Starting phenix.real_space_refine
on Fri Aug 22 17:34:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jhu_36294/08_2025/8jhu_36294.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jhu_36294/08_2025/8jhu_36294.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jhu_36294/08_2025/8jhu_36294.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jhu_36294/08_2025/8jhu_36294.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jhu_36294/08_2025/8jhu_36294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jhu_36294/08_2025/8jhu_36294.map"
  }
  resolution = 3.1
  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=   0.005 sd=   0.118
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      16      5.16       5
     C    4159      2.51       5
     N    1117      2.21       5
     O    1262      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  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: 6554
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 811, 6554
          Classifications: {'peptide': 811}
          Link IDs: {'PCIS': 4, 'PTRANS': 32, 'TRANS': 774}
          Chain breaks: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLU A 709 " occ=0.61
      ... (7 atoms not shown)
      pdb=" OE2 GLU A 709 " occ=0.61
  Time building chain proxies: 1.39, per 1000 atoms: 0.21
  Number of scatterers: 6554
  At special positions: 0
  Unit cell: (85.244, 114.784, 78.492, 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      16     16.00
     O    1262      8.00
     N    1117      7.00
     C    4159      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: 0.33
  Conformation dependent library (CDL) restraints added in 299.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1550

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 3 sheets defined
      53.5% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 34
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 94 through 103
    Processing helix  chain 'A' and resid 136 through 166
      removed outlier: 4.937A  pdb=" N   ALA A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   GLU A 164 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER A 166 " --> pdb=" O   ASN A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 183
      removed outlier: 3.642A  pdb=" N   ALA A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 204
      removed outlier: 3.626A  pdb=" N   ILE A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 225
      removed outlier: 3.516A  pdb=" N   GLN A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 243
    Processing helix  chain 'A' and resid 267 through 271
    Processing helix  chain 'A' and resid 272 through 294
      removed outlier: 3.664A  pdb=" N   ILE A 293 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 361
      removed outlier: 3.730A  pdb=" N   VAL A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 369
    Processing helix  chain 'A' and resid 373 through 388
    Processing helix  chain 'A' and resid 392 through 397
    Processing helix  chain 'A' and resid 398 through 400
      No H-bonds generated for 'chain 'A' and resid 398 through 400'
    Processing helix  chain 'A' and resid 410 through 424
    Processing helix  chain 'A' and resid 427 through 439
      removed outlier: 4.201A  pdb=" N   VAL A 431 " --> pdb=" O   ILE A 427 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE A 432 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 472
      removed outlier: 3.541A  pdb=" N   ALA A 472 " --> pdb=" O   LYS A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
      removed outlier: 4.570A  pdb=" N   THR A 488 " --> pdb=" O   GLN A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 503
      removed outlier: 3.902A  pdb=" N   GLN A 493 " --> pdb=" O   ARG A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 524
    Processing helix  chain 'A' and resid 527 through 531
    Processing helix  chain 'A' and resid 533 through 544
      removed outlier: 3.503A  pdb=" N   ALA A 538 " --> pdb=" O   PRO A 534 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LYS A 539 " --> pdb=" O   THR A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 585
      removed outlier: 4.111A  pdb=" N   ALA A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 615
    Processing helix  chain 'A' and resid 615 through 620
    Processing helix  chain 'A' and resid 637 through 650
      removed outlier: 3.733A  pdb=" N   GLU A 647 " --> pdb=" O   GLN A 643 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A 649 " --> pdb=" O   VAL A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 659
      removed outlier: 3.526A  pdb=" N   LYS A 655 " --> pdb=" O   LYS A 651 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   TYR A 657 " --> pdb=" O   ALA A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 683
      removed outlier: 3.881A  pdb=" N   TRP A 676 " --> pdb=" O   ARG A 672 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS A 677 " --> pdb=" O   ARG A 673 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   ASN A 678 " --> pdb=" O   ASP A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 716
    Processing helix  chain 'A' and resid 732 through 737
      removed outlier: 3.599A  pdb=" N   ILE A 736 " --> pdb=" O   GLY A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 776
    Processing helix  chain 'A' and resid 777 through 786
    Processing helix  chain 'A' and resid 805 through 809
      removed outlier: 3.707A  pdb=" N   GLN A 809 " --> pdb=" O   TYR A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 827
    Processing helix  chain 'A' and resid 839 through 854
    Processing helix  chain 'A' and resid 856 through 868
    Processing helix  chain 'A' and resid 870 through 874
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42
      removed outlier: 6.790A  pdb=" N   ILE A   4 " --> pdb=" O   LYS A  40 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   LEU A  42 " --> pdb=" O   ILE A   4 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   LEU A   6 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LYS A   3 " --> pdb=" O   HIS A 447 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ASP A 449 " --> pdb=" O   LYS A   3 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   TYR A   5 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   HIS A 451 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   LEU A   7 " --> pdb=" O   HIS A 451 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   THR A 446 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ASN A 477 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LEU A 448 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   THR A 479 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ILE A 450 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59
      removed outlier: 6.698A  pdb=" N   SER A  82 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   VAL A 113 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   TYR A  84 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 699 through 703
      removed outlier: 3.772A  pdb=" N   GLY A 633 " --> pdb=" O   TYR A 702 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ILE A 590 " --> pdb=" O   LYS A 630 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   ALA A 632 " --> pdb=" O   ILE A 590 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   SER A 592 " --> pdb=" O   ALA A 632 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LEU A 591 " --> pdb=" O   CYS A 721 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL A 720 " --> pdb=" O   TYR A 745 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   VAL A 744 " --> pdb=" O   ASP A 767 " (cutoff:3.500A)

    279 hydrogen bonds defined for protein.
    798 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1363
        1.33 -     1.45: 1417
        1.45 -     1.57: 3872
        1.57 -     1.69: 1
        1.69 -     1.81: 24
  Bond restraints: 6677
  Sorted by residual:
  bond pdb=" CE1 HIS A 661 "
       pdb=" NE2 HIS A 661 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.67e+01
  bond pdb=" N   VAL A 693 "
       pdb=" CA  VAL A 693 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.14e-02 7.69e+03 8.09e+00
  bond pdb=" CB  PRO A 815 "
       pdb=" CG  PRO A 815 "
    ideal  model  delta    sigma   weight residual
    1.492  1.626 -0.134 5.00e-02 4.00e+02 7.24e+00
  bond pdb=" CA  ALA A 692 "
       pdb=" CB  ALA A 692 "
    ideal  model  delta    sigma   weight residual
    1.535  1.493  0.042 1.71e-02 3.42e+03 6.02e+00
  bond pdb=" N   LYS A 659 "
       pdb=" CA  LYS A 659 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.028 1.29e-02 6.01e+03 4.84e+00
  ... (remaining 6672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 8900
        2.44 -     4.87: 93
        4.87 -     7.31: 6
        7.31 -     9.74: 2
        9.74 -    12.18: 3
  Bond angle restraints: 9004
  Sorted by residual:
  angle pdb=" CA  PRO A 815 "
        pdb=" N   PRO A 815 "
        pdb=" CD  PRO A 815 "
      ideal   model   delta    sigma   weight residual
     112.00  101.70   10.30 1.40e+00 5.10e-01 5.41e+01
  angle pdb=" N   GLU A 689 "
        pdb=" CA  GLU A 689 "
        pdb=" C   GLU A 689 "
      ideal   model   delta    sigma   weight residual
     110.80   98.62   12.18 2.13e+00 2.20e-01 3.27e+01
  angle pdb=" N   ASN A 695 "
        pdb=" CA  ASN A 695 "
        pdb=" C   ASN A 695 "
      ideal   model   delta    sigma   weight residual
     110.28  102.31    7.97 1.48e+00 4.57e-01 2.90e+01
  angle pdb=" N   SER A 670 "
        pdb=" CA  SER A 670 "
        pdb=" C   SER A 670 "
      ideal   model   delta    sigma   weight residual
     114.75  107.98    6.77 1.26e+00 6.30e-01 2.89e+01
  angle pdb=" N   PRO A 662 "
        pdb=" CA  PRO A 662 "
        pdb=" C   PRO A 662 "
      ideal   model   delta    sigma   weight residual
     110.40  116.85   -6.45 1.61e+00 3.86e-01 1.61e+01
  ... (remaining 8999 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3636
       17.96 -    35.91: 386
       35.91 -    53.87: 87
       53.87 -    71.83: 18
       71.83 -    89.79: 6
  Dihedral angle restraints: 4133
    sinusoidal: 1738
      harmonic: 2395
  Sorted by residual:
  dihedral pdb=" CA  ALA A 685 "
           pdb=" C   ALA A 685 "
           pdb=" N   LYS A 686 "
           pdb=" CA  LYS A 686 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.68   18.32     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  ASP A 674 "
           pdb=" C   ASP A 674 "
           pdb=" N   TYR A 675 "
           pdb=" CA  TYR A 675 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.92   18.08     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CB  GLU A  62 "
           pdb=" CG  GLU A  62 "
           pdb=" CD  GLU A  62 "
           pdb=" OE1 GLU A  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.79   89.79     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 4130 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 806
       0.049 -    0.098: 151
       0.098 -    0.147: 31
       0.147 -    0.197: 3
       0.197 -    0.246: 2
  Chirality restraints: 993
  Sorted by residual:
  chirality pdb=" CA  LEU A 694 "
            pdb=" N   LEU A 694 "
            pdb=" C   LEU A 694 "
            pdb=" CB  LEU A 694 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  PRO A 662 "
            pdb=" N   PRO A 662 "
            pdb=" C   PRO A 662 "
            pdb=" CB  PRO A 662 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  TYR A 663 "
            pdb=" N   TYR A 663 "
            pdb=" C   TYR A 663 "
            pdb=" CB  TYR A 663 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.87e-01
  ... (remaining 990 not shown)

  Planarity restraints: 1165
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 688 "   -0.028 2.00e-02 2.50e+03   5.71e-02 3.26e+01
        pdb=" C   LYS A 688 "    0.099 2.00e-02 2.50e+03
        pdb=" O   LYS A 688 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   GLU A 689 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 814 "    0.088 5.00e-02 4.00e+02   1.26e-01 2.55e+01
        pdb=" N   PRO A 815 "   -0.218 5.00e-02 4.00e+02
        pdb=" CA  PRO A 815 "    0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO A 815 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 695 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.23e+00
        pdb=" C   ASN A 695 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ASN A 695 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ASN A 696 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1162 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 482
        2.74 -     3.28: 6620
        3.28 -     3.82: 11187
        3.82 -     4.36: 13620
        4.36 -     4.90: 23081
  Nonbonded interactions: 54990
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  12 "
            pdb=" OG1 THR A  17 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER A  67 "
            pdb=" OD2 ASP A 425 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OG  SER A  59 "
            pdb=" O   PRO A  61 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   THR A 108 "
            pdb=" OG1 THR A 108 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OH  TYR A 745 "
            pdb=" OG  SER A 821 "
     model   vdw
     2.282 3.040
  ... (remaining 54985 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.61 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.134   6677  Z= 0.165
  Angle     :  0.589  12.178   9004  Z= 0.344
  Chirality :  0.042   0.246    993
  Planarity :  0.005   0.126   1165
  Dihedral  : 15.641  89.785   2583
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.35 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 18.52 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.27 (0.31), residues: 803
  helix:  1.40 (0.28), residues: 381
  sheet: -1.28 (0.56), residues: 81
  loop : -1.77 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 681 
 TYR   0.009   0.001   TYR A 495 
 PHE   0.008   0.001   PHE A 219 
 TRP   0.008   0.001   TRP A  41 
 HIS   0.005   0.001   HIS A 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6677)
  covalent geometry    : angle       0.58866 ( 9004)
  hydrogen bonds       : bond        0.18226 (  279)
  hydrogen bonds       : angle       5.71093 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.238 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.0822
  time to fit residues: 8.8460
Evaluate side-chains
  78 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  655 LYS
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  695 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0020
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0170
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.9030

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

Flipped N/Q/H residues before XYZ refinement:
A  97 GLN
A 504 ASN
** A 510 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 = 0.3698 r_free = 0.3698 target = 0.151329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.122031 restraints weight = 7414.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.78
r_work: 0.3391 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6677  Z= 0.152
  Angle     :  0.515   7.027   9004  Z= 0.270
  Chirality :  0.041   0.128    993
  Planarity :  0.005   0.072   1165
  Dihedral  :  4.909  57.657    886
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.87 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.16 (0.31), residues: 803
  helix:  1.43 (0.28), residues: 391
  sheet: -1.50 (0.57), residues: 77
  loop : -1.65 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 681 
 TYR   0.011   0.001   TYR A 491 
 PHE   0.013   0.001   PHE A 756 
 TRP   0.011   0.002   TRP A  41 
 HIS   0.002   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6677)
  covalent geometry    : angle       0.51509 ( 9004)
  hydrogen bonds       : bond        0.03656 (  279)
  hydrogen bonds       : angle       4.13326 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LYS cc_start: 0.7937 (tppp) cc_final: 0.7405 (tptt)
REVERT: A  614 ASP cc_start: 0.7818 (m-30) cc_final: 0.7456 (m-30)
REVERT: A  681 ARG cc_start: 0.7413 (ttp80) cc_final: 0.7179 (ttp80)
  outliers start: 13
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0595
  time to fit residues: 7.0788
Evaluate side-chains
  78 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  504 ASN
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  754 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 29 optimal weight:    0.0980
   chunk 3 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 510 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.144823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.115392 restraints weight = 7304.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.74
r_work: 0.3310 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6677  Z= 0.174
  Angle     :  0.526   7.136   9004  Z= 0.275
  Chirality :  0.041   0.131    993
  Planarity :  0.005   0.057   1165
  Dihedral  :  4.519  44.405    878
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.15 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.33 (0.30), residues: 803
  helix:  1.36 (0.27), residues: 389
  sheet: -1.92 (0.57), residues: 77
  loop : -1.73 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 681 
 TYR   0.012   0.001   TYR A 177 
 PHE   0.016   0.002   PHE A 219 
 TRP   0.013   0.002   TRP A  41 
 HIS   0.002   0.001   HIS A 872 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6677)
  covalent geometry    : angle       0.52606 ( 9004)
  hydrogen bonds       : bond        0.03699 (  279)
  hydrogen bonds       : angle       4.14133 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.8011 (t0) cc_final: 0.7504 (t0)
REVERT: A  372 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7645 (mm-30)
REVERT: A  404 TYR cc_start: 0.8794 (m-80) cc_final: 0.8365 (m-80)
REVERT: A  498 ASP cc_start: 0.8289 (m-30) cc_final: 0.8064 (m-30)
REVERT: A  597 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7941 (mtm110)
REVERT: A  681 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7205 (ttp80)
REVERT: A  711 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6065 (tp)
REVERT: A  839 ASP cc_start: 0.5673 (OUTLIER) cc_final: 0.4536 (m-30)
  outliers start: 18
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0588
  time to fit residues: 7.7569
Evaluate side-chains
  81 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  751 VAL
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain A residue  839 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 39 optimal weight:    0.1980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.144948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.114858 restraints weight = 7444.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.79
r_work: 0.3323 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6677  Z= 0.133
  Angle     :  0.492   8.539   9004  Z= 0.256
  Chirality :  0.040   0.132    993
  Planarity :  0.004   0.051   1165
  Dihedral  :  4.108  18.851    876
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.15 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.25 (0.30), residues: 803
  helix:  1.52 (0.27), residues: 388
  sheet: -2.08 (0.55), residues: 77
  loop : -1.75 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 648 
 TYR   0.010   0.001   TYR A 259 
 PHE   0.013   0.001   PHE A 756 
 TRP   0.011   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6677)
  covalent geometry    : angle       0.49167 ( 9004)
  hydrogen bonds       : bond        0.03181 (  279)
  hydrogen bonds       : angle       4.01824 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.8019 (t0) cc_final: 0.7470 (t0)
REVERT: A  372 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7664 (mm-30)
REVERT: A  398 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8065 (mm-30)
REVERT: A  433 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7148 (mm-30)
REVERT: A  498 ASP cc_start: 0.8259 (m-30) cc_final: 0.8028 (m-30)
REVERT: A  597 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8078 (mtm110)
REVERT: A  681 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7275 (ttp80)
REVERT: A  711 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6091 (tp)
REVERT: A  839 ASP cc_start: 0.5526 (OUTLIER) cc_final: 0.4436 (m-30)
  outliers start: 17
  outliers final: 6
  residues processed: 89
  average time/residue: 0.0695
  time to fit residues: 8.5663
Evaluate side-chains
  79 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  620 HIS
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain A residue  839 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.139223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.108624 restraints weight = 7502.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.85
r_work: 0.3298 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6677  Z= 0.136
  Angle     :  0.492   8.854   9004  Z= 0.255
  Chirality :  0.040   0.133    993
  Planarity :  0.004   0.052   1165
  Dihedral  :  4.131  17.960    876
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.83 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.17 (0.30), residues: 803
  helix:  1.60 (0.27), residues: 388
  sheet: -2.16 (0.55), residues: 77
  loop : -1.71 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 648 
 TYR   0.009   0.001   TYR A 259 
 PHE   0.013   0.001   PHE A 219 
 TRP   0.011   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6677)
  covalent geometry    : angle       0.49232 ( 9004)
  hydrogen bonds       : bond        0.03139 (  279)
  hydrogen bonds       : angle       3.98869 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TRP cc_start: 0.7239 (OUTLIER) cc_final: 0.7025 (p-90)
REVERT: A  356 ASN cc_start: 0.8011 (t0) cc_final: 0.7431 (t0)
REVERT: A  372 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7698 (mm-30)
REVERT: A  404 TYR cc_start: 0.8775 (m-80) cc_final: 0.8361 (m-80)
REVERT: A  433 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7198 (mm-30)
REVERT: A  498 ASP cc_start: 0.8286 (m-30) cc_final: 0.8042 (m-30)
REVERT: A  681 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7177 (ttp80)
REVERT: A  711 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6152 (tp)
REVERT: A  839 ASP cc_start: 0.5740 (OUTLIER) cc_final: 0.4646 (m-30)
  outliers start: 17
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0622
  time to fit residues: 8.1449
Evaluate side-chains
  85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TRP
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  636 GLN
Chi-restraints excluded: chain A residue  649 PHE
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain A residue  839 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 78 optimal weight:    0.3980
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0370
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    0.2980
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.146562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.116584 restraints weight = 7387.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.78
r_work: 0.3357 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6677  Z= 0.100
  Angle     :  0.470   9.928   9004  Z= 0.241
  Chirality :  0.039   0.134    993
  Planarity :  0.004   0.053   1165
  Dihedral  :  3.953  17.730    876
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.34 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.02 (0.31), residues: 803
  helix:  1.80 (0.28), residues: 388
  sheet: -2.09 (0.55), residues: 77
  loop : -1.66 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 825 
 TYR   0.011   0.001   TYR A 177 
 PHE   0.010   0.001   PHE A 756 
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6677)
  covalent geometry    : angle       0.47031 ( 9004)
  hydrogen bonds       : bond        0.02835 (  279)
  hydrogen bonds       : angle       3.89309 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7902 (t0) cc_final: 0.7251 (t0)
REVERT: A  372 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7712 (mm-30)
REVERT: A  381 GLU cc_start: 0.8161 (tt0) cc_final: 0.7927 (mt-10)
REVERT: A  433 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7101 (mm-30)
REVERT: A  681 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7223 (ttp80)
REVERT: A  839 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.4611 (m-30)
  outliers start: 14
  outliers final: 6
  residues processed: 91
  average time/residue: 0.0613
  time to fit residues: 7.9852
Evaluate side-chains
  78 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  636 GLN
Chi-restraints excluded: chain A residue  649 PHE
Chi-restraints excluded: chain A residue  839 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 75 optimal weight:    0.0870
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 678 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.139366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.108123 restraints weight = 7404.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.89
r_work: 0.3188 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6677  Z= 0.129
  Angle     :  0.496  10.220   9004  Z= 0.255
  Chirality :  0.040   0.132    993
  Planarity :  0.004   0.052   1165
  Dihedral  :  4.050  17.886    876
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 20.16 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.00 (0.31), residues: 803
  helix:  1.78 (0.27), residues: 389
  sheet: -2.18 (0.55), residues: 77
  loop : -1.65 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 648 
 TYR   0.018   0.001   TYR A 177 
 PHE   0.013   0.001   PHE A 219 
 TRP   0.010   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6677)
  covalent geometry    : angle       0.49584 ( 9004)
  hydrogen bonds       : bond        0.03032 (  279)
  hydrogen bonds       : angle       3.94487 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7934 (t0) cc_final: 0.7269 (t0)
REVERT: A  372 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7685 (mm-30)
REVERT: A  381 GLU cc_start: 0.8173 (tt0) cc_final: 0.7922 (mt-10)
REVERT: A  404 TYR cc_start: 0.8768 (m-80) cc_final: 0.8350 (m-80)
REVERT: A  433 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7164 (mm-30)
REVERT: A  666 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6443 (mpp80)
REVERT: A  681 ARG cc_start: 0.7479 (ttp80) cc_final: 0.7211 (ttp80)
REVERT: A  711 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6027 (tp)
REVERT: A  839 ASP cc_start: 0.5429 (OUTLIER) cc_final: 0.4287 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 85
  average time/residue: 0.0585
  time to fit residues: 7.1041
Evaluate side-chains
  82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  636 GLN
Chi-restraints excluded: chain A residue  649 PHE
Chi-restraints excluded: chain A residue  666 ARG
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  839 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 79 optimal weight:    0.0670
   chunk 28 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0070
   chunk 12 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0770
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.2494

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.146548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.115852 restraints weight = 7420.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.85
r_work: 0.3390 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6677  Z= 0.093
  Angle     :  0.459   9.490   9004  Z= 0.236
  Chirality :  0.039   0.133    993
  Planarity :  0.004   0.053   1165
  Dihedral  :  3.815  17.287    876
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 20.30 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.21 (0.31), residues: 803
  helix:  1.98 (0.28), residues: 389
  sheet: -2.07 (0.56), residues: 76
  loop : -1.58 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 729 
 TYR   0.017   0.001   TYR A 177 
 PHE   0.009   0.001   PHE A 756 
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 6677)
  covalent geometry    : angle       0.45873 ( 9004)
  hydrogen bonds       : bond        0.02638 (  279)
  hydrogen bonds       : angle       3.81042 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7913 (t0) cc_final: 0.7267 (t0)
REVERT: A  381 GLU cc_start: 0.8156 (tt0) cc_final: 0.7932 (mt-10)
REVERT: A  711 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6175 (tp)
REVERT: A  839 ASP cc_start: 0.5167 (OUTLIER) cc_final: 0.4437 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0694
  time to fit residues: 8.3240
Evaluate side-chains
  81 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  636 GLN
Chi-restraints excluded: chain A residue  649 PHE
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  839 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.136041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.105685 restraints weight = 7549.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.86
r_work: 0.3309 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6677  Z= 0.149
  Angle     :  0.521  10.942   9004  Z= 0.268
  Chirality :  0.041   0.129    993
  Planarity :  0.004   0.050   1165
  Dihedral  :  4.108  18.092    876
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 20.44 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.02 (0.31), residues: 803
  helix:  1.82 (0.27), residues: 388
  sheet: -2.19 (0.55), residues: 77
  loop : -1.66 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 648 
 TYR   0.013   0.001   TYR A 177 
 PHE   0.028   0.002   PHE A  11 
 TRP   0.010   0.001   TRP A  41 
 HIS   0.002   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6677)
  covalent geometry    : angle       0.52117 ( 9004)
  hydrogen bonds       : bond        0.03159 (  279)
  hydrogen bonds       : angle       3.98238 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7972 (t0) cc_final: 0.7364 (t0)
REVERT: A  404 TYR cc_start: 0.8834 (m-80) cc_final: 0.8376 (m-80)
REVERT: A  433 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7314 (mm-30)
REVERT: A  711 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6189 (tp)
REVERT: A  839 ASP cc_start: 0.5606 (OUTLIER) cc_final: 0.4583 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 86
  average time/residue: 0.0545
  time to fit residues: 6.8519
Evaluate side-chains
  83 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  636 GLN
Chi-restraints excluded: chain A residue  649 PHE
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  839 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0980
   chunk 74 optimal weight:    0.1980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
** A 510 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 = 0.3512 r_free = 0.3512 target = 0.138282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.107973 restraints weight = 7435.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.85
r_work: 0.3337 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6677  Z= 0.112
  Angle     :  0.490  10.459   9004  Z= 0.252
  Chirality :  0.040   0.132    993
  Planarity :  0.004   0.049   1165
  Dihedral  :  4.001  16.747    876
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 20.58 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.10 (0.31), residues: 803
  helix:  1.88 (0.27), residues: 390
  sheet: -2.17 (0.55), residues: 77
  loop : -1.63 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 681 
 TYR   0.012   0.001   TYR A 177 
 PHE   0.024   0.001   PHE A  11 
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6677)
  covalent geometry    : angle       0.49002 ( 9004)
  hydrogen bonds       : bond        0.02894 (  279)
  hydrogen bonds       : angle       3.93171 (  798)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7957 (t0) cc_final: 0.7290 (t0)
REVERT: A  381 GLU cc_start: 0.8177 (tt0) cc_final: 0.7937 (mt-10)
REVERT: A  711 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6209 (tp)
REVERT: A  839 ASP cc_start: 0.5575 (OUTLIER) cc_final: 0.4364 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0609
  time to fit residues: 7.2295
Evaluate side-chains
  81 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  593 PHE
Chi-restraints excluded: chain A residue  636 GLN
Chi-restraints excluded: chain A residue  649 PHE
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  839 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 78 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
** A 510 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 = 0.3472 r_free = 0.3472 target = 0.134745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.104625 restraints weight = 7467.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.83
r_work: 0.3312 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6677  Z= 0.162
  Angle     :  0.534  10.391   9004  Z= 0.276
  Chirality :  0.042   0.163    993
  Planarity :  0.004   0.048   1165
  Dihedral  :  4.247  18.480    876
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 20.44 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.06 (0.30), residues: 803
  helix:  1.73 (0.27), residues: 391
  sheet: -2.35 (0.54), residues: 77
  loop : -1.66 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 681 
 TYR   0.013   0.001   TYR A 177 
 PHE   0.025   0.002   PHE A  11 
 TRP   0.016   0.002   TRP A  41 
 HIS   0.002   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 6677)
  covalent geometry    : angle       0.53369 ( 9004)
  hydrogen bonds       : bond        0.03251 (  279)
  hydrogen bonds       : angle       4.05887 (  798)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1564.84 seconds
wall clock time: 27 minutes 34.86 seconds (1654.86 seconds total)