Starting phenix.real_space_refine
on Tue Mar  3 15:41:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8drn_27678/03_2026/8drn_27678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8drn_27678/03_2026/8drn_27678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8drn_27678/03_2026/8drn_27678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8drn_27678/03_2026/8drn_27678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8drn_27678/03_2026/8drn_27678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8drn_27678/03_2026/8drn_27678.cif"
  }
  resolution = 4.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.045
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      24      5.16       5
     C    4234      2.51       5
     N    1130      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6578
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "F"
      Number of atoms: 3257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3257
          Classifications: {'peptide': 404}
          Link IDs: {'PTRANS': 17, 'TRANS': 386}
  Time building chain proxies: 1.54, per 1000 atoms: 0.23
  Number of scatterers: 6578
  At special positions: 0
  Unit cell: (107.944, 76.504, 88.032, 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      24     16.00
     O    1190      8.00
     N    1130      7.00
     C    4234      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: 0.65
  Conformation dependent library (CDL) restraints added in 255.9 milliseconds
  

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      33.2% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 402 through 411
      removed outlier: 3.507A  pdb=" N   TRP A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'A' and resid 439 through 445
      removed outlier: 3.723A  pdb=" N   LEU A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 468
    Processing helix  chain 'A' and resid 484 through 495
    Processing helix  chain 'A' and resid 509 through 515
      removed outlier: 3.635A  pdb=" N   ILE A 512 " --> pdb=" O   PRO A 509 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TYR A 513 " --> pdb=" O   LEU A 510 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU A 515 " --> pdb=" O   ILE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 542
      removed outlier: 4.238A  pdb=" N   GLY A 539 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG A 541 " --> pdb=" O   ASP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 566
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 3.911A  pdb=" N   LYS A 588 " --> pdb=" O   ASN A 585 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LYS A 589 " --> pdb=" O   SER A 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 585 through 589'
    Processing helix  chain 'A' and resid 633 through 638
      removed outlier: 3.509A  pdb=" N   GLN A 636 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   HIS A 637 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
      removed outlier: 3.627A  pdb=" N   ILE A 658 " --> pdb=" O   PRO A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 684
      removed outlier: 3.568A  pdb=" N   CYS A 684 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 707
      removed outlier: 3.770A  pdb=" N   ILE A 704 " --> pdb=" O   PRO A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 730
      removed outlier: 3.936A  pdb=" N   PHE A 728 " --> pdb=" O   PRO A 724 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   CYS A 730 " --> pdb=" O   GLU A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 753
    Processing helix  chain 'A' and resid 770 through 776
    Processing helix  chain 'A' and resid 787 through 793
    Processing helix  chain 'A' and resid 795 through 808
    Processing helix  chain 'F' and resid 401 through 409
      removed outlier: 3.547A  pdb=" N   TRP F 409 " --> pdb=" O   LEU F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 410 through 418
    Processing helix  chain 'F' and resid 437 through 443
      removed outlier: 3.921A  pdb=" N   PHE F 441 " --> pdb=" O   PRO F 437 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE F 443 " --> pdb=" O   THR F 439 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 460 through 466
      removed outlier: 3.946A  pdb=" N   ILE F 463 " --> pdb=" O   PRO F 460 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 482 through 492
    Processing helix  chain 'F' and resid 509 through 513
      removed outlier: 3.833A  pdb=" N   LEU F 513 " --> pdb=" O   MET F 510 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 534 through 538
      removed outlier: 3.801A  pdb=" N   SER F 537 " --> pdb=" O   THR F 534 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 557 through 564
      removed outlier: 3.711A  pdb=" N   VAL F 561 " --> pdb=" O   PRO F 557 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 582 through 587
    Processing helix  chain 'F' and resid 605 through 611
      removed outlier: 4.098A  pdb=" N   PHE F 609 " --> pdb=" O   PRO F 605 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 629 through 636
      removed outlier: 3.524A  pdb=" N   SER F 632 " --> pdb=" O   GLU F 629 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLN F 634 " --> pdb=" O   VAL F 631 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 653 through 659
      removed outlier: 3.934A  pdb=" N   ILE F 656 " --> pdb=" O   PRO F 653 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU F 659 " --> pdb=" O   ILE F 656 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 699 through 705
      removed outlier: 3.699A  pdb=" N   ILE F 702 " --> pdb=" O   PRO F 699 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 723 through 728
    Processing helix  chain 'F' and resid 745 through 749
      removed outlier: 3.540A  pdb=" N   ILE F 748 " --> pdb=" O   SER F 745 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLY F 749 " --> pdb=" O   PRO F 746 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 745 through 749'
    Processing helix  chain 'F' and resid 768 through 772
      removed outlier: 4.126A  pdb=" N   LEU F 771 " --> pdb=" O   PRO F 768 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY F 772 " --> pdb=" O   PRO F 769 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 768 through 772'
    Processing helix  chain 'F' and resid 785 through 790
    Processing helix  chain 'F' and resid 793 through 802
      removed outlier: 3.816A  pdb=" N   ALA F 802 " --> pdb=" O   GLU F 798 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422
      removed outlier: 6.638A  pdb=" N   LEU A 428 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   LYS A 452 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   LEU A 430 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   GLU A 454 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   LEU A 432 " --> pdb=" O   GLU A 454 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LEU A 474 " --> pdb=" O   HIS A 499 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   LYS A 501 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU A 521 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   LYS A 552 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU A 523 " --> pdb=" O   LYS A 552 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   LEU A 572 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   ILE A 599 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.843A  pdb=" N   ILE A 574 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 618 through 620
    Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 668
      removed outlier: 7.012A  pdb=" N   LEU A 667 " --> pdb=" O   ASP A 691 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 735 through 737
      removed outlier: 6.819A  pdb=" N   LEU A 736 " --> pdb=" O   GLU A 760 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ILE A 759 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 419 through 420
      removed outlier: 5.701A  pdb=" N   LEU F 426 " --> pdb=" O   SER F 448 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS F 450 " --> pdb=" O   LEU F 426 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   LEU F 428 " --> pdb=" O   LYS F 450 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLU F 452 " --> pdb=" O   LEU F 428 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU F 430 " --> pdb=" O   GLU F 452 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEU F 449 " --> pdb=" O   CYS F 473 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   HIS F 475 " --> pdb=" O   LEU F 449 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU F 451 " --> pdb=" O   HIS F 475 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU F 472 " --> pdb=" O   SER F 497 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   LYS F 499 " --> pdb=" O   LEU F 472 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   LEU F 474 " --> pdb=" O   LYS F 499 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   MET F 570 " --> pdb=" O   GLU F 595 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   VAL F 597 " --> pdb=" O   MET F 570 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   VAL F 572 " --> pdb=" O   VAL F 597 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   LEU F 594 " --> pdb=" O   ASP F 618 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   LYS F 620 " --> pdb=" O   LEU F 594 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   LEU F 596 " --> pdb=" O   LYS F 620 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   LEU F 617 " --> pdb=" O   LYS F 643 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU F 688 " --> pdb=" O   SER F 712 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   PHE F 711 " --> pdb=" O   LYS F 735 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 457 through 458
      removed outlier: 6.568A  pdb=" N   VAL F 457 " --> pdb=" O   LYS F 480 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    142 hydrogen bonds defined for protein.
    306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.85

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1885
        1.33 -     1.46: 912
        1.46 -     1.58: 3861
        1.58 -     1.70: 1
        1.70 -     1.82: 34
  Bond restraints: 6693
  Sorted by residual:
  bond pdb=" N   TRP F 645 "
       pdb=" CA  TRP F 645 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.16e-02 7.43e+03 8.95e+00
  bond pdb=" CA  HIS F 573 "
       pdb=" CB  HIS F 573 "
    ideal  model  delta    sigma   weight residual
    1.526  1.564 -0.037 1.53e-02 4.27e+03 6.00e+00
  bond pdb=" N   ASP A 444 "
       pdb=" CA  ASP A 444 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.28e-02 6.10e+03 5.91e+00
  bond pdb=" N   GLN A 570 "
       pdb=" CA  GLN A 570 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.031 1.37e-02 5.33e+03 4.97e+00
  bond pdb=" N   GLY F 523 "
       pdb=" CA  GLY F 523 "
    ideal  model  delta    sigma   weight residual
    1.449  1.480 -0.031 1.45e-02 4.76e+03 4.43e+00
  ... (remaining 6688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 8760
        2.34 -     4.69: 246
        4.69 -     7.03: 35
        7.03 -     9.38: 17
        9.38 -    11.72: 4
  Bond angle restraints: 9062
  Sorted by residual:
  angle pdb=" CB  MET F 432 "
        pdb=" CG  MET F 432 "
        pdb=" SD  MET F 432 "
      ideal   model   delta    sigma   weight residual
     112.70  124.42  -11.72 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" CB  GLU A 449 "
        pdb=" CG  GLU A 449 "
        pdb=" CD  GLU A 449 "
      ideal   model   delta    sigma   weight residual
     112.60  119.20   -6.60 1.70e+00 3.46e-01 1.51e+01
  angle pdb=" CA  MET A 434 "
        pdb=" CB  MET A 434 "
        pdb=" CG  MET A 434 "
      ideal   model   delta    sigma   weight residual
     114.10  121.61   -7.51 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" CA  LYS A 622 "
        pdb=" CB  LYS A 622 "
        pdb=" CG  LYS A 622 "
      ideal   model   delta    sigma   weight residual
     114.10  121.59   -7.49 2.00e+00 2.50e-01 1.40e+01
  angle pdb=" CA  MET F 432 "
        pdb=" CB  MET F 432 "
        pdb=" CG  MET F 432 "
      ideal   model   delta    sigma   weight residual
     114.10  121.40   -7.30 2.00e+00 2.50e-01 1.33e+01
  ... (remaining 9057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 3644
       17.88 -    35.76: 399
       35.76 -    53.64: 95
       53.64 -    71.52: 13
       71.52 -    89.39: 5
  Dihedral angle restraints: 4156
    sinusoidal: 1754
      harmonic: 2402
  Sorted by residual:
  dihedral pdb=" CA  LYS F 587 "
           pdb=" C   LYS F 587 "
           pdb=" N   MET F 588 "
           pdb=" CA  MET F 588 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.53   22.47     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  GLU F 505 "
           pdb=" C   GLU F 505 "
           pdb=" N   LEU F 506 "
           pdb=" CA  LEU F 506 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  GLU A 429 "
           pdb=" C   GLU A 429 "
           pdb=" N   LEU A 430 "
           pdb=" CA  LEU A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.27   19.73     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 4153 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1027
       0.098 -    0.195: 55
       0.195 -    0.293: 1
       0.293 -    0.390: 0
       0.390 -    0.488: 1
  Chirality restraints: 1084
  Sorted by residual:
  chirality pdb=" CB  ILE A 629 "
            pdb=" CA  ILE A 629 "
            pdb=" CG1 ILE A 629 "
            pdb=" CG2 ILE A 629 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.16    0.49 2.00e-01 2.50e+01 5.94e+00
  chirality pdb=" CB  ILE F 759 "
            pdb=" CA  ILE F 759 "
            pdb=" CG1 ILE F 759 "
            pdb=" CG2 ILE F 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CG  LEU A 723 "
            pdb=" CB  LEU A 723 "
            pdb=" CD1 LEU A 723 "
            pdb=" CD2 LEU A 723 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.28e-01
  ... (remaining 1081 not shown)

  Planarity restraints: 1137
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 475 "   -0.032 2.00e-02 2.50e+03   2.93e-02 2.15e+01
        pdb=" CG  TRP A 475 "    0.080 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 475 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 475 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 475 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 475 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 475 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 475 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 475 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 475 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 687 "   -0.023 2.00e-02 2.50e+03   2.12e-02 8.95e+00
        pdb=" CG  TYR F 687 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 687 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 687 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 687 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 687 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 687 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F 687 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F 488 "   -0.012 2.00e-02 2.50e+03   1.81e-02 5.72e+00
        pdb=" CG  PHE F 488 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE F 488 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE F 488 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE F 488 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE F 488 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE F 488 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1134 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1498
        2.79 -     3.32: 6482
        3.32 -     3.85: 11414
        3.85 -     4.37: 14444
        4.37 -     4.90: 22664
  Nonbonded interactions: 56502
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 689 "
            pdb=" OG  SER F 691 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   LEU A 405 "
            pdb=" ND2 ASN A 409 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" O   ARG A 419 "
            pdb=" NH1 ARG A 419 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   GLN A 560 "
            pdb=" OG1 THR A 563 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OE1 GLU A 429 "
            pdb=" NZ  LYS A 452 "
     model   vdw
     2.297 3.120
  ... (remaining 56497 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:             7.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     7.410
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   6693  Z= 0.216
  Angle     :  0.981  11.724   9062  Z= 0.510
  Chirality :  0.050   0.488   1084
  Planarity :  0.005   0.041   1137
  Dihedral  : 15.665  89.395   2580
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 21.58 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.29), residues: 807
  helix: -2.79 (0.28), residues: 248
  sheet: -2.18 (0.53), residues: 113
  loop : -0.96 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 419 
 TYR   0.053   0.003   TYR F 687 
 PHE   0.041   0.002   PHE F 488 
 TRP   0.080   0.006   TRP A 475 
 HIS   0.007   0.001   HIS F 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6693)
  covalent geometry    : angle       0.98052 ( 9062)
  hydrogen bonds       : bond        0.21590 (  142)
  hydrogen bonds       : angle       8.69398 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 280
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  404 GLN cc_start: 0.7410 (tm-30) cc_final: 0.7150 (tm-30)
REVERT: A  414 ASP cc_start: 0.9263 (m-30) cc_final: 0.9055 (m-30)
REVERT: A  454 GLU cc_start: 0.8379 (tt0) cc_final: 0.7941 (tm-30)
REVERT: A  473 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8287 (tt0)
REVERT: A  479 THR cc_start: 0.8730 (m) cc_final: 0.8258 (p)
REVERT: A  518 LEU cc_start: 0.8894 (tp) cc_final: 0.8160 (tp)
REVERT: A  547 LYS cc_start: 0.7844 (mttp) cc_final: 0.7594 (mptt)
REVERT: A  601 CYS cc_start: 0.8010 (t) cc_final: 0.7640 (m)
REVERT: A  624 ASN cc_start: 0.8451 (m-40) cc_final: 0.7962 (m110)
REVERT: A  682 PHE cc_start: 0.8169 (m-80) cc_final: 0.7755 (m-80)
REVERT: A  694 HIS cc_start: 0.8789 (m170) cc_final: 0.8583 (m170)
REVERT: A  801 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.7229 (tmt170)
REVERT: A  803 TRP cc_start: 0.8431 (m100) cc_final: 0.8221 (m100)
REVERT: F  421 ASN cc_start: 0.7637 (p0) cc_final: 0.7373 (p0)
REVERT: F  486 LEU cc_start: 0.7943 (mt) cc_final: 0.7508 (tt)
REVERT: F  503 MET cc_start: 0.7456 (mmt) cc_final: 0.6148 (tpp)
REVERT: F  511 TYR cc_start: 0.7217 (m-80) cc_final: 0.6135 (m-80)
REVERT: F  518 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6826 (mt-10)
REVERT: F  567 LEU cc_start: 0.8318 (tp) cc_final: 0.7984 (tp)
REVERT: F  588 MET cc_start: 0.7919 (mmp) cc_final: 0.7575 (mmm)
REVERT: F  633 PHE cc_start: 0.8834 (m-80) cc_final: 0.8073 (m-80)
REVERT: F  642 LEU cc_start: 0.7101 (tp) cc_final: 0.6216 (tt)
REVERT: F  649 ILE cc_start: 0.8160 (mt) cc_final: 0.7050 (mm)
REVERT: F  735 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7454 (mtmm)
REVERT: F  756 TYR cc_start: 0.7701 (t80) cc_final: 0.6893 (t80)
REVERT: F  764 PHE cc_start: 0.7230 (m-10) cc_final: 0.6911 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 282
  average time/residue: 0.0905
  time to fit residues: 32.7210
Evaluate side-chains
  181 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0030
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.6796

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

Flipped N/Q/H residues before XYZ refinement:
A 624 ASN
A 650 HIS
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 706 GLN
F 799 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.120771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.101914 restraints weight = 20576.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.104466 restraints weight = 13222.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.106283 restraints weight = 9475.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.107640 restraints weight = 7205.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.108627 restraints weight = 5775.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.4173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6693  Z= 0.216
  Angle     :  0.803  10.368   9062  Z= 0.398
  Chirality :  0.050   0.295   1084
  Planarity :  0.006   0.074   1137
  Dihedral  :  5.424  18.805    864
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 23.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.47 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.65 (0.29), residues: 807
  helix: -2.48 (0.29), residues: 257
  sheet: -2.52 (0.47), residues: 134
  loop : -0.82 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F 514 
 TYR   0.027   0.003   TYR F 511 
 PHE   0.026   0.003   PHE A 433 
 TRP   0.039   0.005   TRP F 645 
 HIS   0.008   0.002   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 6693)
  covalent geometry    : angle       0.80287 ( 9062)
  hydrogen bonds       : bond        0.04682 (  142)
  hydrogen bonds       : angle       6.87043 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  404 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7866 (tm-30)
REVERT: A  416 LEU cc_start: 0.8816 (tp) cc_final: 0.8613 (tp)
REVERT: A  475 TRP cc_start: 0.8055 (m-10) cc_final: 0.7770 (m-10)
REVERT: A  518 LEU cc_start: 0.7628 (tp) cc_final: 0.7261 (tp)
REVERT: A  557 LYS cc_start: 0.7812 (tptt) cc_final: 0.7265 (tmtt)
REVERT: A  571 LYS cc_start: 0.7342 (tttp) cc_final: 0.7100 (ttpt)
REVERT: A  665 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7233 (tm-30)
REVERT: A  682 PHE cc_start: 0.7662 (m-80) cc_final: 0.7439 (m-80)
REVERT: A  733 LEU cc_start: 0.9123 (mp) cc_final: 0.8845 (mp)
REVERT: F  428 LEU cc_start: 0.8536 (mt) cc_final: 0.8239 (mt)
REVERT: F  452 GLU cc_start: 0.7491 (tp30) cc_final: 0.6688 (tp30)
REVERT: F  550 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7466 (mttm)
REVERT: F  570 MET cc_start: 0.8075 (mmm) cc_final: 0.7608 (mmm)
REVERT: F  573 HIS cc_start: 0.7540 (m170) cc_final: 0.7062 (m170)
REVERT: F  588 MET cc_start: 0.8114 (mmp) cc_final: 0.7737 (mmm)
REVERT: F  594 LEU cc_start: 0.9238 (tp) cc_final: 0.8967 (tp)
REVERT: F  595 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8094 (mm-30)
REVERT: F  633 PHE cc_start: 0.8243 (m-80) cc_final: 0.7760 (m-80)
REVERT: F  687 TYR cc_start: 0.8046 (t80) cc_final: 0.7653 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0748
  time to fit residues: 20.6342
Evaluate side-chains
  140 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0570
   chunk 27 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    1.2104

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

Flipped N/Q/H residues before XYZ refinement:
A 431 HIS
A 657 GLN
A 711 GLN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.119023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.100599 restraints weight = 20661.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.102971 restraints weight = 13102.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.104770 restraints weight = 9366.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.106081 restraints weight = 7154.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.107020 restraints weight = 5783.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6693  Z= 0.171
  Angle     :  0.718   9.135   9062  Z= 0.355
  Chirality :  0.048   0.242   1084
  Planarity :  0.004   0.036   1137
  Dihedral  :  5.225  16.340    864
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 21.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.37 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.29), residues: 807
  helix: -2.36 (0.29), residues: 262
  sheet: -2.43 (0.46), residues: 135
  loop : -0.91 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG F 686 
 TYR   0.032   0.003   TYR A 648 
 PHE   0.029   0.002   PHE A 433 
 TRP   0.020   0.003   TRP F 645 
 HIS   0.005   0.001   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6693)
  covalent geometry    : angle       0.71830 ( 9062)
  hydrogen bonds       : bond        0.04032 (  142)
  hydrogen bonds       : angle       6.62939 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  416 LEU cc_start: 0.8761 (tp) cc_final: 0.8525 (tp)
REVERT: A  475 TRP cc_start: 0.8293 (m-10) cc_final: 0.8058 (m-10)
REVERT: A  518 LEU cc_start: 0.7733 (tp) cc_final: 0.7327 (tp)
REVERT: A  571 LYS cc_start: 0.7818 (tttp) cc_final: 0.7379 (ttpt)
REVERT: A  647 TRP cc_start: 0.7404 (p90) cc_final: 0.7011 (p90)
REVERT: A  666 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7501 (mtm180)
REVERT: A  682 PHE cc_start: 0.7567 (m-80) cc_final: 0.7284 (m-80)
REVERT: A  733 LEU cc_start: 0.9200 (mp) cc_final: 0.8932 (mp)
REVERT: A  773 LEU cc_start: 0.9229 (mm) cc_final: 0.9016 (tp)
REVERT: F  432 MET cc_start: 0.6561 (tpt) cc_final: 0.6146 (tpp)
REVERT: F  570 MET cc_start: 0.8106 (mmm) cc_final: 0.7387 (mmm)
REVERT: F  573 HIS cc_start: 0.7580 (m170) cc_final: 0.7164 (m170)
REVERT: F  588 MET cc_start: 0.8241 (mmp) cc_final: 0.7890 (mmm)
REVERT: F  594 LEU cc_start: 0.9240 (tp) cc_final: 0.8962 (tp)
REVERT: F  633 PHE cc_start: 0.8439 (m-80) cc_final: 0.7834 (m-80)
REVERT: F  642 LEU cc_start: 0.6501 (tp) cc_final: 0.6211 (tt)
REVERT: F  643 LYS cc_start: 0.9000 (ptpp) cc_final: 0.8713 (ptpp)
REVERT: F  644 LEU cc_start: 0.8963 (mt) cc_final: 0.8722 (mt)
REVERT: F  687 TYR cc_start: 0.7999 (t80) cc_final: 0.7566 (t80)
REVERT: F  764 PHE cc_start: 0.7252 (m-10) cc_final: 0.6676 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0631
  time to fit residues: 15.7644
Evaluate side-chains
  133 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0270
   chunk 27 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.1840

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

Flipped N/Q/H residues before XYZ refinement:
A 718 ASN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.117148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.100371 restraints weight = 20912.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.102916 restraints weight = 12838.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.104246 restraints weight = 8469.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.104665 restraints weight = 6836.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.105085 restraints weight = 5923.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.5705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6693  Z= 0.152
  Angle     :  0.664   8.851   9062  Z= 0.330
  Chirality :  0.047   0.269   1084
  Planarity :  0.004   0.037   1137
  Dihedral  :  4.984  16.997    864
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 22.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.47 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.57 (0.30), residues: 807
  helix: -2.38 (0.30), residues: 268
  sheet: -2.59 (0.44), residues: 149
  loop : -0.58 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 666 
 TYR   0.014   0.002   TYR F 756 
 PHE   0.021   0.002   PHE A 433 
 TRP   0.027   0.003   TRP F 645 
 HIS   0.005   0.001   HIS F 573 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6693)
  covalent geometry    : angle       0.66407 ( 9062)
  hydrogen bonds       : bond        0.03703 (  142)
  hydrogen bonds       : angle       6.41262 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  557 LYS cc_start: 0.7771 (tptt) cc_final: 0.7014 (tmtt)
REVERT: A  571 LYS cc_start: 0.8003 (tttp) cc_final: 0.7601 (ttpt)
REVERT: A  682 PHE cc_start: 0.7701 (m-80) cc_final: 0.7316 (m-80)
REVERT: A  733 LEU cc_start: 0.9230 (mp) cc_final: 0.9000 (mp)
REVERT: A  773 LEU cc_start: 0.9299 (mm) cc_final: 0.9057 (tp)
REVERT: F  432 MET cc_start: 0.6314 (tpt) cc_final: 0.6108 (tpp)
REVERT: F  570 MET cc_start: 0.7895 (mmm) cc_final: 0.7460 (mmm)
REVERT: F  588 MET cc_start: 0.8194 (mmp) cc_final: 0.7898 (mmm)
REVERT: F  595 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6683 (mm-30)
REVERT: F  687 TYR cc_start: 0.7955 (t80) cc_final: 0.7439 (t80)
REVERT: F  764 PHE cc_start: 0.7211 (m-10) cc_final: 0.6547 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0756
  time to fit residues: 17.0888
Evaluate side-chains
  133 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0370
   chunk 70 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A 576 ASN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.117708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.101160 restraints weight = 20983.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.102421 restraints weight = 13761.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.104279 restraints weight = 9588.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.104988 restraints weight = 7004.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.105503 restraints weight = 6149.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.5995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6693  Z= 0.129
  Angle     :  0.658  10.673   9062  Z= 0.322
  Chirality :  0.046   0.185   1084
  Planarity :  0.004   0.055   1137
  Dihedral  :  4.904  16.784    864
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 21.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.30), residues: 807
  helix: -2.34 (0.30), residues: 261
  sheet: -2.38 (0.45), residues: 143
  loop : -0.65 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 762 
 TYR   0.025   0.002   TYR A 648 
 PHE   0.025   0.002   PHE A 433 
 TRP   0.044   0.004   TRP F 645 
 HIS   0.005   0.001   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6693)
  covalent geometry    : angle       0.65782 ( 9062)
  hydrogen bonds       : bond        0.03551 (  142)
  hydrogen bonds       : angle       6.27249 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.7877 (tp) cc_final: 0.7405 (tp)
REVERT: A  557 LYS cc_start: 0.7742 (tptt) cc_final: 0.6984 (tmtt)
REVERT: A  571 LYS cc_start: 0.8008 (tttp) cc_final: 0.7559 (ttpt)
REVERT: A  682 PHE cc_start: 0.7663 (m-80) cc_final: 0.7337 (m-80)
REVERT: A  733 LEU cc_start: 0.9233 (mp) cc_final: 0.9032 (mp)
REVERT: A  773 LEU cc_start: 0.9292 (mm) cc_final: 0.8951 (tp)
REVERT: F  426 LEU cc_start: 0.7643 (tp) cc_final: 0.7433 (mm)
REVERT: F  451 LEU cc_start: 0.9343 (mt) cc_final: 0.9078 (mp)
REVERT: F  570 MET cc_start: 0.7891 (mmm) cc_final: 0.7554 (mmm)
REVERT: F  581 MET cc_start: 0.6417 (tpt) cc_final: 0.6146 (tpt)
REVERT: F  588 MET cc_start: 0.8207 (mmp) cc_final: 0.7920 (mmm)
REVERT: F  595 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6775 (mm-30)
REVERT: F  618 ASP cc_start: 0.7875 (t0) cc_final: 0.7563 (t70)
REVERT: F  687 TYR cc_start: 0.7793 (t80) cc_final: 0.7335 (t80)
REVERT: F  764 PHE cc_start: 0.7016 (m-10) cc_final: 0.6364 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0705
  time to fit residues: 16.3056
Evaluate side-chains
  131 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 58 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 18 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0870
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:   20.0000
   chunk 2 optimal weight:    0.0040
   overall best weight:    0.3970

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

Flipped N/Q/H residues before XYZ refinement:
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.119220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.102311 restraints weight = 21022.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.104186 restraints weight = 13863.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.105947 restraints weight = 9316.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.106891 restraints weight = 7014.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.107247 restraints weight = 5831.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.6294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6693  Z= 0.112
  Angle     :  0.645   9.474   9062  Z= 0.311
  Chirality :  0.046   0.173   1084
  Planarity :  0.004   0.054   1137
  Dihedral  :  4.781  16.793    864
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.30), residues: 807
  helix: -2.17 (0.32), residues: 253
  sheet: -2.01 (0.47), residues: 140
  loop : -0.65 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 425 
 TYR   0.035   0.002   TYR F 687 
 PHE   0.022   0.002   PHE A 433 
 TRP   0.050   0.004   TRP A 647 
 HIS   0.007   0.001   HIS F 573 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6693)
  covalent geometry    : angle       0.64478 ( 9062)
  hydrogen bonds       : bond        0.03335 (  142)
  hydrogen bonds       : angle       5.97664 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 PHE cc_start: 0.7460 (t80) cc_final: 0.6771 (t80)
REVERT: A  434 MET cc_start: 0.7701 (mpp) cc_final: 0.7269 (mpp)
REVERT: A  518 LEU cc_start: 0.7800 (tp) cc_final: 0.7343 (tp)
REVERT: A  557 LYS cc_start: 0.7705 (tptt) cc_final: 0.6977 (tmtt)
REVERT: A  571 LYS cc_start: 0.8035 (tttp) cc_final: 0.7607 (ttpt)
REVERT: A  601 CYS cc_start: 0.8538 (m) cc_final: 0.8270 (m)
REVERT: A  682 PHE cc_start: 0.7545 (m-80) cc_final: 0.7157 (m-10)
REVERT: A  733 LEU cc_start: 0.9210 (mp) cc_final: 0.8979 (mp)
REVERT: A  773 LEU cc_start: 0.9282 (mm) cc_final: 0.8922 (tp)
REVERT: F  570 MET cc_start: 0.7894 (mmm) cc_final: 0.7543 (mmm)
REVERT: F  588 MET cc_start: 0.8114 (mmp) cc_final: 0.7794 (mmm)
REVERT: F  595 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: F  764 PHE cc_start: 0.6948 (m-10) cc_final: 0.6303 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0706
  time to fit residues: 16.9724
Evaluate side-chains
  131 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 416 GLN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.115663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.098386 restraints weight = 20287.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.100435 restraints weight = 12287.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.102169 restraints weight = 8124.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.102417 restraints weight = 6066.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.102877 restraints weight = 5631.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.6544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6693  Z= 0.142
  Angle     :  0.658   9.182   9062  Z= 0.323
  Chirality :  0.046   0.244   1084
  Planarity :  0.004   0.047   1137
  Dihedral  :  4.775  18.023    864
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.30), residues: 807
  helix: -2.26 (0.30), residues: 263
  sheet: -1.83 (0.48), residues: 140
  loop : -0.67 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 762 
 TYR   0.022   0.002   TYR F 687 
 PHE   0.021   0.002   PHE A 433 
 TRP   0.052   0.004   TRP A 647 
 HIS   0.006   0.001   HIS F 678 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6693)
  covalent geometry    : angle       0.65833 ( 9062)
  hydrogen bonds       : bond        0.03466 (  142)
  hydrogen bonds       : angle       5.92883 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6522 (mm-30)
REVERT: A  433 PHE cc_start: 0.7625 (t80) cc_final: 0.6848 (t80)
REVERT: A  434 MET cc_start: 0.7931 (mpp) cc_final: 0.7462 (mpp)
REVERT: A  518 LEU cc_start: 0.8089 (tp) cc_final: 0.7688 (tp)
REVERT: A  557 LYS cc_start: 0.7881 (tptt) cc_final: 0.7015 (tmtt)
REVERT: A  571 LYS cc_start: 0.8016 (tttp) cc_final: 0.7596 (ttpt)
REVERT: A  601 CYS cc_start: 0.8657 (m) cc_final: 0.8384 (m)
REVERT: A  682 PHE cc_start: 0.7730 (m-80) cc_final: 0.7478 (m-80)
REVERT: F  424 ASN cc_start: 0.8122 (m-40) cc_final: 0.7813 (m-40)
REVERT: F  486 LEU cc_start: 0.7240 (mt) cc_final: 0.7009 (mt)
REVERT: F  550 LYS cc_start: 0.8349 (mttt) cc_final: 0.7784 (mmtt)
REVERT: F  570 MET cc_start: 0.7922 (mmm) cc_final: 0.7557 (mmm)
REVERT: F  581 MET cc_start: 0.6299 (tpt) cc_final: 0.6042 (tpt)
REVERT: F  588 MET cc_start: 0.8206 (mmp) cc_final: 0.7870 (mmm)
REVERT: F  595 GLU cc_start: 0.7698 (mm-30) cc_final: 0.6957 (mm-30)
REVERT: F  616 GLU cc_start: 0.7718 (tt0) cc_final: 0.7475 (tt0)
REVERT: F  618 ASP cc_start: 0.7656 (t0) cc_final: 0.6952 (t70)
REVERT: F  643 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8181 (ptpp)
REVERT: F  688 LEU cc_start: 0.8452 (tp) cc_final: 0.8206 (tp)
REVERT: F  764 PHE cc_start: 0.7255 (m-10) cc_final: 0.6787 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0674
  time to fit residues: 15.0162
Evaluate side-chains
  126 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0770
   chunk 1 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0970
   overall best weight:    0.5336

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.116927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.099511 restraints weight = 20479.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.101659 restraints weight = 12978.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.103305 restraints weight = 8515.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.103831 restraints weight = 6235.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.104732 restraints weight = 5490.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.6700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6693  Z= 0.117
  Angle     :  0.681  11.490   9062  Z= 0.322
  Chirality :  0.047   0.195   1084
  Planarity :  0.004   0.039   1137
  Dihedral  :  4.691  14.580    864
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.30), residues: 807
  helix: -2.21 (0.30), residues: 257
  sheet: -1.89 (0.48), residues: 141
  loop : -0.60 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 664 
 TYR   0.018   0.002   TYR F 756 
 PHE   0.018   0.002   PHE A 433 
 TRP   0.046   0.004   TRP A 647 
 HIS   0.004   0.001   HIS F 678 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6693)
  covalent geometry    : angle       0.68056 ( 9062)
  hydrogen bonds       : bond        0.03398 (  142)
  hydrogen bonds       : angle       5.93698 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6260 (mm-30)
REVERT: A  433 PHE cc_start: 0.7674 (t80) cc_final: 0.6856 (t80)
REVERT: A  434 MET cc_start: 0.7943 (mpp) cc_final: 0.7575 (mpp)
REVERT: A  518 LEU cc_start: 0.8054 (tp) cc_final: 0.7616 (tp)
REVERT: A  557 LYS cc_start: 0.7745 (tptt) cc_final: 0.6924 (tmtt)
REVERT: A  571 LYS cc_start: 0.7991 (tttp) cc_final: 0.7498 (ttpt)
REVERT: A  591 VAL cc_start: 0.8438 (p) cc_final: 0.8222 (t)
REVERT: A  601 CYS cc_start: 0.8667 (m) cc_final: 0.8434 (m)
REVERT: A  645 LYS cc_start: 0.8322 (mtmt) cc_final: 0.8115 (mtmt)
REVERT: A  733 LEU cc_start: 0.9131 (mp) cc_final: 0.8895 (mp)
REVERT: F  469 LEU cc_start: 0.8371 (tt) cc_final: 0.8030 (mp)
REVERT: F  550 LYS cc_start: 0.8224 (mttt) cc_final: 0.7698 (mmtt)
REVERT: F  581 MET cc_start: 0.6234 (tpt) cc_final: 0.6012 (tpt)
REVERT: F  588 MET cc_start: 0.8113 (mmp) cc_final: 0.7773 (mmm)
REVERT: F  595 GLU cc_start: 0.7780 (mm-30) cc_final: 0.6961 (mm-30)
REVERT: F  616 GLU cc_start: 0.7620 (tt0) cc_final: 0.7381 (tt0)
REVERT: F  618 ASP cc_start: 0.7456 (t0) cc_final: 0.6866 (t70)
REVERT: F  643 LYS cc_start: 0.8723 (ptpp) cc_final: 0.8106 (ptpp)
REVERT: F  764 PHE cc_start: 0.7143 (m-10) cc_final: 0.6703 (m-80)
REVERT: F  790 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6500 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0754
  time to fit residues: 16.8140
Evaluate side-chains
  130 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0470
   chunk 42 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.117334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.099618 restraints weight = 20521.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.102308 restraints weight = 11898.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.104591 restraints weight = 7557.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.104741 restraints weight = 5432.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.105274 restraints weight = 4888.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.6861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6693  Z= 0.116
  Angle     :  0.675  11.616   9062  Z= 0.321
  Chirality :  0.046   0.164   1084
  Planarity :  0.004   0.043   1137
  Dihedral  :  4.639  18.373    864
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 18.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.30), residues: 807
  helix: -2.22 (0.30), residues: 264
  sheet: -2.03 (0.48), residues: 134
  loop : -0.65 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG F 514 
 TYR   0.017   0.002   TYR F 756 
 PHE   0.018   0.002   PHE A 433 
 TRP   0.052   0.004   TRP A 647 
 HIS   0.004   0.001   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6693)
  covalent geometry    : angle       0.67546 ( 9062)
  hydrogen bonds       : bond        0.03415 (  142)
  hydrogen bonds       : angle       5.85555 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 PHE cc_start: 0.7588 (t80) cc_final: 0.6902 (t80)
REVERT: A  434 MET cc_start: 0.7967 (mpp) cc_final: 0.7738 (mpp)
REVERT: A  518 LEU cc_start: 0.8007 (tp) cc_final: 0.7566 (tp)
REVERT: A  557 LYS cc_start: 0.7778 (tptt) cc_final: 0.6958 (tmtt)
REVERT: A  571 LYS cc_start: 0.8022 (tttp) cc_final: 0.7578 (ttpt)
REVERT: A  591 VAL cc_start: 0.8428 (p) cc_final: 0.8214 (t)
REVERT: A  682 PHE cc_start: 0.7637 (m-80) cc_final: 0.7431 (m-10)
REVERT: A  733 LEU cc_start: 0.9133 (mp) cc_final: 0.8910 (mp)
REVERT: F  424 ASN cc_start: 0.8426 (m-40) cc_final: 0.8093 (m-40)
REVERT: F  550 LYS cc_start: 0.8246 (mttt) cc_final: 0.7687 (mmtt)
REVERT: F  581 MET cc_start: 0.6229 (tpt) cc_final: 0.6007 (tpt)
REVERT: F  588 MET cc_start: 0.8029 (mmp) cc_final: 0.7713 (mmm)
REVERT: F  595 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7002 (mm-30)
REVERT: F  616 GLU cc_start: 0.7657 (tt0) cc_final: 0.7395 (tt0)
REVERT: F  618 ASP cc_start: 0.7574 (t0) cc_final: 0.6972 (t70)
REVERT: F  643 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8130 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0664
  time to fit residues: 15.4341
Evaluate side-chains
  124 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0470
   chunk 55 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0070
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 649 ASN
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 740 ASN
F 416 GLN
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.117491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.099816 restraints weight = 20225.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.102455 restraints weight = 11834.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.104744 restraints weight = 7580.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.104819 restraints weight = 5617.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.105325 restraints weight = 5055.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.7011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6693  Z= 0.127
  Angle     :  0.689  11.574   9062  Z= 0.335
  Chirality :  0.046   0.151   1084
  Planarity :  0.004   0.045   1137
  Dihedral  :  4.610  14.845    864
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 18.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.26 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.30), residues: 807
  helix: -2.25 (0.30), residues: 264
  sheet: -2.17 (0.45), residues: 150
  loop : -0.50 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 762 
 TYR   0.018   0.002   TYR A 648 
 PHE   0.022   0.002   PHE F 609 
 TRP   0.074   0.005   TRP A 647 
 HIS   0.008   0.001   HIS F 573 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6693)
  covalent geometry    : angle       0.68875 ( 9062)
  hydrogen bonds       : bond        0.03474 (  142)
  hydrogen bonds       : angle       5.98990 (  306)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 PHE cc_start: 0.7688 (t80) cc_final: 0.6874 (t80)
REVERT: A  434 MET cc_start: 0.7962 (mpp) cc_final: 0.7620 (mpp)
REVERT: A  518 LEU cc_start: 0.7964 (tp) cc_final: 0.7511 (tp)
REVERT: A  557 LYS cc_start: 0.7819 (tptt) cc_final: 0.6955 (tmtt)
REVERT: A  571 LYS cc_start: 0.8030 (tttp) cc_final: 0.7639 (ttpt)
REVERT: A  591 VAL cc_start: 0.8446 (p) cc_final: 0.8194 (t)
REVERT: A  601 CYS cc_start: 0.8713 (m) cc_final: 0.8498 (m)
REVERT: A  733 LEU cc_start: 0.9123 (mp) cc_final: 0.8894 (mp)
REVERT: F  424 ASN cc_start: 0.8504 (m-40) cc_final: 0.8088 (m-40)
REVERT: F  469 LEU cc_start: 0.8408 (tt) cc_final: 0.8128 (mp)
REVERT: F  550 LYS cc_start: 0.8281 (mttt) cc_final: 0.7799 (mmtt)
REVERT: F  573 HIS cc_start: 0.7159 (m170) cc_final: 0.6942 (m170)
REVERT: F  581 MET cc_start: 0.6266 (tpt) cc_final: 0.6012 (tpt)
REVERT: F  588 MET cc_start: 0.8064 (mmp) cc_final: 0.7775 (mmm)
REVERT: F  595 GLU cc_start: 0.7811 (mm-30) cc_final: 0.6981 (mm-30)
REVERT: F  618 ASP cc_start: 0.7680 (t0) cc_final: 0.6863 (t70)
REVERT: F  643 LYS cc_start: 0.8819 (ptpp) cc_final: 0.7721 (ptpp)
REVERT: F  764 PHE cc_start: 0.7010 (m-10) cc_final: 0.6339 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0707
  time to fit residues: 15.9245
Evaluate side-chains
  127 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.115836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.097865 restraints weight = 20266.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.100584 restraints weight = 12000.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.102074 restraints weight = 7796.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.102361 restraints weight = 5997.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.102711 restraints weight = 5528.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.7172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6693  Z= 0.147
  Angle     :  0.716  11.191   9062  Z= 0.346
  Chirality :  0.047   0.157   1084
  Planarity :  0.005   0.047   1137
  Dihedral  :  4.813  18.478    864
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 18.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.30), residues: 807
  helix: -2.29 (0.29), residues: 264
  sheet: -2.08 (0.46), residues: 141
  loop : -0.63 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 514 
 TYR   0.024   0.002   TYR F 756 
 PHE   0.014   0.002   PHE A 433 
 TRP   0.038   0.004   TRP A 803 
 HIS   0.007   0.001   HIS F 573 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6693)
  covalent geometry    : angle       0.71570 ( 9062)
  hydrogen bonds       : bond        0.03731 (  142)
  hydrogen bonds       : angle       5.99542 (  306)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1304.00 seconds
wall clock time: 23 minutes 12.57 seconds (1392.57 seconds total)