Starting phenix.real_space_refine
on Sat May 10 15:15:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jhu_36294/05_2025/8jhu_36294.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jhu_36294/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jhu_36294/05_2025/8jhu_36294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jhu_36294/05_2025/8jhu_36294.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jhu_36294/05_2025/8jhu_36294.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jhu_36294/05_2025/8jhu_36294.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.10, per 1000 atoms: 0.63
  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: 1.55
  Conformation dependent library (CDL) restraints added in 861.6 milliseconds
  

  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: 0.73
  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: 1.78

  Time building geometry restraints manager: 1.85 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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.860
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.700
-------------------------------------------------------------------------------
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 : 10.88
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.008   0.001   TRP A  41 
 HIS   0.005   0.001   HIS A 661 
 PHE   0.008   0.001   PHE A 219 
 TYR   0.009   0.001   TYR A 495 
 ARG   0.006   0.000   ARG A 681 

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

*********************** 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  : 0.685 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1897
  time to fit residues: 20.4476
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  : 0.684 
-------------------------------------------------------------------------------
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 68 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 34 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.156682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.128034 restraints weight = 7285.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.74
r_work: 0.3438 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6677  Z= 0.132
  Angle     :  0.492   7.120   9004  Z= 0.258
  Chirality :  0.040   0.129    993
  Planarity :  0.005   0.072   1165
  Dihedral  :  4.779  55.302    886
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.60 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.31), residues: 803
  helix:  1.51 (0.28), residues: 392
  sheet: -1.49 (0.56), residues: 81
  loop : -1.67 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  41 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.011   0.001   PHE A 756 
 TYR   0.010   0.001   TYR A 491 
 ARG   0.004   0.001   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03696 (  279)
  hydrogen bonds       : angle       4.10467 (  798)
  covalent geometry    : bond        0.00313 ( 6677)
  covalent geometry    : angle       0.49228 ( 9004)

*********************** 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
  85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 LYS cc_start: 0.7899 (tppp) cc_final: 0.7232 (tppt)
REVERT: A  614 ASP cc_start: 0.7829 (m-30) cc_final: 0.7442 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 82
  average time/residue: 0.1761
  time to fit residues: 20.0508
Evaluate side-chains
  75 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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  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 21 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   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 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 = 0.3694 r_free = 0.3694 target = 0.151010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.121586 restraints weight = 7373.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.78
r_work: 0.3383 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1505

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= 0.130
  Angle     :  0.477   6.963   9004  Z= 0.250
  Chirality :  0.040   0.131    993
  Planarity :  0.004   0.056   1165
  Dihedral  :  3.864  19.049    876
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.70 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.31), residues: 803
  helix:  1.60 (0.27), residues: 387
  sheet: -1.63 (0.58), residues: 77
  loop : -1.76 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 416 
 PHE   0.011   0.001   PHE A 219 
 TYR   0.009   0.001   TYR A 259 
 ARG   0.004   0.000   ARG A 648 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03281 (  279)
  hydrogen bonds       : angle       3.96849 (  798)
  covalent geometry    : bond        0.00313 ( 6677)
  covalent geometry    : angle       0.47733 ( 9004)

*********************** 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
  89 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.8037 (t0) cc_final: 0.7542 (t0)
REVERT: A  372 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7684 (mm-30)
REVERT: A  597 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.7814 (mtm-85)
REVERT: A  607 LYS cc_start: 0.7948 (tppp) cc_final: 0.7429 (tptt)
REVERT: A  681 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7138 (ttp80)
REVERT: A  711 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6061 (tp)
REVERT: A  839 ASP cc_start: 0.5469 (OUTLIER) cc_final: 0.4491 (m-30)
  outliers start: 11
  outliers final: 4
  residues processed: 84
  average time/residue: 0.1625
  time to fit residues: 19.2687
Evaluate side-chains
  81 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
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  593 PHE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0060
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.149681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.120249 restraints weight = 7393.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.75
r_work: 0.3374 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6677  Z= 0.114
  Angle     :  0.463   7.617   9004  Z= 0.240
  Chirality :  0.039   0.133    993
  Planarity :  0.004   0.049   1165
  Dihedral  :  3.854  18.605    876
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.83 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.31), residues: 803
  helix:  1.69 (0.27), residues: 389
  sheet: -1.76 (0.57), residues: 77
  loop : -1.68 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 
 PHE   0.011   0.001   PHE A 756 
 TYR   0.010   0.001   TYR A 177 
 ARG   0.002   0.000   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02959 (  279)
  hydrogen bonds       : angle       3.89364 (  798)
  covalent geometry    : bond        0.00273 ( 6677)
  covalent geometry    : angle       0.46290 ( 9004)

*********************** 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
  93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.8030 (t0) cc_final: 0.7419 (t0)
REVERT: A  372 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7652 (mm-30)
REVERT: A  381 GLU cc_start: 0.8179 (tt0) cc_final: 0.7972 (mt-10)
REVERT: A  597 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7879 (mtm110)
REVERT: A  607 LYS cc_start: 0.7902 (tppp) cc_final: 0.7378 (tptt)
REVERT: A  681 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7147 (ttp80)
REVERT: A  711 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6007 (tp)
REVERT: A  839 ASP cc_start: 0.5457 (OUTLIER) cc_final: 0.4461 (m-30)
  outliers start: 14
  outliers final: 6
  residues processed: 90
  average time/residue: 0.1754
  time to fit residues: 21.8740
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  : 0.694 
-------------------------------------------------------------------------------
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  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 21 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.147122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.117227 restraints weight = 7407.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.79
r_work: 0.3297 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1938

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= 0.124
  Angle     :  0.476   8.750   9004  Z= 0.247
  Chirality :  0.040   0.133    993
  Planarity :  0.004   0.050   1165
  Dihedral  :  3.956  17.939    876
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.31), residues: 803
  helix:  1.72 (0.27), residues: 389
  sheet: -1.90 (0.56), residues: 77
  loop : -1.67 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 
 PHE   0.012   0.001   PHE A 219 
 TYR   0.009   0.001   TYR A 491 
 ARG   0.002   0.000   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02978 (  279)
  hydrogen bonds       : angle       3.91268 (  798)
  covalent geometry    : bond        0.00301 ( 6677)
  covalent geometry    : angle       0.47649 ( 9004)

*********************** 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
  94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.8003 (t0) cc_final: 0.7383 (t0)
REVERT: A  372 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7683 (mm-30)
REVERT: A  381 GLU cc_start: 0.8165 (tt0) cc_final: 0.7930 (mt-10)
REVERT: A  398 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8041 (mm-30)
REVERT: A  607 LYS cc_start: 0.7862 (tppp) cc_final: 0.7358 (tptt)
REVERT: A  681 ARG cc_start: 0.7440 (ttp80) cc_final: 0.7190 (ttp80)
REVERT: A  711 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6052 (tp)
REVERT: A  839 ASP cc_start: 0.5490 (OUTLIER) cc_final: 0.4390 (m-30)
  outliers start: 14
  outliers final: 7
  residues processed: 90
  average time/residue: 0.1638
  time to fit residues: 21.0218
Evaluate side-chains
  83 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
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  636 GLN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.152184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.124003 restraints weight = 7250.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.68
r_work: 0.3259 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2141

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   9.520   9004  Z= 0.255
  Chirality :  0.040   0.134    993
  Planarity :  0.004   0.051   1165
  Dihedral  :  4.023  17.732    876
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.52 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.31), residues: 803
  helix:  1.73 (0.27), residues: 389
  sheet: -2.04 (0.55), residues: 77
  loop : -1.69 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  41 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.013   0.001   PHE A 219 
 TYR   0.009   0.001   TYR A 491 
 ARG   0.002   0.000   ARG A 648 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03046 (  279)
  hydrogen bonds       : angle       3.97713 (  798)
  covalent geometry    : bond        0.00330 ( 6677)
  covalent geometry    : angle       0.49180 ( 9004)

*********************** 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: 15
    poor density    : 79
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.8006 (t0) cc_final: 0.7436 (t0)
REVERT: A  372 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7660 (mm-30)
REVERT: A  404 TYR cc_start: 0.8777 (m-80) cc_final: 0.8339 (m-80)
REVERT: A  433 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7134 (mm-30)
REVERT: A  681 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7253 (ttp80)
REVERT: A  711 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6092 (tp)
REVERT: A  839 ASP cc_start: 0.5560 (OUTLIER) cc_final: 0.4393 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 91
  average time/residue: 0.1469
  time to fit residues: 19.5048
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  : 0.692 
-------------------------------------------------------------------------------
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  504 ASN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 38 optimal weight:    0.4980
   chunk 53 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0050
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.156897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.129122 restraints weight = 7185.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 1.66
r_work: 0.3351 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3217
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2116

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= 0.103
  Angle     :  0.474  10.511   9004  Z= 0.242
  Chirality :  0.039   0.133    993
  Planarity :  0.004   0.052   1165
  Dihedral  :  3.920  17.512    876
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.07 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.31), residues: 803
  helix:  1.84 (0.27), residues: 389
  sheet: -1.99 (0.56), residues: 77
  loop : -1.64 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 661 
 PHE   0.011   0.001   PHE A 756 
 TYR   0.008   0.001   TYR A 259 
 ARG   0.004   0.000   ARG A 648 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02810 (  279)
  hydrogen bonds       : angle       3.88300 (  798)
  covalent geometry    : bond        0.00241 ( 6677)
  covalent geometry    : angle       0.47427 ( 9004)

*********************** 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
  91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7942 (t0) cc_final: 0.7299 (t0)
REVERT: A  372 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7715 (mm-30)
REVERT: A  381 GLU cc_start: 0.8140 (tt0) cc_final: 0.7900 (mt-10)
REVERT: A  433 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7084 (mm-30)
REVERT: A  711 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6056 (tp)
REVERT: A  839 ASP cc_start: 0.5422 (OUTLIER) cc_final: 0.4556 (m-30)
  outliers start: 14
  outliers final: 7
  residues processed: 88
  average time/residue: 0.1710
  time to fit residues: 21.0266
Evaluate side-chains
  81 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.6922

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.144083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.113676 restraints weight = 7387.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.82
r_work: 0.3330 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2249

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= 0.125
  Angle     :  0.494  10.774   9004  Z= 0.253
  Chirality :  0.040   0.132    993
  Planarity :  0.004   0.052   1165
  Dihedral  :  3.995  17.105    876
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 19.34 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.31), residues: 803
  helix:  1.81 (0.27), residues: 389
  sheet: -2.08 (0.55), residues: 77
  loop : -1.63 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 708 
 PHE   0.012   0.001   PHE A 219 
 TYR   0.009   0.001   TYR A 177 
 ARG   0.004   0.000   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02976 (  279)
  hydrogen bonds       : angle       3.93867 (  798)
  covalent geometry    : bond        0.00301 ( 6677)
  covalent geometry    : angle       0.49391 ( 9004)

*********************** 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
  93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7950 (t0) cc_final: 0.7285 (t0)
REVERT: A  381 GLU cc_start: 0.8156 (tt0) cc_final: 0.7903 (mt-10)
REVERT: A  404 TYR cc_start: 0.8738 (m-80) cc_final: 0.8278 (m-80)
REVERT: A  433 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7133 (mm-30)
REVERT: A  607 LYS cc_start: 0.8049 (tppp) cc_final: 0.7401 (tppt)
REVERT: A  711 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6094 (tp)
REVERT: A  839 ASP cc_start: 0.5449 (OUTLIER) cc_final: 0.4311 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 90
  average time/residue: 0.1623
  time to fit residues: 20.5165
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  : 0.685 
-------------------------------------------------------------------------------
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  504 ASN
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  754 ASP
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 20 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    0.1980
   chunk 35 optimal weight:    0.3980
   chunk 73 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   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 = 0.3528 r_free = 0.3528 target = 0.139679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.109377 restraints weight = 7440.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.84
r_work: 0.3368 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2290

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= 0.111
  Angle     :  0.484  10.802   9004  Z= 0.248
  Chirality :  0.039   0.133    993
  Planarity :  0.004   0.053   1165
  Dihedral  :  3.954  16.913    876
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.62 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.31), residues: 803
  helix:  1.87 (0.27), residues: 389
  sheet: -2.08 (0.55), residues: 77
  loop : -1.60 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 
 PHE   0.011   0.001   PHE A 756 
 TYR   0.014   0.001   TYR A 177 
 ARG   0.007   0.000   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02858 (  279)
  hydrogen bonds       : angle       3.91201 (  798)
  covalent geometry    : bond        0.00265 ( 6677)
  covalent geometry    : angle       0.48378 ( 9004)

*********************** 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
  85 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7974 (t0) cc_final: 0.7311 (t0)
REVERT: A  381 GLU cc_start: 0.8187 (tt0) cc_final: 0.7947 (mt-10)
REVERT: A  433 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7286 (mm-30)
REVERT: A  607 LYS cc_start: 0.8143 (tppp) cc_final: 0.7529 (tppt)
REVERT: A  711 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6131 (tp)
REVERT: A  839 ASP cc_start: 0.5434 (OUTLIER) cc_final: 0.4295 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 84
  average time/residue: 0.1560
  time to fit residues: 18.7746
Evaluate side-chains
  82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
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  504 ASN
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 51 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3502 r_free = 0.3502 target = 0.137249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.106961 restraints weight = 7484.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.84
r_work: 0.3340 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2416

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= 0.133
  Angle     :  0.505  11.101   9004  Z= 0.259
  Chirality :  0.040   0.132    993
  Planarity :  0.004   0.053   1165
  Dihedral  :  4.054  16.825    876
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 19.34 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.31), residues: 803
  helix:  1.80 (0.27), residues: 389
  sheet: -2.17 (0.55), residues: 77
  loop : -1.62 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 
 PHE   0.014   0.001   PHE A 219 
 TYR   0.011   0.001   TYR A 177 
 ARG   0.007   0.000   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03025 (  279)
  hydrogen bonds       : angle       3.96324 (  798)
  covalent geometry    : bond        0.00324 ( 6677)
  covalent geometry    : angle       0.50472 ( 9004)

********************** 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
  84 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ASN cc_start: 0.7956 (t0) cc_final: 0.7290 (t0)
REVERT: A  381 GLU cc_start: 0.8194 (tt0) cc_final: 0.7951 (mt-10)
REVERT: A  404 TYR cc_start: 0.8811 (m-80) cc_final: 0.8426 (m-80)
REVERT: A  433 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7311 (mm-30)
REVERT: A  607 LYS cc_start: 0.8162 (tppp) cc_final: 0.7548 (tppt)
REVERT: A  711 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6200 (tp)
REVERT: A  839 ASP cc_start: 0.5577 (OUTLIER) cc_final: 0.4400 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 82
  average time/residue: 0.1624
  time to fit residues: 19.1921
Evaluate side-chains
  83 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
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  504 ASN
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  754 ASP
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 49 optimal weight:    0.3980
   chunk 58 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0370
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.139307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.108986 restraints weight = 7539.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.86
r_work: 0.3367 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2368

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= 0.109
  Angle     :  0.486  10.849   9004  Z= 0.249
  Chirality :  0.040   0.132    993
  Planarity :  0.004   0.053   1165
  Dihedral  :  3.962  16.704    876
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 19.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.31), residues: 803
  helix:  1.89 (0.27), residues: 389
  sheet: -2.12 (0.56), residues: 77
  loop : -1.60 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 202 
 PHE   0.011   0.001   PHE A 756 
 TYR   0.012   0.001   TYR A 177 
 ARG   0.007   0.000   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02841 (  279)
  hydrogen bonds       : angle       3.90819 (  798)
  covalent geometry    : bond        0.00259 ( 6677)
  covalent geometry    : angle       0.48604 ( 9004)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3592.42 seconds
wall clock time: 63 minutes 3.63 seconds (3783.63 seconds total)