Starting phenix.real_space_refine
on Fri Aug 22 18:08:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f7d_28903/08_2025/8f7d_28903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f7d_28903/08_2025/8f7d_28903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f7d_28903/08_2025/8f7d_28903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f7d_28903/08_2025/8f7d_28903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f7d_28903/08_2025/8f7d_28903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f7d_28903/08_2025/8f7d_28903.cif"
  }
  resolution = 4.2
  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=   0.003 sd=   0.044
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-2.0-5787/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: 1.99, per 1000 atoms: 0.30
  Number of scatterers: 6578
  At special positions: 0
  Unit cell: (110.04, 73.36, 82.792, 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: 0.47
  Conformation dependent library (CDL) restraints added in 470.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 402 through 411
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'A' and resid 439 through 445
      removed outlier: 3.724A  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: 3.912A  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: 3.508A  pdb=" N   GLN A 636 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   HIS A 637 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
      removed outlier: 3.628A  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: 3.771A  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
    Processing helix  chain 'F' and resid 410 through 418
    Processing helix  chain 'F' and resid 437 through 443
      removed outlier: 3.922A  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: 3.834A  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: 3.540A  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: 3.833A  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: 3.817A  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: 6.824A  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: 7.702A  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: 7.283A  pdb=" N   ILE A 599 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.842A  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: 6.818A  pdb=" N   LEU A 736 " --> pdb=" O   GLU A 760 " (cutoff:3.500A)
      removed outlier: 6.686A  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: 7.012A  pdb=" N   GLU F 452 " --> pdb=" O   LEU F 428 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU F 430 " --> pdb=" O   GLU F 452 " (cutoff:3.500A)
      removed outlier: 6.432A  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: 7.976A  pdb=" N   LYS F 499 " --> pdb=" O   LEU F 472 " (cutoff:3.500A)
      removed outlier: 7.363A  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: 7.350A  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: 6.473A  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: 6.680A  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

    148 hydrogen bonds defined for protein.
    321 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1913
        1.34 -     1.46: 916
        1.46 -     1.58: 3829
        1.58 -     1.70: 1
        1.70 -     1.82: 34
  Bond restraints: 6693
  Sorted by residual:
  bond pdb=" N   ASN A 423 "
       pdb=" CA  ASN A 423 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.17e-02 7.31e+03 9.47e+00
  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 9.06e+00
  bond pdb=" N   THR A 412 "
       pdb=" CA  THR A 412 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.21e-02 6.83e+03 7.87e+00
  bond pdb=" N   LYS A 422 "
       pdb=" CA  LYS A 422 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.25e-02 6.40e+03 7.75e+00
  bond pdb=" N   LEU A 430 "
       pdb=" CA  LEU A 430 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.21e-02 6.83e+03 7.36e+00
  ... (remaining 6688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 8725
        2.35 -     4.69: 286
        4.69 -     7.04: 32
        7.04 -     9.38: 15
        9.38 -    11.73: 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  124.43  -11.73 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  121.60   -7.50 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  121.58   -7.48 2.00e+00 2.50e-01 1.40e+01
  angle pdb=" CA  PHE A 433 "
        pdb=" C   PHE A 433 "
        pdb=" O   PHE A 433 "
      ideal   model   delta    sigma   weight residual
     120.71  116.75    3.96 1.06e+00 8.90e-01 1.40e+01
  ... (remaining 9057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 3658
       17.87 -    35.75: 389
       35.75 -    53.62: 90
       53.62 -    71.50: 14
       71.50 -    89.37: 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  157.55   22.45     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  158.58   21.42     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  SER F 677 "
           pdb=" C   SER F 677 "
           pdb=" N   HIS F 678 "
           pdb=" CA  HIS F 678 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.54  -19.46     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 4153 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1011
       0.098 -    0.195: 71
       0.195 -    0.293: 1
       0.293 -    0.391: 0
       0.391 -    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 5.96e+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 1.64e+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 7.12e-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   2.92e-02 2.13e+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 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 475 "   -0.000 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   2.11e-02 8.94e+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 5.71e+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: 1456
        2.79 -     3.32: 6490
        3.32 -     3.85: 11415
        3.85 -     4.37: 14419
        4.37 -     4.90: 22616
  Nonbonded interactions: 56396
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F 689 "
            pdb=" OG  SER F 691 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLN A 560 "
            pdb=" OG1 THR A 563 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ILE F 556 "
            pdb=" ND2 ASN F 584 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" O   ARG F 775 "
            pdb=" NH1 ARG F 775 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" O   THR F 640 "
            pdb=" N   ARG F 664 "
     model   vdw
     2.334 3.120
  ... (remaining 56391 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:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6126
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      :  0.005   0.102   6693  Z= 0.292
  Angle     :  0.997  11.731   9062  Z= 0.556
  Chirality :  0.053   0.488   1084
  Planarity :  0.005   0.041   1137
  Dihedral  : 15.553  89.372   2580
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 19.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 20.79 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.71 (0.28), residues: 807
  helix: -2.79 (0.28), residues: 248
  sheet: -2.12 (0.53), residues: 113
  loop : -0.99 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 671 
 TYR   0.053   0.003   TYR F 687 
 PHE   0.041   0.002   PHE F 488 
 TRP   0.080   0.005   TRP A 475 
 HIS   0.007   0.001   HIS F 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 6693)
  covalent geometry    : angle       0.99699 ( 9062)
  hydrogen bonds       : bond        0.21588 (  148)
  hydrogen bonds       : angle       8.89012 (  321)

*********************** 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
  284 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 280
  time to evaluate  : 0.211 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.8016 (tp) cc_final: 0.7760 (tp)
REVERT: A  551 LEU cc_start: 0.8946 (mt) cc_final: 0.8682 (mm)
REVERT: A  572 LEU cc_start: 0.8671 (tp) cc_final: 0.8408 (tp)
REVERT: A  592 ASN cc_start: 0.8153 (m-40) cc_final: 0.7555 (t0)
REVERT: A  645 LYS cc_start: 0.8899 (mttt) cc_final: 0.8550 (mttp)
REVERT: A  703 ASP cc_start: 0.7274 (m-30) cc_final: 0.6877 (t0)
REVERT: F  423 HIS cc_start: 0.7386 (m90) cc_final: 0.7132 (m-70)
REVERT: F  430 LEU cc_start: 0.8000 (mt) cc_final: 0.7799 (mp)
REVERT: F  446 LEU cc_start: 0.8320 (mt) cc_final: 0.8035 (mt)
REVERT: F  476 GLN cc_start: 0.8630 (mp10) cc_final: 0.8280 (mp10)
REVERT: F  496 LEU cc_start: 0.7806 (tp) cc_final: 0.7538 (tp)
REVERT: F  524 SER cc_start: 0.6946 (p) cc_final: 0.6098 (p)
REVERT: F  581 MET cc_start: 0.6333 (tpt) cc_final: 0.5908 (tpp)
REVERT: F  598 HIS cc_start: 0.7199 (t-170) cc_final: 0.6853 (t-170)
REVERT: F  666 PHE cc_start: 0.8759 (m-80) cc_final: 0.6929 (m-80)
REVERT: F  715 CYS cc_start: 0.6487 (m) cc_final: 0.6146 (m)
REVERT: F  726 TYR cc_start: 0.6646 (m-80) cc_final: 0.6253 (m-80)
REVERT: F  784 VAL cc_start: 0.6124 (m) cc_final: 0.5588 (m)
REVERT: F  800 MET cc_start: 0.3332 (tpt) cc_final: 0.2796 (mmt)
  outliers start: 4
  outliers final: 0
  residues processed: 282
  average time/residue: 0.1025
  time to fit residues: 36.0349
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  : 0.269 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 409 ASN
A 636 GLN
A 650 HIS
F 407 ASN
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.133153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.115860 restraints weight = 26532.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.117730 restraints weight = 20279.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.118908 restraints weight = 14650.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.119295 restraints weight = 11948.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.119564 restraints weight = 10705.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6370
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6693  Z= 0.174
  Angle     :  0.799  11.247   9062  Z= 0.391
  Chirality :  0.047   0.189   1084
  Planarity :  0.005   0.043   1137
  Dihedral  :  5.274  20.172    864
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 23.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.29), residues: 807
  helix: -2.69 (0.27), residues: 261
  sheet: -2.74 (0.46), residues: 141
  loop : -0.53 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 765 
 TYR   0.024   0.003   TYR F 646 
 PHE   0.033   0.003   PHE F 609 
 TRP   0.047   0.005   TRP A 803 
 HIS   0.009   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 6693)
  covalent geometry    : angle       0.79918 ( 9062)
  hydrogen bonds       : bond        0.05503 (  148)
  hydrogen bonds       : angle       7.46691 (  321)

*********************** 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
  208 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.220 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 ASP cc_start: 0.8061 (m-30) cc_final: 0.7438 (m-30)
REVERT: A  473 GLU cc_start: 0.5981 (mt-10) cc_final: 0.5738 (mm-30)
REVERT: A  495 LEU cc_start: 0.6970 (tp) cc_final: 0.6509 (tp)
REVERT: A  518 LEU cc_start: 0.7443 (tp) cc_final: 0.7186 (tp)
REVERT: A  687 LEU cc_start: 0.7890 (mt) cc_final: 0.7565 (mt)
REVERT: A  713 LEU cc_start: 0.8723 (tp) cc_final: 0.8439 (pp)
REVERT: A  728 PHE cc_start: 0.7405 (m-80) cc_final: 0.6629 (m-80)
REVERT: A  733 LEU cc_start: 0.7997 (tp) cc_final: 0.7777 (tt)
REVERT: A  764 ASN cc_start: 0.6716 (m-40) cc_final: 0.6232 (m110)
REVERT: A  780 LYS cc_start: 0.8041 (pttt) cc_final: 0.7710 (pttm)
REVERT: F  446 LEU cc_start: 0.7972 (mt) cc_final: 0.7714 (mt)
REVERT: F  472 LEU cc_start: 0.9236 (tp) cc_final: 0.8957 (tp)
REVERT: F  573 HIS cc_start: 0.7678 (m90) cc_final: 0.7274 (m-70)
REVERT: F  598 HIS cc_start: 0.7709 (t-170) cc_final: 0.7376 (t-170)
REVERT: F  617 LEU cc_start: 0.7105 (tp) cc_final: 0.6610 (pp)
REVERT: F  618 ASP cc_start: 0.6944 (t0) cc_final: 0.6613 (t70)
REVERT: F  643 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8876 (tptp)
REVERT: F  666 PHE cc_start: 0.9151 (m-80) cc_final: 0.7758 (m-10)
REVERT: F  757 LEU cc_start: 0.7940 (tp) cc_final: 0.7711 (pt)
REVERT: F  759 ILE cc_start: 0.7988 (mm) cc_final: 0.7578 (mm)
REVERT: F  778 LYS cc_start: 0.5058 (mmmt) cc_final: 0.4755 (mmtm)
REVERT: F  800 MET cc_start: 0.3318 (tpt) cc_final: 0.2850 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0805
  time to fit residues: 21.6099
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  : 0.212 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 53 optimal weight:    8.9990
   chunk 27 optimal weight:    0.3980
   chunk 68 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 64 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 416 GLN
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 635 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.131361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.115725 restraints weight = 27056.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.116489 restraints weight = 19787.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.117116 restraints weight = 15337.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.117475 restraints weight = 12792.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.117538 restraints weight = 12555.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6452
moved from start:          0.5389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6693  Z= 0.142
  Angle     :  0.720   8.908   9062  Z= 0.360
  Chirality :  0.046   0.190   1084
  Planarity :  0.005   0.044   1137
  Dihedral  :  5.121  22.375    864
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 19.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.82 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.30), residues: 807
  helix: -2.58 (0.29), residues: 262
  sheet: -2.78 (0.45), residues: 141
  loop : -0.58 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 492 
 TYR   0.038   0.003   TYR F 511 
 PHE   0.024   0.002   PHE F 609 
 TRP   0.029   0.004   TRP F 645 
 HIS   0.008   0.001   HIS F 678 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6693)
  covalent geometry    : angle       0.72003 ( 9062)
  hydrogen bonds       : bond        0.04259 (  148)
  hydrogen bonds       : angle       6.97783 (  321)

*********************** 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
  171 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.159 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  592 ASN cc_start: 0.6939 (t0) cc_final: 0.6737 (t0)
REVERT: A  687 LEU cc_start: 0.7917 (mt) cc_final: 0.7398 (mt)
REVERT: A  713 LEU cc_start: 0.8776 (tp) cc_final: 0.8472 (pp)
REVERT: A  728 PHE cc_start: 0.6970 (m-80) cc_final: 0.6624 (m-80)
REVERT: A  733 LEU cc_start: 0.7880 (tp) cc_final: 0.7578 (tt)
REVERT: A  764 ASN cc_start: 0.6539 (m-40) cc_final: 0.6192 (m110)
REVERT: A  780 LYS cc_start: 0.8175 (pttt) cc_final: 0.7739 (pttm)
REVERT: F  403 LEU cc_start: 0.8363 (tt) cc_final: 0.7603 (mm)
REVERT: F  426 LEU cc_start: 0.7630 (tp) cc_final: 0.6786 (tp)
REVERT: F  581 MET cc_start: 0.8431 (tpp) cc_final: 0.8158 (tpp)
REVERT: F  598 HIS cc_start: 0.7353 (t-170) cc_final: 0.7099 (t-170)
REVERT: F  617 LEU cc_start: 0.6932 (tp) cc_final: 0.6601 (pp)
REVERT: F  618 ASP cc_start: 0.7820 (t0) cc_final: 0.6794 (t70)
REVERT: F  759 ILE cc_start: 0.7621 (mm) cc_final: 0.7211 (mm)
REVERT: F  778 LYS cc_start: 0.4928 (mmmt) cc_final: 0.4608 (mmtm)
REVERT: F  786 ASP cc_start: 0.3261 (p0) cc_final: 0.1973 (t0)
REVERT: F  800 MET cc_start: 0.3205 (tpt) cc_final: 0.2723 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0731
  time to fit residues: 16.1474
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  : 0.163 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0970
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 478 HIS
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 HIS
F 402 GLN
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 482 HIS
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.126622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.109651 restraints weight = 26939.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.111073 restraints weight = 19497.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.112035 restraints weight = 14315.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.112581 restraints weight = 11806.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.112732 restraints weight = 11058.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.6323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6693  Z= 0.197
  Angle     :  0.784  10.385   9062  Z= 0.388
  Chirality :  0.046   0.152   1084
  Planarity :  0.005   0.044   1137
  Dihedral  :  5.202  24.758    864
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 23.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.29 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.09 (0.29), residues: 807
  helix: -2.87 (0.26), residues: 278
  sheet: -2.85 (0.42), residues: 148
  loop : -0.79 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 688 
 TYR   0.027   0.003   TYR F 511 
 PHE   0.039   0.003   PHE F 666 
 TRP   0.058   0.008   TRP A 647 
 HIS   0.005   0.001   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6693)
  covalent geometry    : angle       0.78354 ( 9062)
  hydrogen bonds       : bond        0.04386 (  148)
  hydrogen bonds       : angle       6.91699 (  321)

*********************** 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
  156 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.273 
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: A  495 LEU cc_start: 0.7317 (tp) cc_final: 0.6979 (tp)
REVERT: A  592 ASN cc_start: 0.6707 (t0) cc_final: 0.6503 (t0)
REVERT: A  687 LEU cc_start: 0.8252 (mt) cc_final: 0.7761 (mt)
REVERT: A  713 LEU cc_start: 0.8910 (tp) cc_final: 0.8434 (pp)
REVERT: A  733 LEU cc_start: 0.7872 (tp) cc_final: 0.7588 (tt)
REVERT: A  764 ASN cc_start: 0.6590 (m-40) cc_final: 0.6053 (m110)
REVERT: A  780 LYS cc_start: 0.8352 (pttt) cc_final: 0.7946 (pttm)
REVERT: F  430 LEU cc_start: 0.7991 (mp) cc_final: 0.7690 (mp)
REVERT: F  432 MET cc_start: 0.4253 (mmp) cc_final: 0.3676 (mtt)
REVERT: F  446 LEU cc_start: 0.8077 (mt) cc_final: 0.7868 (mt)
REVERT: F  474 LEU cc_start: 0.9014 (mt) cc_final: 0.8509 (mt)
REVERT: F  510 MET cc_start: 0.6122 (pmm) cc_final: 0.4783 (pmm)
REVERT: F  581 MET cc_start: 0.8439 (tpp) cc_final: 0.8046 (tpp)
REVERT: F  598 HIS cc_start: 0.7334 (t-170) cc_final: 0.7113 (t-170)
REVERT: F  666 PHE cc_start: 0.9137 (m-80) cc_final: 0.7900 (m-80)
REVERT: F  715 CYS cc_start: 0.7109 (m) cc_final: 0.6758 (m)
REVERT: F  759 ILE cc_start: 0.7739 (mm) cc_final: 0.7506 (mm)
REVERT: F  778 LYS cc_start: 0.5206 (mmmt) cc_final: 0.4860 (mmtm)
REVERT: F  800 MET cc_start: 0.2854 (tpt) cc_final: 0.2475 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0684
  time to fit residues: 14.3553
Evaluate side-chains
  108 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 560 GLN
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 475 HIS
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 573 HIS
F 606 HIS
** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.122633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.106018 restraints weight = 27023.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.107816 restraints weight = 18543.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.109247 restraints weight = 13521.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.110232 restraints weight = 10425.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.110965 restraints weight = 8637.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.7303

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= 0.214
  Angle     :  0.800  10.659   9062  Z= 0.398
  Chirality :  0.049   0.272   1084
  Planarity :  0.005   0.051   1137
  Dihedral  :  5.455  24.691    864
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 23.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.61 %
    Favored  : 95.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.17 (0.28), residues: 807
  helix: -3.01 (0.25), residues: 266
  sheet: -2.75 (0.42), residues: 156
  loop : -0.87 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 781 
 TYR   0.034   0.004   TYR F 710 
 PHE   0.022   0.003   PHE A 635 
 TRP   0.048   0.005   TRP F 645 
 HIS   0.006   0.001   HIS F 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 6693)
  covalent geometry    : angle       0.80019 ( 9062)
  hydrogen bonds       : bond        0.04334 (  148)
  hydrogen bonds       : angle       7.11513 (  321)

*********************** 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
  153 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.271 
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: A  495 LEU cc_start: 0.6943 (tp) cc_final: 0.6497 (tp)
REVERT: A  668 TYR cc_start: 0.6624 (m-10) cc_final: 0.5611 (m-10)
REVERT: A  687 LEU cc_start: 0.8498 (mt) cc_final: 0.8131 (mt)
REVERT: A  713 LEU cc_start: 0.8860 (tp) cc_final: 0.8399 (pp)
REVERT: A  780 LYS cc_start: 0.8545 (pttt) cc_final: 0.8172 (pttm)
REVERT: F  510 MET cc_start: 0.6450 (pmm) cc_final: 0.5290 (pmm)
REVERT: F  513 LEU cc_start: 0.7256 (mt) cc_final: 0.6834 (mp)
REVERT: F  573 HIS cc_start: 0.7400 (m-70) cc_final: 0.7156 (m-70)
REVERT: F  581 MET cc_start: 0.8591 (tpp) cc_final: 0.8145 (tpp)
REVERT: F  598 HIS cc_start: 0.7011 (t-170) cc_final: 0.6596 (t-170)
REVERT: F  646 TYR cc_start: 0.5989 (m-10) cc_final: 0.5751 (m-80)
REVERT: F  666 PHE cc_start: 0.9106 (m-80) cc_final: 0.8858 (m-10)
REVERT: F  800 MET cc_start: 0.1915 (tpt) cc_final: 0.1668 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0712
  time to fit residues: 14.9343
Evaluate side-chains
  112 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0270
   chunk 38 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.0044

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

Flipped N/Q/H residues before XYZ refinement:
A 636 GLN
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** 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 = 0.4257 r_free = 0.4257 target = 0.124710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.107371 restraints weight = 27802.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.109232 restraints weight = 19295.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.110547 restraints weight = 14541.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.111646 restraints weight = 11507.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.112143 restraints weight = 9527.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.7594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6693  Z= 0.139
  Angle     :  0.714   9.438   9062  Z= 0.356
  Chirality :  0.046   0.255   1084
  Planarity :  0.005   0.057   1137
  Dihedral  :  5.204  24.315    864
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 21.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.76 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.99 (0.29), residues: 807
  helix: -2.91 (0.27), residues: 266
  sheet: -2.68 (0.42), residues: 156
  loop : -0.73 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 801 
 TYR   0.022   0.003   TYR F 511 
 PHE   0.015   0.002   PHE F 764 
 TRP   0.063   0.006   TRP A 803 
 HIS   0.008   0.001   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6693)
  covalent geometry    : angle       0.71376 ( 9062)
  hydrogen bonds       : bond        0.03924 (  148)
  hydrogen bonds       : angle       6.98325 (  321)

*********************** 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
  152 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  592 ASN cc_start: 0.6814 (t0) cc_final: 0.6492 (t0)
REVERT: A  687 LEU cc_start: 0.8505 (mt) cc_final: 0.8029 (mt)
REVERT: A  713 LEU cc_start: 0.8808 (tp) cc_final: 0.8268 (pp)
REVERT: A  780 LYS cc_start: 0.8534 (pttt) cc_final: 0.8108 (pttm)
REVERT: F  573 HIS cc_start: 0.7464 (m-70) cc_final: 0.7236 (m-70)
REVERT: F  581 MET cc_start: 0.8434 (tpp) cc_final: 0.7972 (tpp)
REVERT: F  646 TYR cc_start: 0.5986 (m-10) cc_final: 0.5728 (m-80)
REVERT: F  666 PHE cc_start: 0.9076 (m-80) cc_final: 0.8827 (m-10)
REVERT: F  778 LYS cc_start: 0.5059 (mmtt) cc_final: 0.4840 (mmtp)
REVERT: F  786 ASP cc_start: 0.2860 (p0) cc_final: 0.1227 (t0)
REVERT: F  800 MET cc_start: 0.2397 (tpt) cc_final: 0.1881 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0657
  time to fit residues: 13.4787
Evaluate side-chains
  112 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 75 optimal weight:    0.3980
   chunk 60 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 592 ASN
** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** 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 = 0.4257 r_free = 0.4257 target = 0.124764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.108747 restraints weight = 26926.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.110328 restraints weight = 19207.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.111189 restraints weight = 13751.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.111601 restraints weight = 11799.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.111724 restraints weight = 11117.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.7738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6693  Z= 0.125
  Angle     :  0.692   9.983   9062  Z= 0.339
  Chirality :  0.046   0.228   1084
  Planarity :  0.005   0.048   1137
  Dihedral  :  5.014  23.023    864
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.05 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.80 (0.29), residues: 807
  helix: -2.76 (0.27), residues: 259
  sheet: -2.57 (0.42), residues: 156
  loop : -0.65 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 417 
 TYR   0.031   0.002   TYR F 710 
 PHE   0.016   0.002   PHE F 667 
 TRP   0.060   0.004   TRP F 645 
 HIS   0.011   0.001   HIS F 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6693)
  covalent geometry    : angle       0.69217 ( 9062)
  hydrogen bonds       : bond        0.03762 (  148)
  hydrogen bonds       : angle       6.72363 (  321)

*********************** 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
  153 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  571 LYS cc_start: 0.8771 (mppt) cc_final: 0.8441 (mptt)
REVERT: A  687 LEU cc_start: 0.8403 (mt) cc_final: 0.7916 (mt)
REVERT: A  713 LEU cc_start: 0.8738 (tp) cc_final: 0.8273 (pp)
REVERT: F  510 MET cc_start: 0.6777 (pmm) cc_final: 0.6196 (pmm)
REVERT: F  513 LEU cc_start: 0.6859 (mt) cc_final: 0.6534 (mt)
REVERT: F  573 HIS cc_start: 0.7478 (m-70) cc_final: 0.7271 (m-70)
REVERT: F  581 MET cc_start: 0.8617 (tpp) cc_final: 0.8128 (tpp)
REVERT: F  646 TYR cc_start: 0.5767 (m-10) cc_final: 0.5526 (m-80)
REVERT: F  659 LEU cc_start: 0.3820 (tp) cc_final: 0.3277 (tp)
REVERT: F  666 PHE cc_start: 0.8994 (m-80) cc_final: 0.7814 (m-10)
REVERT: F  786 ASP cc_start: 0.3109 (p0) cc_final: 0.1579 (t70)
REVERT: F  800 MET cc_start: 0.2858 (tpt) cc_final: 0.2229 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0728
  time to fit residues: 14.9376
Evaluate side-chains
  117 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 409 ASN
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** 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 = 0.4258 r_free = 0.4258 target = 0.124642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.109254 restraints weight = 27405.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.110361 restraints weight = 18373.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.111202 restraints weight = 13677.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.111776 restraints weight = 11924.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.111938 restraints weight = 10512.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.7922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6693  Z= 0.130
  Angle     :  0.672  10.133   9062  Z= 0.334
  Chirality :  0.046   0.266   1084
  Planarity :  0.005   0.049   1137
  Dihedral  :  4.992  22.791    864
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.64 (0.29), residues: 807
  helix: -2.64 (0.28), residues: 254
  sheet: -2.52 (0.43), residues: 156
  loop : -0.56 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 719 
 TYR   0.015   0.002   TYR A 683 
 PHE   0.024   0.002   PHE F 500 
 TRP   0.064   0.004   TRP F 645 
 HIS   0.009   0.001   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6693)
  covalent geometry    : angle       0.67228 ( 9062)
  hydrogen bonds       : bond        0.03683 (  148)
  hydrogen bonds       : angle       6.59006 (  321)

*********************** 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
  149 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  687 LEU cc_start: 0.8498 (mt) cc_final: 0.8037 (mt)
REVERT: A  713 LEU cc_start: 0.8744 (tp) cc_final: 0.8140 (pp)
REVERT: A  780 LYS cc_start: 0.8605 (pttt) cc_final: 0.8129 (pttm)
REVERT: A  787 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5653 (pt0)
REVERT: F  510 MET cc_start: 0.6766 (pmm) cc_final: 0.6498 (pmm)
REVERT: F  513 LEU cc_start: 0.6871 (mt) cc_final: 0.6564 (mt)
REVERT: F  581 MET cc_start: 0.8610 (tpp) cc_final: 0.8087 (tpp)
REVERT: F  646 TYR cc_start: 0.6037 (m-10) cc_final: 0.5762 (m-80)
REVERT: F  666 PHE cc_start: 0.8980 (m-80) cc_final: 0.7726 (m-10)
REVERT: F  736 ILE cc_start: 0.7702 (mm) cc_final: 0.7495 (mm)
REVERT: F  786 ASP cc_start: 0.3201 (p0) cc_final: 0.1722 (t70)
REVERT: F  800 MET cc_start: 0.2875 (tpt) cc_final: 0.2237 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0705
  time to fit residues: 14.6530
Evaluate side-chains
  116 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0570
   chunk 73 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    0.4980
   chunk 79 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** 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 = 0.4265 r_free = 0.4265 target = 0.125408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.108252 restraints weight = 27723.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.110238 restraints weight = 19017.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.111705 restraints weight = 13890.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.112619 restraints weight = 10802.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.113493 restraints weight = 8939.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.8103

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= 0.117
  Angle     :  0.677  10.629   9062  Z= 0.332
  Chirality :  0.045   0.249   1084
  Planarity :  0.005   0.048   1137
  Dihedral  :  4.847  21.928    864
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.63 (0.29), residues: 807
  helix: -2.65 (0.28), residues: 254
  sheet: -2.51 (0.42), residues: 158
  loop : -0.53 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 804 
 TYR   0.015   0.002   TYR F 710 
 PHE   0.019   0.002   PHE F 667 
 TRP   0.085   0.006   TRP A 803 
 HIS   0.012   0.001   HIS F 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6693)
  covalent geometry    : angle       0.67721 ( 9062)
  hydrogen bonds       : bond        0.03658 (  148)
  hydrogen bonds       : angle       6.48785 (  321)

*********************** 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
  150 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  687 LEU cc_start: 0.8471 (mt) cc_final: 0.8040 (mt)
REVERT: A  780 LYS cc_start: 0.8524 (pttt) cc_final: 0.8141 (pttm)
REVERT: F  581 MET cc_start: 0.8594 (tpp) cc_final: 0.8030 (tpp)
REVERT: F  646 TYR cc_start: 0.6036 (m-10) cc_final: 0.5760 (m-80)
REVERT: F  666 PHE cc_start: 0.8975 (m-80) cc_final: 0.7787 (m-10)
REVERT: F  786 ASP cc_start: 0.3307 (p0) cc_final: 0.1974 (t70)
REVERT: F  800 MET cc_start: 0.2978 (tpt) cc_final: 0.2198 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0592
  time to fit residues: 12.4856
Evaluate side-chains
  115 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 20 optimal weight:    0.0870
   chunk 55 optimal weight:    0.0030
   chunk 61 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    0.4968

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

Flipped N/Q/H residues before XYZ refinement:
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** 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 = 0.4277 r_free = 0.4277 target = 0.126238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.109416 restraints weight = 27659.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.111327 restraints weight = 19355.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.112701 restraints weight = 14368.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.113743 restraints weight = 11359.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.114522 restraints weight = 9313.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.8218

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= 0.115
  Angle     :  0.680  12.888   9062  Z= 0.329
  Chirality :  0.045   0.269   1084
  Planarity :  0.004   0.048   1137
  Dihedral  :  4.756  20.946    864
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 17.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.13 %
    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 aren not related in a simple way.
  whole: -2.62 (0.29), residues: 807
  helix: -2.51 (0.29), residues: 259
  sheet: -2.47 (0.42), residues: 158
  loop : -0.61 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 719 
 TYR   0.010   0.001   TYR F 692 
 PHE   0.018   0.002   PHE F 666 
 TRP   0.080   0.004   TRP F 645 
 HIS   0.008   0.001   HIS F 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6693)
  covalent geometry    : angle       0.68043 ( 9062)
  hydrogen bonds       : bond        0.03638 (  148)
  hydrogen bonds       : angle       6.45907 (  321)

********************** 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
  151 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  495 LEU cc_start: 0.6799 (tp) cc_final: 0.6537 (tp)
REVERT: A  687 LEU cc_start: 0.8511 (mt) cc_final: 0.8130 (mt)
REVERT: A  780 LYS cc_start: 0.8496 (pttt) cc_final: 0.8266 (pttm)
REVERT: F  581 MET cc_start: 0.8613 (tpp) cc_final: 0.8034 (tpp)
REVERT: F  646 TYR cc_start: 0.6006 (m-10) cc_final: 0.5762 (m-80)
REVERT: F  666 PHE cc_start: 0.8815 (m-80) cc_final: 0.7639 (m-10)
REVERT: F  786 ASP cc_start: 0.3320 (p0) cc_final: 0.2030 (t70)
REVERT: F  800 MET cc_start: 0.3132 (tpt) cc_final: 0.2397 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0735
  time to fit residues: 15.5074
Evaluate side-chains
  119 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 592 ASN
A 660 ASN
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 622 ASN ** 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 = 0.4225 r_free = 0.4225 target = 0.123041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.106667 restraints weight = 28362.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.108517 restraints weight = 19624.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.109875 restraints weight = 14616.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.110864 restraints weight = 11484.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.111506 restraints weight = 9470.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6817
moved from start:          0.8497

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= 0.148
  Angle     :  0.706  11.675   9062  Z= 0.346
  Chirality :  0.045   0.274   1084
  Planarity :  0.005   0.052   1137
  Dihedral  :  4.883  20.398    864
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 20.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.92 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.72 (0.29), residues: 807
  helix: -2.61 (0.28), residues: 260
  sheet: -2.54 (0.41), residues: 161
  loop : -0.62 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 533 
 TYR   0.021   0.002   TYR F 710 
 PHE   0.014   0.002   PHE F 764 
 TRP   0.071   0.004   TRP F 645 
 HIS   0.010   0.001   HIS F 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6693)
  covalent geometry    : angle       0.70584 ( 9062)
  hydrogen bonds       : bond        0.03692 (  148)
  hydrogen bonds       : angle       6.53718 (  321)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1344.04 seconds
wall clock time: 23 minutes 55.72 seconds (1435.72 seconds total)