Starting phenix.real_space_refine
on Wed Feb  4 04:01:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n64_49048/02_2026/9n64_49048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n64_49048/02_2026/9n64_49048.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/9n64_49048/02_2026/9n64_49048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n64_49048/02_2026/9n64_49048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n64_49048/02_2026/9n64_49048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n64_49048/02_2026/9n64_49048.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=   0.001 sd=   0.032
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       6      5.49       5
     Mg      2      5.21       5
     S      40      5.16       5
     C    5407      2.51       5
     N    1471      2.21       5
     O    1600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 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: 8526
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 549, 4232
          Classifications: {'peptide': 549}
          Link IDs: {'PTRANS': 22, 'TRANS': 526}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4226
          Classifications: {'peptide': 540}
          Link IDs: {'PTRANS': 20, 'TRANS': 519}
          Chain breaks: 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: 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: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.54, per 1000 atoms: 0.18
  Number of scatterers: 8526
  At special positions: 0
  Unit cell: (71.995, 88.935, 137.214, 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       6     15.00
     Mg      2     11.99
     O    1600      8.00
     N    1471      7.00
     C    5407      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: 0.54
  Conformation dependent library (CDL) restraints added in 207.4 milliseconds
  

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 4 sheets defined
      67.4% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 176 through 182
      removed outlier: 3.798A  pdb=" N   LEU A 180 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   GLY A 181 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   SER A 182 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 203
      removed outlier: 4.483A  pdb=" N   LEU A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLY A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 270
      removed outlier: 4.389A  pdb=" N   LEU A 234 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   THR A 235 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ASP A 246 " --> pdb=" O   GLU A 242 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASN A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   HIS A 255 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   HIS A 259 " --> pdb=" O   HIS A 255 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   PHE A 265 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   GLY A 266 " --> pdb=" O   GLY A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 279
    Processing helix  chain 'A' and resid 280 through 320
      removed outlier: 4.529A  pdb=" N   ASP A 291 " --> pdb=" O   ARG A 287 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   THR A 292 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   SER A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ARG A 312 " --> pdb=" O   TRP A 308 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   MET A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 335
    Processing helix  chain 'A' and resid 336 through 338
      No H-bonds generated for 'chain 'A' and resid 336 through 338'
    Processing helix  chain 'A' and resid 339 through 373
      removed outlier: 3.580A  pdb=" N   LYS A 343 " --> pdb=" O   PHE A 339 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A 344 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LYS A 347 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   TRP A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLN A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL A 356 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 380
      removed outlier: 3.711A  pdb=" N   PHE A 380 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 435
      removed outlier: 3.527A  pdb=" N   GLU A 386 " --> pdb=" O   ASN A 382 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLU A 396 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ILE A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A 403 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL A 406 " --> pdb=" O   GLN A 402 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   THR A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 475
      removed outlier: 4.108A  pdb=" N   THR A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE A 447 " --> pdb=" O   ASN A 443 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LEU A 449 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 461 " --> pdb=" O   ALA A 457 " (cutoff:3.500A)
      Proline residue:  A 466  - end of helix
    Processing helix  chain 'A' and resid 475 through 484
      removed outlier: 3.619A  pdb=" N   PHE A 479 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 552
    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: 3.589A  pdb=" N   ALA A 600 " --> pdb=" O   GLN A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 619
      removed outlier: 3.767A  pdb=" N   ILE A 612 " --> pdb=" O   THR A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 626
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 3.770A  pdb=" N   THR A 634 " --> pdb=" O   GLY A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 641
      removed outlier: 3.602A  pdb=" N   SER A 641 " --> pdb=" O   GLU A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 658
    Processing helix  chain 'A' and resid 677 through 687
      removed outlier: 3.711A  pdb=" N   VAL A 681 " --> pdb=" O   SER A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 694
      removed outlier: 4.252A  pdb=" N   TYR A 692 " --> pdb=" O   PRO A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 732
    Processing helix  chain 'A' and resid 734 through 741
    Processing helix  chain 'B' and resid 139 through 144
      removed outlier: 3.612A  pdb=" N   LYS B 143 " --> pdb=" O   TRP B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 167
      removed outlier: 3.943A  pdb=" N   VAL B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ALA B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA B 162 " --> pdb=" O   PHE B 158 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY B 165 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 178
      removed outlier: 4.050A  pdb=" N   TYR B 172 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 181
      No H-bonds generated for 'chain 'B' and resid 179 through 181'
    Processing helix  chain 'B' and resid 187 through 234
      removed outlier: 3.683A  pdb=" N   CYS B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER B 219 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ASN B 222 " --> pdb=" O   MET B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 4.050A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN B 242 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU B 243 " --> pdb=" O   GLY B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 255
    Processing helix  chain 'B' and resid 255 through 261
      removed outlier: 3.585A  pdb=" N   LEU B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 285
    Processing helix  chain 'B' and resid 286 through 292
      removed outlier: 3.696A  pdb=" N   SER B 289 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      Proline residue:  B 290  - end of helix
      No H-bonds generated for 'chain 'B' and resid 286 through 292'
    Processing helix  chain 'B' and resid 306 through 337
      removed outlier: 3.954A  pdb=" N   THR B 312 " --> pdb=" O   LYS B 308 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN B 315 " --> pdb=" O   ASN B 311 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL B 317 " --> pdb=" O   ARG B 313 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   GLN B 322 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ARG B 327 " --> pdb=" O   ASP B 323 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 328 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL B 331 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   VAL B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ARG B 333 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL B 336 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 347 through 384
      removed outlier: 3.831A  pdb=" N   GLN B 361 " --> pdb=" O   GLU B 357 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   CYS B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 397
      removed outlier: 4.072A  pdb=" N   GLN B 388 " --> pdb=" O   HIS B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'B' and resid 412 through 439
      removed outlier: 4.306A  pdb=" N   GLN B 416 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR B 422 " --> pdb=" O   SER B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 449
    Processing helix  chain 'B' and resid 508 through 516
    Processing helix  chain 'B' and resid 535 through 537
      No H-bonds generated for 'chain 'B' and resid 535 through 537'
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 560 through 565
    Processing helix  chain 'B' and resid 572 through 583
      removed outlier: 3.597A  pdb=" N   VAL B 576 " --> pdb=" O   GLU B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 590
      removed outlier: 3.787A  pdb=" N   GLN B 590 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 598
      removed outlier: 3.805A  pdb=" N   THR B 598 " --> pdb=" O   GLY B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 605
    Processing helix  chain 'B' and resid 608 through 622
    Processing helix  chain 'B' and resid 638 through 645
    Processing helix  chain 'B' and resid 647 through 651
      removed outlier: 3.937A  pdb=" N   SER B 650 " --> pdb=" O   ASP B 647 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ARG B 651 " --> pdb=" O   TRP B 648 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 647 through 651'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 528
      removed outlier: 6.904A  pdb=" N   GLN A 522 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   SER A 509 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   LEU A 524 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 583
      removed outlier: 6.885A  pdb=" N   ILE A 712 " --> pdb=" O   GLY A 723 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   GLY A 723 " --> pdb=" O   ILE A 712 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   PHE A 714 " --> pdb=" O   ARG A 721 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 493
      removed outlier: 4.294A  pdb=" N   VAL B 473 " --> pdb=" O   GLY B 524 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLY B 524 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 546 through 549
      removed outlier: 6.367A  pdb=" N   VAL B 547 " --> pdb=" O   ILE B 629 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ASP B 631 " --> pdb=" O   VAL B 547 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL B 549 " --> pdb=" O   ASP B 631 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU B 628 " --> pdb=" O   LEU B 657 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ILE B 659 " --> pdb=" O   LEU B 628 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU B 630 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   THR B 499 " --> pdb=" O   VAL B 658 " (cutoff:3.500A)

    490 hydrogen bonds defined for protein.
    1416 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: 1.19

  Time building geometry restraints manager: 0.73 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: 2778
        1.34 -     1.46: 1646
        1.46 -     1.58: 4179
        1.58 -     1.70: 7
        1.70 -     1.82: 66
  Bond restraints: 8676
  Sorted by residual:
  bond pdb=" C   SER A 286 "
       pdb=" N   ARG A 287 "
    ideal  model  delta    sigma   weight residual
    1.335  1.371 -0.036 1.38e-02 5.25e+03 6.71e+00
  bond pdb=" CA  LEU B 286 "
       pdb=" C   LEU B 286 "
    ideal  model  delta    sigma   weight residual
    1.522  1.564 -0.043 1.72e-02 3.38e+03 6.16e+00
  bond pdb=" C   CYS B 213 "
       pdb=" N   PHE B 214 "
    ideal  model  delta    sigma   weight residual
    1.335  1.366 -0.031 1.31e-02 5.83e+03 5.75e+00
  bond pdb=" C   ASP B 185 "
       pdb=" N   PRO B 186 "
    ideal  model  delta    sigma   weight residual
    1.337  1.366 -0.029 1.24e-02 6.50e+03 5.61e+00
  bond pdb=" C   PHE B 214 "
       pdb=" N   THR B 215 "
    ideal  model  delta    sigma   weight residual
    1.335  1.366 -0.031 1.38e-02 5.25e+03 5.17e+00
  ... (remaining 8671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 11599
        2.68 -     5.35: 126
        5.35 -     8.03: 37
        8.03 -    10.70: 12
       10.70 -    13.38: 1
  Bond angle restraints: 11775
  Sorted by residual:
  angle pdb=" CA  PRO B 301 "
        pdb=" N   PRO B 301 "
        pdb=" CD  PRO B 301 "
      ideal   model   delta    sigma   weight residual
     112.00  105.72    6.28 1.40e+00 5.10e-01 2.01e+01
  angle pdb=" CB  MET B 413 "
        pdb=" CG  MET B 413 "
        pdb=" SD  MET B 413 "
      ideal   model   delta    sigma   weight residual
     112.70  126.08  -13.38 3.00e+00 1.11e-01 1.99e+01
  angle pdb=" CA  GLN A 456 "
        pdb=" CB  GLN A 456 "
        pdb=" CG  GLN A 456 "
      ideal   model   delta    sigma   weight residual
     114.10  122.76   -8.66 2.00e+00 2.50e-01 1.88e+01
  angle pdb=" CB  MET A 730 "
        pdb=" CG  MET A 730 "
        pdb=" SD  MET A 730 "
      ideal   model   delta    sigma   weight residual
     112.70  123.03  -10.33 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" N   SER A 440 "
        pdb=" CA  SER A 440 "
        pdb=" C   SER A 440 "
      ideal   model   delta    sigma   weight residual
     110.41  114.45   -4.04 1.23e+00 6.61e-01 1.08e+01
  ... (remaining 11770 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 4512
       17.54 -    35.08: 545
       35.08 -    52.63: 144
       52.63 -    70.17: 35
       70.17 -    87.71: 15
  Dihedral angle restraints: 5251
    sinusoidal: 2122
      harmonic: 3129
  Sorted by residual:
  dihedral pdb=" CA  MET B 300 "
           pdb=" C   MET B 300 "
           pdb=" N   PRO B 301 "
           pdb=" CA  PRO B 301 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.07  -24.93     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  ASP B 185 "
           pdb=" C   ASP B 185 "
           pdb=" N   PRO B 186 "
           pdb=" CA  PRO B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.04  -19.96     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  ALA B 335 "
           pdb=" C   ALA B 335 "
           pdb=" N   VAL B 336 "
           pdb=" CA  VAL B 336 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.77  -18.23     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 5248 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1089
       0.050 -    0.100: 216
       0.100 -    0.149: 56
       0.149 -    0.199: 5
       0.199 -    0.249: 1
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" CB  ILE A 464 "
            pdb=" CA  ILE A 464 "
            pdb=" CG1 ILE A 464 "
            pdb=" CG2 ILE A 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  PRO B 301 "
            pdb=" N   PRO B 301 "
            pdb=" C   PRO B 301 "
            pdb=" CB  PRO B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CG  LEU A 703 "
            pdb=" CB  LEU A 703 "
            pdb=" CD1 LEU A 703 "
            pdb=" CD2 LEU A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.15e-01
  ... (remaining 1364 not shown)

  Planarity restraints: 1501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 348 "    0.013 2.00e-02 2.50e+03   2.72e-02 7.42e+00
        pdb=" CD  GLU B 348 "   -0.047 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 348 "    0.017 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 348 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 204 "   -0.032 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO A 205 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 205 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 205 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 683 "    0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   GLN A 683 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   GLN A 683 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 684 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1498 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 62
        2.58 -     3.16: 6866
        3.16 -     3.74: 13181
        3.74 -     4.32: 16804
        4.32 -     4.90: 28113
  Nonbonded interactions: 65026
  Sorted by model distance:
  nonbonded pdb=" O3G ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.005 2.170
  nonbonded pdb="MG    MG A 802 "
            pdb=" O   HOH A 902 "
     model   vdw
     2.014 2.170
  nonbonded pdb=" O3B ATP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     2.017 2.170
  nonbonded pdb=" OG  SER A 545 "
            pdb="MG    MG A 802 "
     model   vdw
     2.033 2.170
  nonbonded pdb="MG    MG A 802 "
            pdb=" O   HOH A 901 "
     model   vdw
     2.041 2.170
  ... (remaining 65021 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.060
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.380
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
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   0.087   8676  Z= 0.189
  Angle     :  0.793  13.376  11775  Z= 0.395
  Chirality :  0.044   0.249   1367
  Planarity :  0.005   0.049   1501
  Dihedral  : 17.193  87.710   3241
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 17.73 %
    Favored  : 81.84 %
  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: -0.69 (0.25), residues: 1079
  helix: -0.36 (0.19), residues: 654
  sheet:  1.15 (0.63), residues: 75
  loop : -0.73 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 235 
 TYR   0.015   0.001   TYR A 309 
 PHE   0.026   0.002   PHE A 206 
 TRP   0.026   0.002   TRP B 139 
 HIS   0.003   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 8676)
  covalent geometry    : angle       0.79280 (11775)
  hydrogen bonds       : bond        0.16328 (  490)
  hydrogen bonds       : angle       6.61130 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A  434 VAL cc_start: 0.7786 (t) cc_final: 0.7566 (t)
REVERT: B  399 MET cc_start: 0.7177 (tmm) cc_final: 0.6904 (tmm)
  outliers start: 4
  outliers final: 2
  residues processed: 108
  average time/residue: 0.0892
  time to fit residues: 13.2953
Evaluate side-chains
  78 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  345 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
A 540 ASN
B 242 GLN
B 406 GLN
B 584 HIS
B 664 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.088290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.073462 restraints weight = 28705.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.075360 restraints weight = 16578.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.076707 restraints weight = 11400.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.077593 restraints weight = 8676.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.078075 restraints weight = 7185.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8676  Z= 0.123
  Angle     :  0.575   8.581  11775  Z= 0.287
  Chirality :  0.039   0.153   1367
  Planarity :  0.003   0.039   1501
  Dihedral  :  8.365  67.789   1250
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.62 %
    Favored  : 80.11 %
  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:  0.41 (0.26), residues: 1079
  helix:  0.64 (0.21), residues: 669
  sheet:  1.08 (0.63), residues: 74
  loop : -0.46 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 235 
 TYR   0.012   0.001   TYR B 422 
 PHE   0.032   0.001   PHE B 158 
 TRP   0.009   0.001   TRP B 648 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8676)
  covalent geometry    : angle       0.57518 (11775)
  hydrogen bonds       : bond        0.05139 (  490)
  hydrogen bonds       : angle       4.37446 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  434 VAL cc_start: 0.7659 (t) cc_final: 0.7444 (t)
REVERT: B  399 MET cc_start: 0.7453 (tmm) cc_final: 0.7079 (tmm)
  outliers start: 21
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0777
  time to fit residues: 11.2172
Evaluate side-chains
  86 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  540 CYS
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  622 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
B 664 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.083913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.069360 restraints weight = 29083.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.071256 restraints weight = 16692.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.072523 restraints weight = 11396.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.073351 restraints weight = 8710.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.073807 restraints weight = 7228.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8676  Z= 0.199
  Angle     :  0.624   8.424  11775  Z= 0.310
  Chirality :  0.041   0.163   1367
  Planarity :  0.003   0.035   1501
  Dihedral  :  8.085  64.840   1247
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.70 %
    Favored  : 79.03 %
  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:  0.72 (0.26), residues: 1079
  helix:  0.92 (0.21), residues: 674
  sheet:  0.71 (0.63), residues: 76
  loop : -0.32 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 312 
 TYR   0.013   0.001   TYR B 422 
 PHE   0.025   0.002   PHE B 158 
 TRP   0.006   0.001   TRP A 413 
 HIS   0.003   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 8676)
  covalent geometry    : angle       0.62379 (11775)
  hydrogen bonds       : bond        0.05137 (  490)
  hydrogen bonds       : angle       4.30543 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  434 VAL cc_start: 0.7865 (t) cc_final: 0.7628 (t)
REVERT: B  399 MET cc_start: 0.7651 (tmm) cc_final: 0.7298 (tmm)
  outliers start: 21
  outliers final: 15
  residues processed: 93
  average time/residue: 0.0848
  time to fit residues: 10.9163
Evaluate side-chains
  87 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  540 CYS
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  622 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0770
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.086587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.071932 restraints weight = 28960.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.073891 restraints weight = 16415.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.075180 restraints weight = 11094.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.076133 restraints weight = 8471.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.076565 restraints weight = 6935.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8676  Z= 0.112
  Angle     :  0.558   8.487  11775  Z= 0.273
  Chirality :  0.039   0.171   1367
  Planarity :  0.003   0.032   1501
  Dihedral  :  7.613  71.705   1247
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.24 %
    Favored  : 79.35 %
  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:  1.09 (0.27), residues: 1079
  helix:  1.29 (0.21), residues: 670
  sheet:  0.77 (0.63), residues: 76
  loop : -0.35 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 235 
 TYR   0.010   0.001   TYR B 422 
 PHE   0.009   0.001   PHE B 302 
 TRP   0.006   0.001   TRP A 308 
 HIS   0.002   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8676)
  covalent geometry    : angle       0.55783 (11775)
  hydrogen bonds       : bond        0.04646 (  490)
  hydrogen bonds       : angle       3.95242 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  434 VAL cc_start: 0.7761 (t) cc_final: 0.7517 (t)
REVERT: A  730 MET cc_start: 0.8429 (mmm) cc_final: 0.8074 (mmm)
REVERT: B  399 MET cc_start: 0.7569 (tmm) cc_final: 0.7234 (tmm)
  outliers start: 13
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0740
  time to fit residues: 9.3974
Evaluate side-chains
  90 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  675 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0870
   chunk 44 optimal weight:    0.0670
   chunk 34 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 104 optimal weight:    0.2980
   chunk 94 optimal weight:    0.9980
   chunk 69 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
A 402 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.087359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.072710 restraints weight = 28736.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.074658 restraints weight = 16279.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.076037 restraints weight = 11034.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.076950 restraints weight = 8325.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.077485 restraints weight = 6840.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8676  Z= 0.105
  Angle     :  0.543   8.847  11775  Z= 0.264
  Chirality :  0.038   0.189   1367
  Planarity :  0.003   0.029   1501
  Dihedral  :  7.312  84.235   1247
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.68 %
    Favored  : 78.70 %
  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:  1.26 (0.27), residues: 1079
  helix:  1.43 (0.21), residues: 672
  sheet:  0.82 (0.63), residues: 76
  loop : -0.28 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 235 
 TYR   0.013   0.001   TYR B 415 
 PHE   0.027   0.001   PHE B 158 
 TRP   0.007   0.001   TRP A 308 
 HIS   0.002   0.000   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 8676)
  covalent geometry    : angle       0.54339 (11775)
  hydrogen bonds       : bond        0.04293 (  490)
  hydrogen bonds       : angle       3.80403 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A  434 VAL cc_start: 0.7731 (t) cc_final: 0.7481 (t)
REVERT: B  399 MET cc_start: 0.7531 (tmm) cc_final: 0.7194 (tmm)
  outliers start: 15
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0807
  time to fit residues: 10.4048
Evaluate side-chains
  90 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  641 CYS
Chi-restraints excluded: chain B residue  675 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0040
   chunk 79 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.1196

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.086042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.071396 restraints weight = 28543.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.073331 restraints weight = 16305.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.074625 restraints weight = 11074.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.075523 restraints weight = 8441.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.075894 restraints weight = 6958.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8676  Z= 0.132
  Angle     :  0.564   9.374  11775  Z= 0.273
  Chirality :  0.039   0.156   1367
  Planarity :  0.003   0.027   1501
  Dihedral  :  7.198  86.549   1247
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.46 %
    Favored  : 77.95 %
  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:  1.37 (0.27), residues: 1079
  helix:  1.53 (0.21), residues: 670
  sheet:  0.80 (0.63), residues: 76
  loop : -0.25 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 312 
 TYR   0.009   0.001   TYR B 422 
 PHE   0.026   0.001   PHE B 158 
 TRP   0.006   0.001   TRP A 308 
 HIS   0.002   0.001   HIS A 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8676)
  covalent geometry    : angle       0.56447 (11775)
  hydrogen bonds       : bond        0.04394 (  490)
  hydrogen bonds       : angle       3.84383 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A  434 VAL cc_start: 0.7815 (t) cc_final: 0.7567 (t)
REVERT: A  730 MET cc_start: 0.8415 (mmm) cc_final: 0.8041 (mmm)
REVERT: B  399 MET cc_start: 0.7640 (tmm) cc_final: 0.7309 (tmm)
  outliers start: 24
  outliers final: 18
  residues processed: 97
  average time/residue: 0.0688
  time to fit residues: 9.6822
Evaluate side-chains
  95 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  214 PHE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  675 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:    0.2980
   chunk 70 optimal weight:    0.1980
   chunk 102 optimal weight:    0.4980
   chunk 101 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 3 optimal weight:   20.0000
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
A 451 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.087315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.072595 restraints weight = 28966.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.074544 restraints weight = 16422.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.075905 restraints weight = 11123.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.076745 restraints weight = 8409.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.077385 restraints weight = 6956.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8676  Z= 0.104
  Angle     :  0.555   9.745  11775  Z= 0.266
  Chirality :  0.038   0.149   1367
  Planarity :  0.003   0.026   1501
  Dihedral  :  7.070  88.443   1247
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.89 %
    Favored  : 78.05 %
  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:  1.49 (0.27), residues: 1079
  helix:  1.63 (0.21), residues: 670
  sheet:  0.81 (0.63), residues: 76
  loop : -0.20 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 235 
 TYR   0.009   0.001   TYR B 422 
 PHE   0.046   0.001   PHE B 158 
 TRP   0.008   0.001   TRP A 308 
 HIS   0.002   0.000   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8676)
  covalent geometry    : angle       0.55501 (11775)
  hydrogen bonds       : bond        0.04209 (  490)
  hydrogen bonds       : angle       3.73699 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  434 VAL cc_start: 0.7771 (t) cc_final: 0.7519 (t)
REVERT: A  730 MET cc_start: 0.8419 (mmm) cc_final: 0.8125 (mmm)
REVERT: B  218 MET cc_start: 0.8548 (mmt) cc_final: 0.8298 (mmt)
REVERT: B  399 MET cc_start: 0.7668 (tmm) cc_final: 0.7319 (tmm)
  outliers start: 19
  outliers final: 17
  residues processed: 95
  average time/residue: 0.0760
  time to fit residues: 10.2567
Evaluate side-chains
  97 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  675 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 14 optimal weight:    0.3980
   chunk 73 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 18 optimal weight:    0.1980
   chunk 24 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.087336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.072638 restraints weight = 28652.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.074580 restraints weight = 16311.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.075804 restraints weight = 11076.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.076769 restraints weight = 8527.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.077346 restraints weight = 6989.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8676  Z= 0.105
  Angle     :  0.555  10.321  11775  Z= 0.264
  Chirality :  0.038   0.151   1367
  Planarity :  0.003   0.028   1501
  Dihedral  :  6.929  85.974   1247
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.78 %
    Favored  : 78.27 %
  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 (0.27), residues: 1079
  helix:  1.69 (0.21), residues: 670
  sheet:  0.84 (0.63), residues: 76
  loop : -0.19 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 312 
 TYR   0.009   0.001   TYR B 422 
 PHE   0.052   0.001   PHE B 158 
 TRP   0.024   0.001   TRP B 648 
 HIS   0.002   0.000   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 8676)
  covalent geometry    : angle       0.55517 (11775)
  hydrogen bonds       : bond        0.04076 (  490)
  hydrogen bonds       : angle       3.70586 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.7920 (p) cc_final: 0.7600 (t)
REVERT: A  242 GLU cc_start: 0.8409 (tt0) cc_final: 0.8147 (tt0)
REVERT: A  434 VAL cc_start: 0.7758 (t) cc_final: 0.7555 (t)
REVERT: A  730 MET cc_start: 0.8442 (mmm) cc_final: 0.8173 (mmm)
REVERT: B  218 MET cc_start: 0.8525 (mmt) cc_final: 0.8305 (mmt)
REVERT: B  399 MET cc_start: 0.7661 (tmm) cc_final: 0.7313 (tmm)
  outliers start: 18
  outliers final: 16
  residues processed: 93
  average time/residue: 0.0779
  time to fit residues: 10.0194
Evaluate side-chains
  95 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  284 PHE
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  675 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0770
   chunk 100 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
A 402 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.086494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.071763 restraints weight = 28721.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.073670 restraints weight = 16411.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.075042 restraints weight = 11195.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.075857 restraints weight = 8446.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.076515 restraints weight = 7006.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8676  Z= 0.123
  Angle     :  0.571  10.338  11775  Z= 0.273
  Chirality :  0.039   0.145   1367
  Planarity :  0.003   0.028   1501
  Dihedral  :  6.854  83.464   1247
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.35 %
    Favored  : 78.27 %
  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:  1.56 (0.27), residues: 1079
  helix:  1.71 (0.21), residues: 670
  sheet:  0.83 (0.63), residues: 76
  loop : -0.22 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 235 
 TYR   0.008   0.001   TYR B 422 
 PHE   0.052   0.001   PHE B 158 
 TRP   0.013   0.001   TRP B 648 
 HIS   0.002   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8676)
  covalent geometry    : angle       0.57072 (11775)
  hydrogen bonds       : bond        0.04163 (  490)
  hydrogen bonds       : angle       3.75749 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.7969 (p) cc_final: 0.7667 (t)
REVERT: A  242 GLU cc_start: 0.8413 (tt0) cc_final: 0.8167 (tt0)
REVERT: A  730 MET cc_start: 0.8460 (mmm) cc_final: 0.8197 (mmm)
REVERT: B  218 MET cc_start: 0.8564 (mmt) cc_final: 0.8348 (mmt)
REVERT: B  399 MET cc_start: 0.7675 (tmm) cc_final: 0.7332 (tmm)
  outliers start: 22
  outliers final: 18
  residues processed: 98
  average time/residue: 0.0742
  time to fit residues: 10.5562
Evaluate side-chains
  98 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  675 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 99 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
A 402 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.086850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.072136 restraints weight = 28758.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.074055 restraints weight = 16419.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.075406 restraints weight = 11196.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.076255 restraints weight = 8483.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.076896 restraints weight = 7012.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8676  Z= 0.116
  Angle     :  0.577  10.975  11775  Z= 0.273
  Chirality :  0.038   0.149   1367
  Planarity :  0.003   0.029   1501
  Dihedral  :  6.803  81.943   1247
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.11 %
    Favored  : 77.73 %
  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:  1.58 (0.27), residues: 1079
  helix:  1.73 (0.21), residues: 670
  sheet:  0.84 (0.63), residues: 76
  loop : -0.23 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 273 
 TYR   0.009   0.001   TYR B 422 
 PHE   0.052   0.001   PHE B 158 
 TRP   0.015   0.001   TRP B 648 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8676)
  covalent geometry    : angle       0.57670 (11775)
  hydrogen bonds       : bond        0.04147 (  490)
  hydrogen bonds       : angle       3.73747 ( 1416)

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

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

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2158 Ramachandran restraints generated.
    1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.7973 (p) cc_final: 0.7679 (t)
REVERT: A  242 GLU cc_start: 0.8398 (tt0) cc_final: 0.8152 (tt0)
REVERT: A  730 MET cc_start: 0.8442 (mmm) cc_final: 0.8188 (mmm)
REVERT: B  218 MET cc_start: 0.8547 (mmt) cc_final: 0.8340 (mmt)
REVERT: B  399 MET cc_start: 0.7690 (tmm) cc_final: 0.7356 (tmm)
  outliers start: 20
  outliers final: 20
  residues processed: 96
  average time/residue: 0.0708
  time to fit residues: 9.6974
Evaluate side-chains
  100 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  452 ASN
Chi-restraints excluded: chain B residue  622 VAL
Chi-restraints excluded: chain B residue  675 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.086719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.072109 restraints weight = 28396.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.073998 restraints weight = 16222.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.075338 restraints weight = 11077.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.076163 restraints weight = 8380.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.076460 restraints weight = 6937.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8676  Z= 0.115
  Angle     :  0.579  11.053  11775  Z= 0.273
  Chirality :  0.038   0.150   1367
  Planarity :  0.003   0.029   1501
  Dihedral  :  6.734  80.265   1247
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.57 %
    Favored  : 78.05 %
  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:  1.61 (0.27), residues: 1079
  helix:  1.77 (0.21), residues: 670
  sheet:  0.84 (0.64), residues: 76
  loop : -0.25 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 235 
 TYR   0.009   0.001   TYR B 422 
 PHE   0.050   0.001   PHE B 158 
 TRP   0.016   0.001   TRP B 648 
 HIS   0.002   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8676)
  covalent geometry    : angle       0.57902 (11775)
  hydrogen bonds       : bond        0.04126 (  490)
  hydrogen bonds       : angle       3.72608 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1124.86 seconds
wall clock time: 20 minutes 9.38 seconds (1209.38 seconds total)