" N   THR A 184 "
        pdb=" CA  THR A 184 "
        pdb=" C   THR A 184 "
      ideal   model   delta    sigma   weight residual
     113.02  102.38   10.64 1.49e+00 4.50e-01 5.10e+01
  angle pdb=" CB  GLU B 166 "
        pdb=" CG  GLU B 166 "
        pdb=" CD  GLU B 166 "
      ideal   model   delta    sigma   weight residual
     112.60  119.40   -6.80 1.70e+00 3.46e-01 1.60e+01
  angle pdb=" C   THR A 184 "
        pdb=" CA  THR A 184 "
        pdb=" CB  THR A 184 "
      ideal   model   delta    sigma   weight residual
     110.44  104.06    6.38 1.68e+00 3.54e-01 1.44e+01
  angle pdb=" CA  GLU B 166 "
        pdb=" CB  GLU B 166 "
        pdb=" CG  GLU B 166 "
      ideal   model   delta    sigma   weight residual
     114.10  121.21   -7.11 2.00e+00 2.50e-01 1.26e+01
  angle pdb=" CA  GLU A 459 "
        pdb=" CB  GLU A 459 "
        pdb=" CG  GLU A 459 "
      ideal   model   delta    sigma   weight residual
     114.10  120.57   -6.47 2.00e+00 2.50e-01 1.05e+01
  ... (remaining 12133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 4566
       17.20 -    34.40: 584
       34.40 -    51.61: 190
       51.61 -    68.81: 42
       68.81 -    86.01: 16
  Dihedral angle restraints: 5398
    sinusoidal: 2178
      harmonic: 3220
  Sorted by residual:
  dihedral pdb=" C   THR A 184 "
           pdb=" N   THR A 184 "
           pdb=" CA  THR A 184 "
           pdb=" CB  THR A 184 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -110.33  -11.67     0      2.50e+00 1.60e-01 2.18e+01
  dihedral pdb=" CA  SER B 418 "
           pdb=" C   SER B 418 "
           pdb=" N   VAL B 419 "
           pdb=" CA  VAL B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.94  -18.06     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" N   GLU A 183 "
           pdb=" C   GLU A 183 "
           pdb=" CA  GLU A 183 "
           pdb=" CB  GLU A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.08    8.72     0      2.50e+00 1.60e-01 1.22e+01
  ... (remaining 5395 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 824
       0.027 -    0.054: 361
       0.054 -    0.080: 133
       0.080 -    0.107: 56
       0.107 -    0.134: 30
  Chirality restraints: 1404
  Sorted by residual:
  chirality pdb=" CA  ILE B 629 "
            pdb=" N   ILE B 629 "
            pdb=" C   ILE B 629 "
            pdb=" CB  ILE B 629 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CG  LEU B 385 "
            pdb=" CB  LEU B 385 "
            pdb=" CD1 LEU B 385 "
            pdb=" CD2 LEU B 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CG  LEU A 493 "
            pdb=" CB  LEU A 493 "
            pdb=" CD1 LEU A 493 "
            pdb=" CD2 LEU A 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 1401 not shown)

  Planarity restraints: 1551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 184 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.13e+01
        pdb=" C   THR A 184 "    0.058 2.00e-02 2.50e+03
        pdb=" O   THR A 184 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ARG A 185 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 299 "   -0.011 2.00e-02 2.50e+03   1.54e-02 3.56e+00
        pdb=" CG  HIS B 299 "    0.033 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 299 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 299 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 299 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 299 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 181 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.52e+00
        pdb=" C   GLY A 181 "    0.032 2.00e-02 2.50e+03
        pdb=" O   GLY A 181 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER A 182 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1548 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1561
        2.76 -     3.30: 8443
        3.30 -     3.83: 14779
        3.83 -     4.37: 15400
        4.37 -     4.90: 27690
  Nonbonded interactions: 67873
  Sorted by model distance:
  nonbonded pdb=" CB  GLU A 272 "
            pdb=" SG  CYS A 488 "
     model   vdw
     2.228 3.800
  nonbonded pdb=" OH  TYR A 686 "
            pdb=" O   LEU A 705 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   SER B 474 "
            pdb=" OG1 THR B 523 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OD2 ASP A 637 "
            pdb=" OG  SER A 641 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   TYR B 566 "
            pdb=" NH2 ARG B 623 "
     model   vdw
     2.339 3.120
  ... (remaining 67868 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.470
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
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      :  0.004   0.102   8940  Z= 0.224
  Angle     :  0.633  10.636  12138  Z= 0.320
  Chirality :  0.040   0.134   1404
  Planarity :  0.003   0.034   1551
  Dihedral  : 17.748  86.011   3332
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 23.68 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.10 %
  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:  2.15 (0.25), residues: 1117
  helix:  2.24 (0.19), residues: 726
  sheet:  2.06 (0.67), residues: 71
  loop : -0.67 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 662 
 TYR   0.012   0.001   TYR B 282 
 PHE   0.011   0.001   PHE A 306 
 TRP   0.006   0.001   TRP B 263 
 HIS   0.020   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8940)
  covalent geometry    : angle       0.63303 (12138)
  hydrogen bonds       : bond        0.14255 (  564)
  hydrogen bonds       : angle       4.85865 ( 1653)

*********************** 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
  54 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1060
  time to fit residues: 8.3421
Evaluate side-chains
  49 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0040
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.5150

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

Flipped N/Q/H residues before XYZ refinement:
A 578 HIS
B 681 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.076506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.059504 restraints weight = 30230.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 3.51
r_work: 0.2946 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8940  Z= 0.114
  Angle     :  0.499   8.320  12138  Z= 0.253
  Chirality :  0.037   0.134   1404
  Planarity :  0.003   0.032   1551
  Dihedral  :  8.661  81.792   1284
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 21.37 %
    Favored  : 76.95 %
  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:  2.73 (0.26), residues: 1117
  helix:  2.71 (0.20), residues: 732
  sheet:  1.83 (0.66), residues: 60
  loop : -0.37 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 287 
 TYR   0.010   0.001   TYR B 282 
 PHE   0.006   0.001   PHE A 276 
 TRP   0.005   0.001   TRP A 413 
 HIS   0.010   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 8940)
  covalent geometry    : angle       0.49947 (12138)
  hydrogen bonds       : bond        0.04947 (  564)
  hydrogen bonds       : angle       3.66393 ( 1653)

*********************** 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
  68 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 MET cc_start: 0.9158 (mpp) cc_final: 0.8828 (mpp)
REVERT: B  388 GLN cc_start: 0.8893 (tp40) cc_final: 0.8674 (tt0)
  outliers start: 16
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0862
  time to fit residues: 8.5309
Evaluate side-chains
  55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  315 CYS
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  658 VAL
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:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.075227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.057949 restraints weight = 30530.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 3.51
r_work: 0.2940 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8940  Z= 0.142
  Angle     :  0.500   6.779  12138  Z= 0.252
  Chirality :  0.038   0.129   1404
  Planarity :  0.003   0.032   1551
  Dihedral  :  7.520  77.199   1284
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 21.79 %
    Favored  : 76.00 %
  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:  2.96 (0.26), residues: 1117
  helix:  2.89 (0.20), residues: 731
  sheet:  1.82 (0.64), residues: 73
  loop : -0.36 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 373 
 TYR   0.012   0.001   TYR B 282 
 PHE   0.009   0.001   PHE B 345 
 TRP   0.005   0.001   TRP A 413 
 HIS   0.011   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8940)
  covalent geometry    : angle       0.50025 (12138)
  hydrogen bonds       : bond        0.05223 (  564)
  hydrogen bonds       : angle       3.55366 ( 1653)

*********************** 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
  73 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 52
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  285 MET cc_start: 0.9090 (mpp) cc_final: 0.8757 (mpp)
REVERT: A  332 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9322 (mp)
  outliers start: 21
  outliers final: 12
  residues processed: 71
  average time/residue: 0.0726
  time to fit residues: 8.0471
Evaluate side-chains
  60 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  428 TYR
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  658 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0470
   chunk 43 optimal weight:    0.0170
   chunk 61 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
B 384 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.076411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.059268 restraints weight = 30447.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 3.51
r_work: 0.2973 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8940  Z= 0.105
  Angle     :  0.486   7.436  12138  Z= 0.240
  Chirality :  0.037   0.125   1404
  Planarity :  0.002   0.032   1551
  Dihedral  :  7.182  79.214   1284
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 22.00 %
    Favored  : 75.79 %
  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:  3.11 (0.26), residues: 1117
  helix:  3.02 (0.20), residues: 731
  sheet:  1.87 (0.68), residues: 62
  loop : -0.23 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 287 
 TYR   0.009   0.001   TYR A 686 
 PHE   0.007   0.001   PHE B 412 
 TRP   0.005   0.001   TRP A 413 
 HIS   0.013   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 8940)
  covalent geometry    : angle       0.48553 (12138)
  hydrogen bonds       : bond        0.04662 (  564)
  hydrogen bonds       : angle       3.34661 ( 1653)

*********************** 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
  72 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 PHE cc_start: 0.7948 (m-80) cc_final: 0.7701 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 69
  average time/residue: 0.0749
  time to fit residues: 7.7961
Evaluate side-chains
  61 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  428 TYR
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  658 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:    0.0670
   chunk 89 optimal weight:    5.9990
   chunk 87 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.0920

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.074809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.057834 restraints weight = 30574.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.52
r_work: 0.2947 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8940  Z= 0.136
  Angle     :  0.506   8.590  12138  Z= 0.249
  Chirality :  0.037   0.125   1404
  Planarity :  0.002   0.031   1551
  Dihedral  :  7.021  77.535   1284
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 22.11 %
    Favored  : 75.05 %
  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:  3.17 (0.26), residues: 1117
  helix:  3.04 (0.20), residues: 731
  sheet:  1.92 (0.64), residues: 74
  loop : -0.26 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 287 
 TYR   0.011   0.001   TYR B 282 
 PHE   0.008   0.001   PHE A 207 
 TRP   0.005   0.001   TRP B 648 
 HIS   0.013   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8940)
  covalent geometry    : angle       0.50607 (12138)
  hydrogen bonds       : bond        0.04948 (  564)
  hydrogen bonds       : angle       3.40797 ( 1653)

*********************** 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
  76 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 49
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 PHE cc_start: 0.8022 (m-80) cc_final: 0.7796 (m-80)
REVERT: A  332 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9332 (mp)
REVERT: B  285 MET cc_start: 0.8788 (mmm) cc_final: 0.8410 (mtt)
REVERT: B  621 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8925 (tp)
REVERT: B  643 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7904 (tp-100)
  outliers start: 27
  outliers final: 18
  residues processed: 73
  average time/residue: 0.0658
  time to fit residues: 7.3423
Evaluate side-chains
  67 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  428 TYR
Chi-restraints excluded: chain B residue  621 LEU
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  643 GLN
Chi-restraints excluded: chain B residue  658 VAL
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:    0.9990
   chunk 106 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 32 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.078040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.061030 restraints weight = 30214.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 3.59
r_work: 0.2954 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8940  Z= 0.115
  Angle     :  0.503   8.000  12138  Z= 0.245
  Chirality :  0.037   0.126   1404
  Planarity :  0.002   0.031   1551
  Dihedral  :  6.855  78.045   1284
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 22.95 %
    Favored  : 74.84 %
  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:  3.22 (0.26), residues: 1117
  helix:  3.09 (0.19), residues: 731
  sheet:  1.84 (0.69), residues: 62
  loop : -0.14 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 373 
 TYR   0.008   0.001   TYR B 282 
 PHE   0.007   0.001   PHE A 207 
 TRP   0.005   0.001   TRP B 648 
 HIS   0.014   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8940)
  covalent geometry    : angle       0.50253 (12138)
  hydrogen bonds       : bond        0.04781 (  564)
  hydrogen bonds       : angle       3.32203 ( 1653)

*********************** 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
  70 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 49
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 PHE cc_start: 0.7958 (m-80) cc_final: 0.7748 (m-80)
REVERT: B  643 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7917 (tp-100)
  outliers start: 21
  outliers final: 19
  residues processed: 66
  average time/residue: 0.0768
  time to fit residues: 7.6804
Evaluate side-chains
  65 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  428 TYR
Chi-restraints excluded: chain B residue  592 MET
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  643 GLN
Chi-restraints excluded: chain B residue  658 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0870
   chunk 96 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A 261 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 = 0.3543 r_free = 0.3543 target = 0.078627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.061764 restraints weight = 30172.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 3.59
r_work: 0.2968 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8940  Z= 0.107
  Angle     :  0.493   8.432  12138  Z= 0.242
  Chirality :  0.037   0.124   1404
  Planarity :  0.002   0.030   1551
  Dihedral  :  6.663  77.508   1284
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.32 %
    Favored  : 75.05 %
  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:  3.31 (0.26), residues: 1117
  helix:  3.18 (0.20), residues: 724
  sheet:  1.85 (0.68), residues: 62
  loop : -0.07 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 287 
 TYR   0.009   0.001   TYR A 686 
 PHE   0.007   0.001   PHE B 412 
 TRP   0.005   0.001   TRP B 648 
 HIS   0.015   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8940)
  covalent geometry    : angle       0.49333 (12138)
  hydrogen bonds       : bond        0.04580 (  564)
  hydrogen bonds       : angle       3.25343 ( 1653)

*********************** 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
  71 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 46
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 MET cc_start: 0.9121 (mpp) cc_final: 0.8876 (mpp)
REVERT: B  643 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7904 (tp-100)
  outliers start: 25
  outliers final: 20
  residues processed: 67
  average time/residue: 0.0569
  time to fit residues: 5.8236
Evaluate side-chains
  67 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  428 TYR
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  643 GLN
Chi-restraints excluded: chain B residue  658 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 98 optimal weight:    0.2980
   chunk 64 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.075602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.058810 restraints weight = 30098.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 3.50
r_work: 0.2968 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8940  Z= 0.112
  Angle     :  0.493   8.655  12138  Z= 0.241
  Chirality :  0.036   0.124   1404
  Planarity :  0.002   0.030   1551
  Dihedral  :  6.471  76.543   1284
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.32 %
    Favored  : 75.05 %
  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:  3.33 (0.26), residues: 1117
  helix:  3.19 (0.20), residues: 724
  sheet:  1.84 (0.68), residues: 62
  loop : -0.06 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 373 
 TYR   0.009   0.001   TYR B 282 
 PHE   0.008   0.001   PHE B 412 
 TRP   0.005   0.001   TRP B 648 
 HIS   0.015   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8940)
  covalent geometry    : angle       0.49282 (12138)
  hydrogen bonds       : bond        0.04575 (  564)
  hydrogen bonds       : angle       3.24358 ( 1653)

*********************** 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
  74 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 49
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  196 MET cc_start: 0.9305 (mtp) cc_final: 0.9082 (ttm)
REVERT: B  643 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7888 (tp-100)
  outliers start: 25
  outliers final: 20
  residues processed: 71
  average time/residue: 0.0622
  time to fit residues: 6.9176
Evaluate side-chains
  69 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  428 TYR
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  643 GLN
Chi-restraints excluded: chain B residue  658 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0970
   chunk 70 optimal weight:    0.0770
   chunk 75 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 46 optimal weight:    9.9990
   chunk 97 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0470
   overall best weight:    0.3634

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.079784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.063016 restraints weight = 29877.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 3.57
r_work: 0.2999 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8940  Z= 0.100
  Angle     :  0.501   9.152  12138  Z= 0.242
  Chirality :  0.036   0.126   1404
  Planarity :  0.002   0.030   1551
  Dihedral  :  6.214  75.791   1284
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 22.95 %
    Favored  : 74.84 %
  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:  3.42 (0.26), residues: 1117
  helix:  3.24 (0.20), residues: 724
  sheet:  2.03 (0.65), residues: 72
  loop : -0.07 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 623 
 TYR   0.009   0.001   TYR A 686 
 PHE   0.007   0.001   PHE B 412 
 TRP   0.005   0.001   TRP B 648 
 HIS   0.016   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 8940)
  covalent geometry    : angle       0.50092 (12138)
  hydrogen bonds       : bond        0.04191 (  564)
  hydrogen bonds       : angle       3.13996 ( 1653)

*********************** 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
  72 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 HIS cc_start: 0.8777 (t-170) cc_final: 0.8575 (t-170)
  outliers start: 21
  outliers final: 15
  residues processed: 70
  average time/residue: 0.0674
  time to fit residues: 7.2239
Evaluate side-chains
  65 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  428 TYR
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  658 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 87 optimal weight:    0.2980
   chunk 89 optimal weight:    5.9990
   chunk 105 optimal weight:    5.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.079038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.062122 restraints weight = 30012.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 3.58
r_work: 0.2974 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8940  Z= 0.113
  Angle     :  0.508   9.103  12138  Z= 0.246
  Chirality :  0.037   0.127   1404
  Planarity :  0.002   0.030   1551
  Dihedral  :  6.078  74.376   1284
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 23.79 %
    Favored  : 74.84 %
  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 (0.26), residues: 1117
  helix:  3.26 (0.20), residues: 721
  sheet:  1.92 (0.69), residues: 62
  loop :  0.02 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 373 
 TYR   0.009   0.001   TYR B 282 
 PHE   0.010   0.001   PHE B 284 
 TRP   0.005   0.001   TRP B 648 
 HIS   0.016   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8940)
  covalent geometry    : angle       0.50841 (12138)
  hydrogen bonds       : bond        0.04388 (  564)
  hydrogen bonds       : angle       3.18784 ( 1653)

********************** 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
  63 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 13
  residues processed: 61
  average time/residue: 0.0619
  time to fit residues: 5.7610
Evaluate side-chains
  62 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  428 TYR
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  658 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 102 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0670
   chunk 89 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0470
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
A 498 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.077036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.060402 restraints weight = 29714.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 3.47
r_work: 0.3012 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8940  Z= 0.101
  Angle     :  0.502   9.316  12138  Z= 0.243
  Chirality :  0.036   0.125   1404
  Planarity :  0.002   0.030   1551
  Dihedral  :  5.964  74.305   1284
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 23.58 %
    Favored  : 74.53 %
  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:  3.48 (0.26), residues: 1117
  helix:  3.29 (0.19), residues: 724
  sheet:  2.08 (0.65), residues: 72
  loop : -0.06 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 373 
 TYR   0.008   0.001   TYR A 686 
 PHE   0.013   0.001   PHE B 284 
 TRP   0.008   0.001   TRP A 214 
 HIS   0.016   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 8940)
  covalent geometry    : angle       0.50219 (12138)
  hydrogen bonds       : bond        0.04160 (  564)
  hydrogen bonds       : angle       3.12271 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1565.39 seconds
wall clock time: 27 minutes 38.29 seconds (1658.29 seconds total)