Starting phenix.real_space_refine
on Fri Aug 22 21:10:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t46_41021/08_2025/8t46_41021.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t46_41021/08_2025/8t46_41021.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t46_41021/08_2025/8t46_41021.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t46_41021/08_2025/8t46_41021.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t46_41021/08_2025/8t46_41021.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t46_41021/08_2025/8t46_41021.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4980      2.51       5
     N    1394      2.21       5
     O    1478      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7885
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 562, 3661
          Classifications: {'peptide': 562}
          Incomplete info: {'truncation_to_alanine': 204}
          Link IDs: {'PTRANS': 18, 'TRANS': 543}
          Chain breaks: 1
          Unresolved chain link angles: 13
          Unresolved non-hydrogen bonds: 725
          Unresolved non-hydrogen angles: 937
          Unresolved non-hydrogen dihedrals: 586
          Unresolved non-hydrogen chiralities: 76
          Planarities with less than four sites: {'HIS:plan': 7, 'GLU:plan': 16, 'GLN:plan1': 24, 'PHE:plan': 6, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 5, 'ARG:plan': 11, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 400
    Chain: "B"
      Number of atoms: 4224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4224
          Classifications: {'peptide': 551}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 20, 'TRANS': 530}
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 62
  Time building chain proxies: 2.04, per 1000 atoms: 0.26
  Number of scatterers: 7885
  At special positions: 0
  Unit cell: (73.832, 122.494, 139.274, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    1478      8.00
     N    1394      7.00
     C    4980      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: 0.69
  Conformation dependent library (CDL) restraints added in 442.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2050

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      73.5% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 173 through 181
      removed outlier: 4.138A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 202
      removed outlier: 4.139A  pdb=" N   LEU A 189 " --> pdb=" O   ARG A 185 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   MET A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 217
      removed outlier: 4.319A  pdb=" N   PHE A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 270
      removed outlier: 3.668A  pdb=" N   ASN A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 280
      No H-bonds generated for 'chain 'A' and resid 278 through 280'
    Processing helix  chain 'A' and resid 281 through 324
      removed outlier: 4.010A  pdb=" N   MET A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   THR A 289 " --> pdb=" O   MET A 285 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   GLU A 290 " --> pdb=" O   SER A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 340
      removed outlier: 4.767A  pdb=" N   VAL A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A 335 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
    Processing helix  chain 'A' and resid 340 through 373
      removed outlier: 3.959A  pdb=" N   LYS A 347 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   TRP A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   TYR A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 382 through 421
      removed outlier: 4.255A  pdb=" N   THR A 399 " --> pdb=" O   GLN A 395 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LEU A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLY A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 437
      removed outlier: 3.750A  pdb=" N   LEU A 427 " --> pdb=" O   LYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 462
    Processing helix  chain 'A' and resid 464 through 484
      removed outlier: 3.577A  pdb=" N   LYS A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG A 484 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 552
    Processing helix  chain 'A' and resid 573 through 580
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 608 through 619
    Processing helix  chain 'A' and resid 621 through 627
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 3.716A  pdb=" N   ASP A 633 " --> pdb=" O   GLN A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 641
      removed outlier: 3.554A  pdb=" N   GLY A 640 " --> pdb=" O   ASP A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 660
    Processing helix  chain 'A' and resid 674 through 687
    Processing helix  chain 'A' and resid 688 through 694
      removed outlier: 3.891A  pdb=" N   TYR A 692 " --> pdb=" O   PRO A 689 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ARG A 694 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 708
      removed outlier: 3.705A  pdb=" N   GLN A 708 " --> pdb=" O   SER A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 733
    Processing helix  chain 'A' and resid 734 through 741
    Processing helix  chain 'B' and resid 132 through 146
    Processing helix  chain 'B' and resid 148 through 167
    Processing helix  chain 'B' and resid 167 through 181
      removed outlier: 4.040A  pdb=" N   HIS B 171 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 234
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.820A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 262
      removed outlier: 4.811A  pdb=" N   THR B 257 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   THR B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 289
      removed outlier: 3.930A  pdb=" N   LEU B 266 " --> pdb=" O   ASN B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 298
    Processing helix  chain 'B' and resid 299 through 346
      removed outlier: 3.616A  pdb=" N   GLU B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL B 331 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   VAL B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   GLN B 340 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   THR B 341 " --> pdb=" O   GLY B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 402
      removed outlier: 4.159A  pdb=" N   ARG B 354 " --> pdb=" O   HIS B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 437
      removed outlier: 4.491A  pdb=" N   GLY B 420 " --> pdb=" O   GLN B 416 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   TYR B 422 " --> pdb=" O   SER B 418 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   VAL B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   TYR B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   GLY B 431 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU B 434 " --> pdb=" O   TYR B 430 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 448
    Processing helix  chain 'B' and resid 509 through 515
      removed outlier: 3.661A  pdb=" N   ALA B 513 " --> pdb=" O   LYS B 509 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU B 515 " --> pdb=" O   THR B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 518
      No H-bonds generated for 'chain 'B' and resid 516 through 518'
    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
      removed outlier: 3.950A  pdb=" N   HIS B 543 " --> pdb=" O   HIS B 539 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   SER B 544 " --> pdb=" O   CYS B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 573 through 583
      removed outlier: 4.091A  pdb=" N   MET B 577 " --> pdb=" O   ASP B 573 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA B 578 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   ALA B 579 " --> pdb=" O   LYS B 575 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA B 580 " --> pdb=" O   VAL B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 592
      removed outlier: 3.520A  pdb=" N   GLN B 590 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLU B 591 " --> pdb=" O   ASP B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 623
      removed outlier: 4.238A  pdb=" N   ARG B 623 " --> pdb=" O   ARG B 619 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 637
      removed outlier: 4.082A  pdb=" N   ALA B 636 " --> pdb=" O   GLU B 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 647
      removed outlier: 3.668A  pdb=" N   GLU B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 652
    Processing helix  chain 'B' and resid 662 through 668
      removed outlier: 4.008A  pdb=" N   THR B 665 " --> pdb=" O   ARG B 662 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLN B 667 " --> pdb=" O   GLN B 664 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 519 through 524
      removed outlier: 5.745A  pdb=" N   GLN A 522 " --> pdb=" O   PHE A 510 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   PHE A 510 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 508 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   PHE A 505 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU A 563 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   ASP A 507 " --> pdb=" O   GLN A 561 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   GLN A 561 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584
      removed outlier: 3.812A  pdb=" N   VAL A 584 " --> pdb=" O   ILE A 665 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASP A 667 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LEU A 664 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   ILE A 699 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   LEU A 666 " --> pdb=" O   ILE A 699 " (cutoff:3.500A)
      removed outlier: 5.916A  pdb=" N   THR A 534 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   GLU A 716 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   ILE A 720 " --> pdb=" O   GLU A 716 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 489 through 492
      removed outlier: 4.910A  pdb=" N   LEU B 489 " --> pdb=" O   ASP B 472 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   PHE B 470 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   LEU B 528 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   ASP B 472 " --> pdb=" O   GLN B 526 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   GLN B 526 " --> pdb=" O   ASP B 472 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 546 through 548
      removed outlier: 6.963A  pdb=" N   VAL B 547 " --> pdb=" O   ILE B 629 " (cutoff:3.500A)
      removed outlier: 8.377A  pdb=" N   ASP B 631 " --> pdb=" O   VAL B 547 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   THR B 499 " --> pdb=" O   VAL B 658 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ALA B 660 " --> pdb=" O   THR B 499 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   LEU B 501 " --> pdb=" O   ALA B 660 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ALA B 500 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)

    589 hydrogen bonds defined for protein.
    1728 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: 1.50

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2690
        1.34 -     1.46: 1645
        1.46 -     1.58: 3610
        1.58 -     1.70: 0
        1.70 -     1.81: 56
  Bond restraints: 8001
  Sorted by residual:
  bond pdb=" N   GLU A 201 "
       pdb=" CA  GLU A 201 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.70e+00
  bond pdb=" N   ASP B 573 "
       pdb=" CA  ASP B 573 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.032 1.28e-02 6.10e+03 6.07e+00
  bond pdb=" N   LEU B 385 "
       pdb=" CA  LEU B 385 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.20e-02 6.94e+03 5.85e+00
  bond pdb=" N   ASN B 222 "
       pdb=" CA  ASN B 222 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.19e-02 7.06e+03 5.73e+00
  bond pdb=" N   MET A 202 "
       pdb=" CA  MET A 202 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.64e+00
  ... (remaining 7996 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 10760
        2.33 -     4.65: 99
        4.65 -     6.98: 18
        6.98 -     9.31: 6
        9.31 -    11.63: 1
  Bond angle restraints: 10884
  Sorted by residual:
  angle pdb=" C   LYS B 575 "
        pdb=" N   VAL B 576 "
        pdb=" CA  VAL B 576 "
      ideal   model   delta    sigma   weight residual
     122.63  117.56    5.07 1.19e+00 7.06e-01 1.81e+01
  angle pdb=" CB  MET B 218 "
        pdb=" CG  MET B 218 "
        pdb=" SD  MET B 218 "
      ideal   model   delta    sigma   weight residual
     112.70  124.33  -11.63 3.00e+00 1.11e-01 1.50e+01
  angle pdb=" N   THR A 223 "
        pdb=" CA  THR A 223 "
        pdb=" C   THR A 223 "
      ideal   model   delta    sigma   weight residual
     113.01  108.69    4.32 1.20e+00 6.94e-01 1.30e+01
  angle pdb=" CA  MET B 218 "
        pdb=" CB  MET B 218 "
        pdb=" CG  MET B 218 "
      ideal   model   delta    sigma   weight residual
     114.10  120.50   -6.40 2.00e+00 2.50e-01 1.03e+01
  angle pdb=" C   MET A 202 "
        pdb=" N   ALA A 203 "
        pdb=" CA  ALA A 203 "
      ideal   model   delta    sigma   weight residual
     122.06  116.22    5.84 1.86e+00 2.89e-01 9.86e+00
  ... (remaining 10879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 4134
       17.50 -    35.00: 457
       35.00 -    52.50: 141
       52.50 -    70.01: 18
       70.01 -    87.51: 10
  Dihedral angle restraints: 4760
    sinusoidal: 1574
      harmonic: 3186
  Sorted by residual:
  dihedral pdb=" CA  ARG A 287 "
           pdb=" C   ARG A 287 "
           pdb=" N   VAL A 288 "
           pdb=" CA  VAL A 288 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.76  -20.24     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  ASP B 472 "
           pdb=" CB  ASP B 472 "
           pdb=" CG  ASP B 472 "
           pdb=" OD1 ASP B 472 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.39   58.39     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  ASN A 283 "
           pdb=" C   ASN A 283 "
           pdb=" N   ILE A 284 "
           pdb=" CA  ILE A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.20  -16.80     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 4757 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1033
       0.048 -    0.096: 218
       0.096 -    0.144: 49
       0.144 -    0.192: 3
       0.192 -    0.240: 1
  Chirality restraints: 1304
  Sorted by residual:
  chirality pdb=" CG  LEU A 327 "
            pdb=" CB  LEU A 327 "
            pdb=" CD1 LEU A 327 "
            pdb=" CD2 LEU A 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  MET A 374 "
            pdb=" N   MET A 374 "
            pdb=" C   MET A 374 "
            pdb=" CB  MET A 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.03e-01
  chirality pdb=" CA  LEU B 385 "
            pdb=" N   LEU B 385 "
            pdb=" C   LEU B 385 "
            pdb=" CB  LEU B 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.94e-01
  ... (remaining 1301 not shown)

  Planarity restraints: 1421
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 306 "   -0.015 2.00e-02 2.50e+03   2.99e-02 8.91e+00
        pdb=" C   PHE A 306 "    0.052 2.00e-02 2.50e+03
        pdb=" O   PHE A 306 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU A 307 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 301 "    0.014 2.00e-02 2.50e+03   2.90e-02 8.40e+00
        pdb=" C   GLU A 301 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLU A 301 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN A 302 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 305 "    0.014 2.00e-02 2.50e+03   2.85e-02 8.10e+00
        pdb=" C   LEU A 305 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   LEU A 305 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE A 306 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1418 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2131
        2.80 -     3.33: 7880
        3.33 -     3.85: 12995
        3.85 -     4.38: 13091
        4.38 -     4.90: 23591
  Nonbonded interactions: 59688
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 278 "
            pdb=" OG1 THR A 281 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   PHE B 158 "
            pdb=" OG  SER B 206 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG  SER A 440 "
            pdb=" OD1 ASN A 443 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OE1 GLU B 307 "
            pdb=" OH  TYR B 376 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   PRO B 461 "
            pdb=" OH  TYR B 541 "
     model   vdw
     2.324 3.040
  ... (remaining 59683 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:             5.230
  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:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8001  Z= 0.191
  Angle     :  0.633  11.634  10884  Z= 0.354
  Chirality :  0.041   0.240   1304
  Planarity :  0.006   0.047   1421
  Dihedral  : 16.789  87.506   2710
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.08 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 27.97 %
    Favored  : 71.75 %
  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 aren not related in a simple way.
  whole:  1.31 (0.25), residues: 1107
  helix:  1.28 (0.19), residues: 757
  sheet:  0.94 (0.69), residues: 64
  loop : -0.08 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 226 
 TYR   0.021   0.001   TYR A 481 
 PHE   0.009   0.001   PHE B 491 
 TRP   0.006   0.001   TRP A 214 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8001)
  covalent geometry    : angle       0.63340 (10884)
  hydrogen bonds       : bond        0.14003 (  589)
  hydrogen bonds       : angle       5.49461 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7847 (tt0)
REVERT: A  451 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8070 (tm-30)
REVERT: A  465 TYR cc_start: 0.6256 (t80) cc_final: 0.6047 (t80)
REVERT: B  424 GLN cc_start: 0.9013 (tt0) cc_final: 0.8592 (tp40)
  outliers start: 2
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0840
  time to fit residues: 13.1882
Evaluate side-chains
  85 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0070
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.1804

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 251 ASN
A 302 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.133111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.101979 restraints weight = 16091.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.101893 restraints weight = 9228.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.103513 restraints weight = 6781.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.103686 restraints weight = 5833.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.104029 restraints weight = 5427.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8001  Z= 0.162
  Angle     :  0.521   6.597  10884  Z= 0.271
  Chirality :  0.038   0.134   1304
  Planarity :  0.003   0.045   1421
  Dihedral  :  3.363  15.355   1183
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 27.13 %
    Favored  : 68.81 %
  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 aren not related in a simple way.
  whole:  2.22 (0.26), residues: 1107
  helix:  1.93 (0.19), residues: 767
  sheet:  0.80 (0.71), residues: 63
  loop :  0.49 (0.38), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 368 
 TYR   0.013   0.001   TYR B 366 
 PHE   0.011   0.001   PHE B 470 
 TRP   0.013   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8001)
  covalent geometry    : angle       0.52068 (10884)
  hydrogen bonds       : bond        0.04923 (  589)
  hydrogen bonds       : angle       3.84155 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7399 (t-100) cc_final: 0.6962 (t-100)
REVERT: A  242 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7978 (tt0)
REVERT: A  285 MET cc_start: 0.7736 (mpp) cc_final: 0.7369 (mpp)
REVERT: A  335 LEU cc_start: 0.7966 (tt) cc_final: 0.7354 (tp)
REVERT: A  451 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8346 (tm-30)
REVERT: A  465 TYR cc_start: 0.6047 (t80) cc_final: 0.5706 (t80)
REVERT: A  469 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6954 (mm110)
REVERT: B  179 ILE cc_start: 0.8431 (mm) cc_final: 0.8211 (mm)
REVERT: B  399 MET cc_start: 0.8745 (tpp) cc_final: 0.8036 (ttm)
  outliers start: 29
  outliers final: 15
  residues processed: 112
  average time/residue: 0.0732
  time to fit residues: 12.1342
Evaluate side-chains
  92 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  469 GLN
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  680 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   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 302 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.135035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.103151 restraints weight = 15917.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.103404 restraints weight = 9229.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.105668 restraints weight = 6660.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.105741 restraints weight = 5203.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.105849 restraints weight = 4934.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8001  Z= 0.115
  Angle     :  0.469   6.616  10884  Z= 0.242
  Chirality :  0.036   0.130   1304
  Planarity :  0.003   0.043   1421
  Dihedral  :  3.164  14.949   1183
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 27.83 %
    Favored  : 67.97 %
  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 aren not related in a simple way.
  whole:  2.63 (0.26), residues: 1107
  helix:  2.29 (0.19), residues: 761
  sheet:  0.61 (0.80), residues: 50
  loop :  0.59 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 226 
 TYR   0.016   0.001   TYR A 481 
 PHE   0.010   0.001   PHE A 447 
 TRP   0.010   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8001)
  covalent geometry    : angle       0.46862 (10884)
  hydrogen bonds       : bond        0.04335 (  589)
  hydrogen bonds       : angle       3.51597 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 86
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7319 (t-100) cc_final: 0.6828 (t-100)
REVERT: A  242 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8023 (tt0)
REVERT: A  285 MET cc_start: 0.7721 (mpp) cc_final: 0.7159 (mpp)
REVERT: A  335 LEU cc_start: 0.7930 (tt) cc_final: 0.7301 (tp)
REVERT: A  451 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8328 (tm-30)
REVERT: B  399 MET cc_start: 0.8700 (tpp) cc_final: 0.8073 (ttm)
REVERT: B  453 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8786 (mm)
  outliers start: 30
  outliers final: 19
  residues processed: 111
  average time/residue: 0.0821
  time to fit residues: 13.0114
Evaluate side-chains
  100 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  560 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 110 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 99 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 101 optimal weight:    0.1980
   chunk 62 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 80 optimal weight:    0.3980
   chunk 36 optimal weight:    7.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.138161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.104523 restraints weight = 16290.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.107871 restraints weight = 8490.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.110046 restraints weight = 5645.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.111321 restraints weight = 4387.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.111950 restraints weight = 3777.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8001  Z= 0.108
  Angle     :  0.461   7.126  10884  Z= 0.236
  Chirality :  0.036   0.131   1304
  Planarity :  0.003   0.042   1421
  Dihedral  :  3.056  14.536   1183
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 27.83 %
    Favored  : 68.11 %
  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 aren not related in a simple way.
  whole:  2.83 (0.26), residues: 1107
  helix:  2.44 (0.19), residues: 766
  sheet:  0.63 (0.82), residues: 50
  loop :  0.63 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 333 
 TYR   0.013   0.001   TYR A 465 
 PHE   0.010   0.001   PHE A 447 
 TRP   0.009   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8001)
  covalent geometry    : angle       0.46147 (10884)
  hydrogen bonds       : bond        0.04069 (  589)
  hydrogen bonds       : angle       3.36318 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 87
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7253 (t-100) cc_final: 0.6829 (t-100)
REVERT: A  242 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7971 (tt0)
REVERT: A  285 MET cc_start: 0.7792 (mpp) cc_final: 0.7219 (mpp)
REVERT: A  287 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.8166 (mmm160)
REVERT: A  335 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7332 (tp)
REVERT: B  399 MET cc_start: 0.8714 (tpp) cc_final: 0.8052 (ttm)
REVERT: B  453 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8800 (mm)
  outliers start: 29
  outliers final: 19
  residues processed: 109
  average time/residue: 0.0894
  time to fit residues: 14.1177
Evaluate side-chains
  101 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.134970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.103627 restraints weight = 15675.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.103767 restraints weight = 8966.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.105092 restraints weight = 6688.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.105966 restraints weight = 5284.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.105970 restraints weight = 4742.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8001  Z= 0.116
  Angle     :  0.464   7.374  10884  Z= 0.239
  Chirality :  0.036   0.131   1304
  Planarity :  0.003   0.041   1421
  Dihedral  :  3.044  14.425   1183
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 26.57 %
    Favored  : 68.11 %
  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 aren not related in a simple way.
  whole:  2.87 (0.26), residues: 1107
  helix:  2.48 (0.19), residues: 767
  sheet:  0.58 (0.83), residues: 50
  loop :  0.66 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 333 
 TYR   0.013   0.001   TYR B 366 
 PHE   0.016   0.001   PHE A 275 
 TRP   0.010   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8001)
  covalent geometry    : angle       0.46418 (10884)
  hydrogen bonds       : bond        0.04155 (  589)
  hydrogen bonds       : angle       3.36552 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 81
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7423 (t-100) cc_final: 0.6925 (t-100)
REVERT: A  242 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8013 (tt0)
REVERT: A  285 MET cc_start: 0.7790 (mpp) cc_final: 0.7267 (mpp)
REVERT: A  287 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8253 (mmm160)
REVERT: A  335 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7396 (tp)
REVERT: A  404 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7417 (tp30)
REVERT: B  399 MET cc_start: 0.8734 (tpp) cc_final: 0.8178 (ttm)
REVERT: B  453 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8775 (mm)
  outliers start: 38
  outliers final: 30
  residues processed: 113
  average time/residue: 0.0710
  time to fit residues: 12.1236
Evaluate side-chains
  113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 108 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0570
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.1302

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.132689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.098404 restraints weight = 15634.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.101482 restraints weight = 8577.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.103468 restraints weight = 5907.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.104753 restraints weight = 4676.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.105321 restraints weight = 4063.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8001  Z= 0.153
  Angle     :  0.508   7.774  10884  Z= 0.260
  Chirality :  0.038   0.133   1304
  Planarity :  0.003   0.042   1421
  Dihedral  :  3.162  14.785   1183
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 25.59 %
    Favored  : 68.25 %
  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 aren not related in a simple way.
  whole:  2.78 (0.26), residues: 1107
  helix:  2.39 (0.19), residues: 766
  sheet:  0.75 (0.80), residues: 57
  loop :  0.64 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 333 
 TYR   0.014   0.001   TYR B 366 
 PHE   0.016   0.001   PHE A 275 
 TRP   0.011   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8001)
  covalent geometry    : angle       0.50774 (10884)
  hydrogen bonds       : bond        0.04651 (  589)
  hydrogen bonds       : angle       3.53887 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 79
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7573 (t-100) cc_final: 0.7171 (t-100)
REVERT: A  242 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8020 (tt0)
REVERT: A  285 MET cc_start: 0.7809 (mpp) cc_final: 0.7254 (mpp)
REVERT: A  335 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7446 (tp)
REVERT: A  404 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7480 (tp30)
REVERT: B  399 MET cc_start: 0.8774 (tpp) cc_final: 0.8349 (ttm)
  outliers start: 44
  outliers final: 31
  residues processed: 117
  average time/residue: 0.0653
  time to fit residues: 11.6057
Evaluate side-chains
  112 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:    0.0050
   chunk 17 optimal weight:    0.0980
   chunk 76 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 49 optimal weight:    0.2980
   overall best weight:    0.4394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.135802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.102506 restraints weight = 15607.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.105846 restraints weight = 8011.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.107988 restraints weight = 5286.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.109312 restraints weight = 4090.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.110154 restraints weight = 3495.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8001  Z= 0.107
  Angle     :  0.472   7.034  10884  Z= 0.243
  Chirality :  0.036   0.128   1304
  Planarity :  0.003   0.041   1421
  Dihedral  :  3.051  14.543   1183
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 27.69 %
    Favored  : 67.83 %
  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 aren not related in a simple way.
  whole:  2.96 (0.26), residues: 1107
  helix:  2.56 (0.19), residues: 766
  sheet:  0.75 (0.79), residues: 57
  loop :  0.62 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 287 
 TYR   0.014   0.001   TYR B 366 
 PHE   0.017   0.001   PHE A 275 
 TRP   0.010   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8001)
  covalent geometry    : angle       0.47249 (10884)
  hydrogen bonds       : bond        0.04006 (  589)
  hydrogen bonds       : angle       3.30849 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 85
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7483 (t-100) cc_final: 0.7077 (t-100)
REVERT: A  242 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7992 (tt0)
REVERT: A  285 MET cc_start: 0.7804 (mpp) cc_final: 0.7253 (mpp)
REVERT: A  335 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7449 (tp)
REVERT: A  404 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7398 (tp30)
REVERT: B  399 MET cc_start: 0.8727 (tpp) cc_final: 0.8225 (ttm)
  outliers start: 32
  outliers final: 25
  residues processed: 110
  average time/residue: 0.0724
  time to fit residues: 11.8211
Evaluate side-chains
  107 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  656 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 54 optimal weight:   50.0000
   chunk 95 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   chunk 7 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 83 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.134447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.100825 restraints weight = 15587.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.103900 restraints weight = 8565.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.105912 restraints weight = 5898.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.107104 restraints weight = 4670.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.107900 restraints weight = 4059.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8001  Z= 0.120
  Angle     :  0.494   7.894  10884  Z= 0.251
  Chirality :  0.037   0.139   1304
  Planarity :  0.003   0.040   1421
  Dihedral  :  3.051  14.554   1183
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 28.53 %
    Favored  : 66.99 %
  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 aren not related in a simple way.
  whole:  2.91 (0.26), residues: 1107
  helix:  2.52 (0.19), residues: 766
  sheet:  0.73 (0.79), residues: 57
  loop :  0.59 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.017   0.001   TYR B 366 
 PHE   0.018   0.001   PHE A 275 
 TRP   0.009   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8001)
  covalent geometry    : angle       0.49395 (10884)
  hydrogen bonds       : bond        0.04154 (  589)
  hydrogen bonds       : angle       3.34508 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7486 (t-100) cc_final: 0.7113 (t-100)
REVERT: A  242 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8024 (tt0)
REVERT: A  285 MET cc_start: 0.7843 (mpp) cc_final: 0.7279 (mpp)
REVERT: A  335 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7448 (tp)
REVERT: A  404 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7420 (tp30)
REVERT: B  399 MET cc_start: 0.8755 (tpp) cc_final: 0.8298 (ttm)
  outliers start: 32
  outliers final: 29
  residues processed: 109
  average time/residue: 0.0690
  time to fit residues: 11.3182
Evaluate side-chains
  111 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 80
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  498 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 110 optimal weight:    0.0870
   chunk 46 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 49 optimal weight:   20.0000
   chunk 86 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.6962

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.134178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.100538 restraints weight = 15482.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.103633 restraints weight = 8417.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.105600 restraints weight = 5764.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.106682 restraints weight = 4573.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.107587 restraints weight = 3999.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8001  Z= 0.121
  Angle     :  0.496   7.970  10884  Z= 0.252
  Chirality :  0.037   0.131   1304
  Planarity :  0.003   0.040   1421
  Dihedral  :  3.059  14.541   1183
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 27.83 %
    Favored  : 66.85 %
  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 aren not related in a simple way.
  whole:  2.88 (0.26), residues: 1107
  helix:  2.50 (0.19), residues: 766
  sheet:  0.71 (0.79), residues: 57
  loop :  0.59 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 287 
 TYR   0.019   0.001   TYR B 366 
 PHE   0.016   0.001   PHE A 275 
 TRP   0.009   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8001)
  covalent geometry    : angle       0.49559 (10884)
  hydrogen bonds       : bond        0.04140 (  589)
  hydrogen bonds       : angle       3.33907 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 82
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7512 (t-100) cc_final: 0.7163 (t-100)
REVERT: A  242 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8038 (tt0)
REVERT: A  285 MET cc_start: 0.7869 (mpp) cc_final: 0.7292 (mpp)
REVERT: A  335 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7403 (tp)
REVERT: A  404 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7379 (tp30)
REVERT: B  399 MET cc_start: 0.8752 (tpp) cc_final: 0.8291 (ttm)
  outliers start: 38
  outliers final: 32
  residues processed: 113
  average time/residue: 0.0613
  time to fit residues: 10.7657
Evaluate side-chains
  111 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 77
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  498 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  656 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0970
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.135419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.101044 restraints weight = 15987.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.104307 restraints weight = 8540.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.106405 restraints weight = 5783.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.107728 restraints weight = 4534.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.108374 restraints weight = 3918.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8001  Z= 0.127
  Angle     :  0.515   8.205  10884  Z= 0.261
  Chirality :  0.037   0.140   1304
  Planarity :  0.003   0.040   1421
  Dihedral  :  3.123  16.278   1183
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.67 %
    Favored  : 66.57 %
  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 aren not related in a simple way.
  whole:  2.84 (0.26), residues: 1107
  helix:  2.47 (0.19), residues: 766
  sheet:  0.71 (0.79), residues: 57
  loop :  0.58 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.023   0.001   TYR B 366 
 PHE   0.020   0.001   PHE A 275 
 TRP   0.010   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8001)
  covalent geometry    : angle       0.51471 (10884)
  hydrogen bonds       : bond        0.04205 (  589)
  hydrogen bonds       : angle       3.34578 ( 1728)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 78
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7546 (t-100) cc_final: 0.7163 (t-100)
REVERT: A  242 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8059 (tt0)
REVERT: A  285 MET cc_start: 0.7907 (mpp) cc_final: 0.7250 (mpp)
REVERT: A  335 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7423 (tp)
REVERT: A  404 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7403 (tp30)
REVERT: B  399 MET cc_start: 0.8724 (tpp) cc_final: 0.8314 (ttm)
  outliers start: 34
  outliers final: 31
  residues processed: 107
  average time/residue: 0.0640
  time to fit residues: 10.5965
Evaluate side-chains
  111 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 78
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  299 HIS
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  498 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 109 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 32 optimal weight:   30.0000
   chunk 92 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.135187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.102152 restraints weight = 15615.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.105358 restraints weight = 8166.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.107414 restraints weight = 5436.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.108734 restraints weight = 4235.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.109396 restraints weight = 3634.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8001  Z= 0.121
  Angle     :  0.503   8.168  10884  Z= 0.256
  Chirality :  0.037   0.136   1304
  Planarity :  0.003   0.040   1421
  Dihedral  :  3.084  15.002   1183
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 28.81 %
    Favored  : 66.57 %
  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 aren not related in a simple way.
  whole:  2.87 (0.26), residues: 1107
  helix:  2.49 (0.19), residues: 766
  sheet:  0.71 (0.79), residues: 57
  loop :  0.60 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.024   0.001   TYR B 366 
 PHE   0.019   0.001   PHE A 275 
 TRP   0.009   0.001   TRP B 367 
 HIS   0.007   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8001)
  covalent geometry    : angle       0.50264 (10884)
  hydrogen bonds       : bond        0.04099 (  589)
  hydrogen bonds       : angle       3.29479 ( 1728)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1594.26 seconds
wall clock time: 28 minutes 13.78 seconds (1693.78 seconds total)