Starting phenix.real_space_refine
on Tue Feb 11 21:54:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8drn_27678/02_2025/8drn_27678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8drn_27678/02_2025/8drn_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_27678/02_2025/8drn_27678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8drn_27678/02_2025/8drn_27678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8drn_27678/02_2025/8drn_27678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8drn_27678/02_2025/8drn_27678.cif"
  }
  resolution = 4.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.66, per 1000 atoms: 0.86
  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: 1.46
  Conformation dependent library (CDL) restraints added in 888.8 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: 0.91
  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: 2.17

  Time building geometry restraints manager: 1.71 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:             7.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.480
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.830
-------------------------------------------------------------------------------
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= 0.285
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.080   0.006   TRP A 475 
 HIS   0.007   0.001   HIS F 669 
 PHE   0.041   0.002   PHE F 488 
 TYR   0.053   0.003   TYR F 687 
 ARG   0.006   0.001   ARG A 419 

*********************** 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  : 0.827 
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: 0.7149 (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: 0.8584 (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: 0.8450 (m-40) cc_final: 0.7962 (m110)
REVERT: A  682 PHE cc_start: 0.8170 (m-80) cc_final: 0.7755 (m-80)
REVERT: A  694 HIS cc_start: 0.8789 (m170) cc_final: 0.8582 (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: 0.7374 (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: 0.7218 (m-80) cc_final: 0.6135 (m-80)
REVERT: F  518 GLU cc_start: 0.7342 (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: 0.7051 (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: 0.2136
  time to fit residues: 76.0072
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  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0030
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.5396

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.121742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.102815 restraints weight = 20208.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.105580 restraints weight = 12626.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.107533 restraints weight = 8786.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6693  Z= 0.317
  Angle     :  0.788  10.398   9062  Z= 0.390
  Chirality :  0.049   0.302   1084
  Planarity :  0.006   0.073   1137
  Dihedral  :  5.368  19.308    864
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 23.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.42 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.29), residues: 807
  helix: -2.46 (0.29), residues: 249
  sheet: -2.47 (0.48), residues: 132
  loop : -0.70 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.005   TRP F 645 
 HIS   0.007   0.001   HIS F 598 
 PHE   0.025   0.003   PHE A 433 
 TYR   0.025   0.003   TYR F 511 
 ARG   0.006   0.001   ARG F 514 

*********************** 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
  206 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 0.772 
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: 0.8189 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: A  475 TRP cc_start: 0.8004 (m-10) cc_final: 0.7572 (m-10)
REVERT: A  518 LEU cc_start: 0.7737 (tp) cc_final: 0.7362 (tp)
REVERT: A  557 LYS cc_start: 0.7961 (tptt) cc_final: 0.7406 (tmtt)
REVERT: A  571 LYS cc_start: 0.7195 (tttp) cc_final: 0.6958 (ttpt)
REVERT: A  645 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8236 (mtpp)
REVERT: A  682 PHE cc_start: 0.7735 (m-80) cc_final: 0.7450 (m-80)
REVERT: A  733 LEU cc_start: 0.9162 (mp) cc_final: 0.8941 (mp)
REVERT: A  801 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7577 (tmt170)
REVERT: F  428 LEU cc_start: 0.8557 (mt) cc_final: 0.8269 (mt)
REVERT: F  452 GLU cc_start: 0.7528 (tp30) cc_final: 0.6840 (tp30)
REVERT: F  550 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7270 (mttm)
REVERT: F  570 MET cc_start: 0.8052 (mmm) cc_final: 0.7678 (mmm)
REVERT: F  573 HIS cc_start: 0.7707 (m170) cc_final: 0.7242 (m170)
REVERT: F  588 MET cc_start: 0.8065 (mmp) cc_final: 0.7574 (mmm)
REVERT: F  633 PHE cc_start: 0.8269 (m-80) cc_final: 0.7783 (m-80)
REVERT: F  647 ASN cc_start: 0.6730 (t0) cc_final: 0.5961 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1875
  time to fit residues: 50.7622
Evaluate side-chains
  145 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 79 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 431 HIS
A 576 ASN
A 657 GLN
A 711 GLN
F 799 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.121237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.102565 restraints weight = 20349.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.105262 restraints weight = 12338.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.107215 restraints weight = 8532.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.4884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6693  Z= 0.205
  Angle     :  0.693   9.204   9062  Z= 0.342
  Chirality :  0.047   0.255   1084
  Planarity :  0.004   0.033   1137
  Dihedral  :  5.083  17.347    864
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 19.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.29 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.29), residues: 807
  helix: -2.27 (0.31), residues: 250
  sheet: -2.60 (0.47), residues: 125
  loop : -0.81 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP F 645 
 HIS   0.006   0.001   HIS A 694 
 PHE   0.017   0.002   PHE F 500 
 TYR   0.024   0.003   TYR F 511 
 ARG   0.003   0.000   ARG F 637 

*********************** 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
  187 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.612 
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: 0.7762 (tp) cc_final: 0.7390 (tp)
REVERT: A  571 LYS cc_start: 0.7585 (tttp) cc_final: 0.7299 (ttpt)
REVERT: A  647 TRP cc_start: 0.7528 (p90) cc_final: 0.6963 (p90)
REVERT: A  665 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7345 (tm-30)
REVERT: A  682 PHE cc_start: 0.7508 (m-80) cc_final: 0.7202 (m-80)
REVERT: A  694 HIS cc_start: 0.8105 (m170) cc_final: 0.7891 (m170)
REVERT: F  432 MET cc_start: 0.6523 (tpt) cc_final: 0.6126 (tpp)
REVERT: F  550 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7509 (mttm)
REVERT: F  570 MET cc_start: 0.8055 (mmm) cc_final: 0.7646 (mmm)
REVERT: F  573 HIS cc_start: 0.7597 (m170) cc_final: 0.7108 (m170)
REVERT: F  588 MET cc_start: 0.8258 (mmp) cc_final: 0.7946 (mmm)
REVERT: F  594 LEU cc_start: 0.9240 (tp) cc_final: 0.8369 (tp)
REVERT: F  595 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7934 (mm-30)
REVERT: F  616 GLU cc_start: 0.8373 (pt0) cc_final: 0.7954 (pp20)
REVERT: F  633 PHE cc_start: 0.8410 (m-80) cc_final: 0.7795 (m-80)
REVERT: F  642 LEU cc_start: 0.6690 (tp) cc_final: 0.6476 (tt)
REVERT: F  644 LEU cc_start: 0.8874 (mt) cc_final: 0.8536 (mt)
REVERT: F  647 ASN cc_start: 0.6940 (t0) cc_final: 0.6224 (t0)
REVERT: F  687 TYR cc_start: 0.8105 (t80) cc_final: 0.7704 (t80)
REVERT: F  706 GLN cc_start: 0.6639 (tp-100) cc_final: 0.6432 (tp-100)
REVERT: F  764 PHE cc_start: 0.7162 (m-10) cc_final: 0.6630 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1627
  time to fit residues: 41.2731
Evaluate side-chains
  142 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 19 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 718 ASN ** 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 = 0.4024 r_free = 0.4024 target = 0.119620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.101081 restraints weight = 20543.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.103825 restraints weight = 12336.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.105716 restraints weight = 8459.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.5394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6693  Z= 0.218
  Angle     :  0.684  11.201   9062  Z= 0.333
  Chirality :  0.047   0.278   1084
  Planarity :  0.005   0.060   1137
  Dihedral  :  4.844  16.129    864
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 21.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.55 %
    Favored  : 96.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.30), residues: 807
  helix: -2.22 (0.30), residues: 262
  sheet: -2.37 (0.47), residues: 133
  loop : -0.74 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 647 
 HIS   0.004   0.001   HIS A 737 
 PHE   0.013   0.002   PHE F 500 
 TYR   0.022   0.002   TYR F 511 
 ARG   0.005   0.000   ARG A 541 

*********************** 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
  168 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 TRP cc_start: 0.8199 (m-10) cc_final: 0.7949 (m-10)
REVERT: A  495 LEU cc_start: 0.7976 (tp) cc_final: 0.7704 (tt)
REVERT: A  518 LEU cc_start: 0.7799 (tp) cc_final: 0.7551 (tp)
REVERT: A  557 LYS cc_start: 0.7703 (tptt) cc_final: 0.6868 (tmtt)
REVERT: A  571 LYS cc_start: 0.7778 (tttp) cc_final: 0.7373 (ttpt)
REVERT: A  601 CYS cc_start: 0.8542 (m) cc_final: 0.8228 (m)
REVERT: A  666 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7439 (mtm110)
REVERT: A  682 PHE cc_start: 0.7563 (m-80) cc_final: 0.7249 (m-80)
REVERT: A  733 LEU cc_start: 0.9196 (mp) cc_final: 0.8942 (mp)
REVERT: A  773 LEU cc_start: 0.9370 (tp) cc_final: 0.9072 (tp)
REVERT: A  804 ARG cc_start: 0.6917 (ptm160) cc_final: 0.6659 (tmt170)
REVERT: F  432 MET cc_start: 0.6510 (tpt) cc_final: 0.6290 (tpp)
REVERT: F  570 MET cc_start: 0.8007 (mmm) cc_final: 0.7573 (mmm)
REVERT: F  573 HIS cc_start: 0.7325 (m170) cc_final: 0.7105 (m170)
REVERT: F  588 MET cc_start: 0.8117 (mmp) cc_final: 0.7783 (mmm)
REVERT: F  594 LEU cc_start: 0.9247 (tp) cc_final: 0.8434 (tp)
REVERT: F  595 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8012 (mm-30)
REVERT: F  616 GLU cc_start: 0.8263 (pt0) cc_final: 0.8005 (pp20)
REVERT: F  643 LYS cc_start: 0.8997 (ptpp) cc_final: 0.8539 (ptpp)
REVERT: F  670 ASN cc_start: 0.6945 (t0) cc_final: 0.6427 (t0)
REVERT: F  687 TYR cc_start: 0.8114 (t80) cc_final: 0.7790 (t80)
REVERT: F  764 PHE cc_start: 0.7296 (m-10) cc_final: 0.6715 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1598
  time to fit residues: 36.5762
Evaluate side-chains
  135 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 73 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.118139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.100713 restraints weight = 20514.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.102872 restraints weight = 12517.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.104626 restraints weight = 8449.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.5800

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= 0.222
  Angle     :  0.661   9.308   9062  Z= 0.329
  Chirality :  0.046   0.199   1084
  Planarity :  0.004   0.040   1137
  Dihedral  :  4.812  16.254    864
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 22.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.30), residues: 807
  helix: -2.22 (0.30), residues: 261
  sheet: -2.35 (0.46), residues: 139
  loop : -0.69 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.004   TRP A 647 
 HIS   0.004   0.001   HIS F 606 
 PHE   0.012   0.002   PHE F 500 
 TYR   0.019   0.002   TYR F 756 
 ARG   0.004   0.000   ARG A 762 

*********************** 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
  166 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.7705 (tp) cc_final: 0.7451 (tp)
REVERT: A  557 LYS cc_start: 0.7810 (tptt) cc_final: 0.6894 (tmtt)
REVERT: A  571 LYS cc_start: 0.7996 (tttp) cc_final: 0.7545 (ttpt)
REVERT: A  624 ASN cc_start: 0.7770 (m-40) cc_final: 0.7456 (m-40)
REVERT: A  682 PHE cc_start: 0.7701 (m-80) cc_final: 0.7403 (m-80)
REVERT: F  426 LEU cc_start: 0.7672 (tp) cc_final: 0.7408 (mm)
REVERT: F  570 MET cc_start: 0.8054 (mmm) cc_final: 0.7496 (mmm)
REVERT: F  588 MET cc_start: 0.8120 (mmp) cc_final: 0.7828 (mmm)
REVERT: F  594 LEU cc_start: 0.9290 (tp) cc_final: 0.8465 (tp)
REVERT: F  595 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8019 (mm-30)
REVERT: F  616 GLU cc_start: 0.8211 (pt0) cc_final: 0.7966 (pp20)
REVERT: F  618 ASP cc_start: 0.7061 (t0) cc_final: 0.6461 (t70)
REVERT: F  764 PHE cc_start: 0.7306 (m-10) cc_final: 0.6590 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1634
  time to fit residues: 37.1322
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  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   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 = 0.3993 r_free = 0.3993 target = 0.117612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.100370 restraints weight = 20468.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.101661 restraints weight = 14020.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.103690 restraints weight = 9735.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.6193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6693  Z= 0.228
  Angle     :  0.661  10.633   9062  Z= 0.326
  Chirality :  0.046   0.173   1084
  Planarity :  0.005   0.058   1137
  Dihedral  :  4.826  19.084    864
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 21.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.30), residues: 807
  helix: -2.11 (0.31), residues: 256
  sheet: -2.21 (0.49), residues: 133
  loop : -0.77 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP A 411 
 HIS   0.005   0.001   HIS A 694 
 PHE   0.021   0.002   PHE F 666 
 TYR   0.027   0.002   TYR F 687 
 ARG   0.003   0.000   ARG F 425 

*********************** 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
  156 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.7806 (tp) cc_final: 0.7393 (tp)
REVERT: A  557 LYS cc_start: 0.7800 (tptt) cc_final: 0.6897 (tmtt)
REVERT: A  571 LYS cc_start: 0.8028 (tttp) cc_final: 0.7615 (ttpt)
REVERT: A  601 CYS cc_start: 0.8670 (m) cc_final: 0.8451 (m)
REVERT: A  682 PHE cc_start: 0.7592 (m-80) cc_final: 0.7285 (m-80)
REVERT: A  733 LEU cc_start: 0.9116 (mp) cc_final: 0.8880 (mp)
REVERT: F  426 LEU cc_start: 0.7806 (tp) cc_final: 0.7597 (mm)
REVERT: F  513 LEU cc_start: 0.7805 (mt) cc_final: 0.7032 (mt)
REVERT: F  550 LYS cc_start: 0.8339 (mttt) cc_final: 0.7634 (mmtt)
REVERT: F  570 MET cc_start: 0.8013 (mmm) cc_final: 0.7708 (mmm)
REVERT: F  594 LEU cc_start: 0.9250 (tp) cc_final: 0.8447 (tp)
REVERT: F  595 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8133 (mm-30)
REVERT: F  618 ASP cc_start: 0.7318 (t0) cc_final: 0.6472 (t70)
REVERT: F  764 PHE cc_start: 0.7174 (m-10) cc_final: 0.6362 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1638
  time to fit residues: 35.0758
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  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0060
   chunk 48 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 694 HIS ** 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 = 0.3961 r_free = 0.3961 target = 0.116294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.098577 restraints weight = 20343.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.101064 restraints weight = 11767.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.102857 restraints weight = 7641.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.6433

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= 0.207
  Angle     :  0.676  10.283   9062  Z= 0.331
  Chirality :  0.047   0.176   1084
  Planarity :  0.004   0.051   1137
  Dihedral  :  4.830  16.945    864
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 20.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.30), residues: 807
  helix: -2.06 (0.32), residues: 248
  sheet: -1.96 (0.49), residues: 130
  loop : -0.75 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.004   TRP A 647 
 HIS   0.007   0.001   HIS F 573 
 PHE   0.019   0.002   PHE A 443 
 TYR   0.022   0.002   TYR F 687 
 ARG   0.003   0.000   ARG F 514 

*********************** 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
  158 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6568 (mm-30)
REVERT: A  518 LEU cc_start: 0.8041 (tp) cc_final: 0.7631 (tp)
REVERT: A  557 LYS cc_start: 0.7887 (tptt) cc_final: 0.6992 (tmtt)
REVERT: A  571 LYS cc_start: 0.7875 (tttp) cc_final: 0.7559 (ttpt)
REVERT: A  624 ASN cc_start: 0.8040 (m110) cc_final: 0.7831 (m-40)
REVERT: A  682 PHE cc_start: 0.7833 (m-80) cc_final: 0.7583 (m-10)
REVERT: F  486 LEU cc_start: 0.7277 (mt) cc_final: 0.7060 (mt)
REVERT: F  498 VAL cc_start: 0.9772 (m) cc_final: 0.9513 (p)
REVERT: F  570 MET cc_start: 0.8027 (mmm) cc_final: 0.7605 (mmm)
REVERT: F  581 MET cc_start: 0.6275 (tpt) cc_final: 0.6066 (tpt)
REVERT: F  588 MET cc_start: 0.8005 (mmp) cc_final: 0.7771 (mmm)
REVERT: F  688 LEU cc_start: 0.8444 (tp) cc_final: 0.8165 (tp)
REVERT: F  764 PHE cc_start: 0.7268 (m-10) cc_final: 0.6418 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1744
  time to fit residues: 37.2298
Evaluate side-chains
  121 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 576 ASN
A 608 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.115047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.097923 restraints weight = 20638.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.099509 restraints weight = 12998.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.101410 restraints weight = 9153.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.6847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6693  Z= 0.328
  Angle     :  0.775   9.160   9062  Z= 0.379
  Chirality :  0.049   0.173   1084
  Planarity :  0.005   0.049   1137
  Dihedral  :  5.251  23.225    864
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 25.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.30), residues: 807
  helix: -2.32 (0.30), residues: 248
  sheet: -2.11 (0.47), residues: 135
  loop : -0.74 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.005   TRP A 647 
 HIS   0.009   0.001   HIS A 694 
 PHE   0.013   0.002   PHE F 500 
 TYR   0.033   0.003   TYR A 648 
 ARG   0.004   0.001   ARG F 425 

*********************** 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
  153 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.7890 (tp) cc_final: 0.7502 (tp)
REVERT: A  557 LYS cc_start: 0.7826 (tptt) cc_final: 0.6979 (tmtt)
REVERT: A  650 HIS cc_start: 0.5901 (m-70) cc_final: 0.5645 (m-70)
REVERT: A  682 PHE cc_start: 0.7708 (m-80) cc_final: 0.7362 (m-10)
REVERT: A  733 LEU cc_start: 0.9123 (mp) cc_final: 0.8865 (mp)
REVERT: F  486 LEU cc_start: 0.7159 (mt) cc_final: 0.6871 (mt)
REVERT: F  498 VAL cc_start: 0.9764 (m) cc_final: 0.9530 (p)
REVERT: F  550 LYS cc_start: 0.8459 (mttt) cc_final: 0.7973 (mmtt)
REVERT: F  764 PHE cc_start: 0.7320 (m-10) cc_final: 0.6617 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1686
  time to fit residues: 35.2351
Evaluate side-chains
  106 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0470
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.7078

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
F 468 ASN
** 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 = 0.3960 r_free = 0.3960 target = 0.116333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.098214 restraints weight = 19998.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.100849 restraints weight = 11719.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.102553 restraints weight = 7799.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.7050

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= 0.212
  Angle     :  0.748  10.021   9062  Z= 0.361
  Chirality :  0.048   0.227   1084
  Planarity :  0.004   0.045   1137
  Dihedral  :  5.032  26.168    864
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 21.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.79 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.29), residues: 807
  helix: -2.23 (0.31), residues: 249
  sheet: -2.12 (0.45), residues: 142
  loop : -0.85 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.004   TRP A 647 
 HIS   0.007   0.001   HIS A 694 
 PHE   0.023   0.002   PHE F 609 
 TYR   0.021   0.002   TYR F 511 
 ARG   0.004   0.000   ARG A 762 

*********************** 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
  152 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.8073 (tp) cc_final: 0.7684 (tp)
REVERT: A  557 LYS cc_start: 0.7786 (tptt) cc_final: 0.6976 (tmtt)
REVERT: A  648 TYR cc_start: 0.7652 (m-80) cc_final: 0.7406 (m-80)
REVERT: A  682 PHE cc_start: 0.7711 (m-80) cc_final: 0.7440 (m-10)
REVERT: F  486 LEU cc_start: 0.7176 (mt) cc_final: 0.6950 (mt)
REVERT: F  581 MET cc_start: 0.6326 (tpt) cc_final: 0.5978 (tpt)
REVERT: F  616 GLU cc_start: 0.8192 (pt0) cc_final: 0.7987 (pp20)
REVERT: F  643 LYS cc_start: 0.9195 (ptpp) cc_final: 0.8910 (ptpp)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1610
  time to fit residues: 33.4200
Evaluate side-chains
  114 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0030
   chunk 71 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.116268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.098104 restraints weight = 20347.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.100494 restraints weight = 12158.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.102766 restraints weight = 8045.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.7146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6693  Z= 0.207
  Angle     :  0.720  10.152   9062  Z= 0.349
  Chirality :  0.047   0.216   1084
  Planarity :  0.004   0.043   1137
  Dihedral  :  4.967  20.688    864
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 20.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.30), residues: 807
  helix: -1.99 (0.33), residues: 229
  sheet: -2.07 (0.45), residues: 142
  loop : -0.53 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.004   TRP A 475 
 HIS   0.007   0.001   HIS A 694 
 PHE   0.020   0.002   PHE F 441 
 TYR   0.016   0.002   TYR F 687 
 ARG   0.003   0.000   ARG F 425 

********************** 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
  149 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.8065 (tp) cc_final: 0.7636 (tp)
REVERT: A  557 LYS cc_start: 0.7781 (tptt) cc_final: 0.6957 (tmtt)
REVERT: A  601 CYS cc_start: 0.8866 (m) cc_final: 0.8615 (m)
REVERT: A  648 TYR cc_start: 0.7864 (m-80) cc_final: 0.7403 (m-80)
REVERT: A  682 PHE cc_start: 0.7724 (m-80) cc_final: 0.7451 (m-10)
REVERT: F  486 LEU cc_start: 0.7195 (mt) cc_final: 0.6990 (mt)
REVERT: F  550 LYS cc_start: 0.8475 (mttt) cc_final: 0.8043 (mmtt)
REVERT: F  581 MET cc_start: 0.6315 (tpt) cc_final: 0.6044 (tpt)
REVERT: F  616 GLU cc_start: 0.8199 (pt0) cc_final: 0.7958 (pp20)
REVERT: F  764 PHE cc_start: 0.7094 (m-10) cc_final: 0.6202 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1775
  time to fit residues: 36.1152
Evaluate side-chains
  114 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0870
   chunk 61 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0770
   chunk 70 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.5116

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.117294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.099324 restraints weight = 20410.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.101039 restraints weight = 12802.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.103083 restraints weight = 8824.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.7284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6693  Z= 0.192
  Angle     :  0.717   9.751   9062  Z= 0.347
  Chirality :  0.046   0.190   1084
  Planarity :  0.005   0.043   1137
  Dihedral  :  4.829  18.400    864
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.00 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.30), residues: 807
  helix: -2.15 (0.32), residues: 238
  sheet: -2.04 (0.45), residues: 147
  loop : -0.63 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A 475 
 HIS   0.008   0.001   HIS A 694 
 PHE   0.018   0.002   PHE F 666 
 TYR   0.016   0.002   TYR F 756 
 ARG   0.006   0.001   ARG F 514 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2425.71 seconds
wall clock time: 44 minutes 48.06 seconds (2688.06 seconds total)