Starting phenix.real_space_refine
on Wed Feb  4 15:02:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7way_32389/02_2026/7way_32389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7way_32389/02_2026/7way_32389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7way_32389/02_2026/7way_32389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7way_32389/02_2026/7way_32389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7way_32389/02_2026/7way_32389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7way_32389/02_2026/7way_32389.cif"
  }
  resolution = 2.9
  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=   0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     P     175      5.49       5
     S      28      5.16       5
     C    6630      2.51       5
     N    2041      2.21       5
     O    2579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11453
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 674
          Classifications: {'DNA': 33}
          Link IDs: {'rna3p': 32}
    Chain: "C"
      Number of atoms: 547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 547
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "D"
      Number of atoms: 2446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 2446
          Classifications: {'RNA': 115}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 12, 'rna3p': 102}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 7786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 960, 7786
          Classifications: {'peptide': 960}
          Link IDs: {'PTRANS': 37, 'TRANS': 922}
          Chain breaks: 2
  Time building chain proxies: 2.26, per 1000 atoms: 0.20
  Number of scatterers: 11453
  At special positions: 0
  Unit cell: (100.58, 141.94, 125.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P     175     15.00
     O    2579      8.00
     N    2041      7.00
     C    6630      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: 1.00
  Conformation dependent library (CDL) restraints added in 422.6 milliseconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      49.6% alpha, 22.4% beta
      61 base pairs and 103 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 17
    Processing helix  chain 'A' and resid 38 through 47
    Processing helix  chain 'A' and resid 60 through 92
    Processing helix  chain 'A' and resid 92 through 101
    Processing helix  chain 'A' and resid 196 through 201
    Processing helix  chain 'A' and resid 210 through 215
    Processing helix  chain 'A' and resid 221 through 272
      removed outlier: 3.644A  pdb=" N   VAL A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASP A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A 249 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLU A 250 " --> pdb=" O   ASP A 246 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LYS A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
    Processing helix  chain 'A' and resid 343 through 358
      removed outlier: 3.689A  pdb=" N   LYS A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 368
    Processing helix  chain 'A' and resid 371 through 378
      removed outlier: 4.135A  pdb=" N   GLN A 375 " --> pdb=" O   GLY A 371 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU A 376 " --> pdb=" O   TYR A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 382
    Processing helix  chain 'A' and resid 384 through 390
    Processing helix  chain 'A' and resid 394 through 411
    Processing helix  chain 'A' and resid 413 through 443
      removed outlier: 3.532A  pdb=" N   VAL A 417 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 466
    Processing helix  chain 'A' and resid 467 through 469
      No H-bonds generated for 'chain 'A' and resid 467 through 469'
    Processing helix  chain 'A' and resid 472 through 493
    Processing helix  chain 'A' and resid 494 through 496
      No H-bonds generated for 'chain 'A' and resid 494 through 496'
    Processing helix  chain 'A' and resid 510 through 513
    Processing helix  chain 'A' and resid 589 through 596
    Processing helix  chain 'A' and resid 697 through 717
    Processing helix  chain 'A' and resid 720 through 724
    Processing helix  chain 'A' and resid 725 through 750
    Processing helix  chain 'A' and resid 770 through 774
    Processing helix  chain 'A' and resid 775 through 790
      removed outlier: 3.550A  pdb=" N   MET A 779 " --> pdb=" O   GLN A 775 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLU A 790 " --> pdb=" O   LYS A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 796
    Processing helix  chain 'A' and resid 818 through 829
    Processing helix  chain 'A' and resid 866 through 876
      removed outlier: 3.981A  pdb=" N   GLU A 876 " --> pdb=" O   ARG A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 885
    Processing helix  chain 'A' and resid 886 through 901
    Processing helix  chain 'A' and resid 921 through 936
      removed outlier: 3.594A  pdb=" N   ALA A 930 " --> pdb=" O   ALA A 926 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 949
      removed outlier: 3.518A  pdb=" N   THR A 949 " --> pdb=" O   GLN A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 973
      removed outlier: 3.887A  pdb=" N   PHE A 958 " --> pdb=" O   ASP A 954 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506
      removed outlier: 3.643A  pdb=" N   GLY A 614 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   THR A 638 " --> pdb=" O   ALA A 612 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLY A 614 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA A 636 " --> pdb=" O   GLY A 614 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL A 616 " --> pdb=" O   PHE A 634 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   PHE A 634 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLU A 618 " --> pdb=" O   ALA A 632 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ALA A 632 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   THR A 620 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   GLU A 630 " --> pdb=" O   THR A 620 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   TYR A 622 " --> pdb=" O   GLN A 628 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLN A 628 " --> pdb=" O   TYR A 622 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU A 633 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 506
      removed outlier: 3.643A  pdb=" N   GLY A 614 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   THR A 638 " --> pdb=" O   ALA A 612 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLY A 614 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA A 636 " --> pdb=" O   GLY A 614 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL A 616 " --> pdb=" O   PHE A 634 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   PHE A 634 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLU A 618 " --> pdb=" O   ALA A 632 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ALA A 632 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   THR A 620 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   GLU A 630 " --> pdb=" O   THR A 620 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   TYR A 622 " --> pdb=" O   GLN A 628 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLN A 628 " --> pdb=" O   TYR A 622 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU A 633 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 13.056A  pdb=" N   CYS A 515 " --> pdb=" O   ASN A 561 " (cutoff:3.500A)
      removed outlier: 10.231A  pdb=" N   ASN A 561 " --> pdb=" O   CYS A 515 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   PHE A 517 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   VAL A 559 " --> pdb=" O   PHE A 517 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   PHE A 556 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 117
      removed outlier: 4.365A  pdb=" N   ILE A 114 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE A 128 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   VAL A 139 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   SER A 126 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 117
      removed outlier: 4.365A  pdb=" N   ILE A 114 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 10.689A  pdb=" N   THR A 153 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 694
      removed outlier: 4.520A  pdb=" N   ALA A 756 " --> pdb=" O   ILE A 658 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   ARG A 660 " --> pdb=" O   ALA A 756 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682
    Processing sheet with id=AA8, first strand: chain 'A' and resid 830 through 832
      removed outlier: 3.747A  pdb=" N   THR A 838 " --> pdb=" O   LEU A 845 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855
    Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 911

    447 hydrogen bonds defined for protein.
    1266 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      151 hydrogen bonds
      290 hydrogen bond angles
      0 basepair planarities
      61 basepair parallelities
      103 stacking parallelities
  Total time for adding SS restraints: 2.69

  Time building geometry restraints manager: 1.24 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: 2340
        1.33 -     1.45: 3480
        1.45 -     1.57: 5834
        1.57 -     1.69: 346
        1.69 -     1.81: 41
  Bond restraints: 12041
  Sorted by residual:
  bond pdb=" CG  LEU A 894 "
       pdb=" CD2 LEU A 894 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.30e+00
  bond pdb=" N   ASN A 528 "
       pdb=" CA  ASN A 528 "
    ideal  model  delta    sigma   weight residual
    1.453  1.466 -0.012 1.22e-02 6.72e+03 1.02e+00
  bond pdb=" CA  ILE A 108 "
       pdb=" CB  ILE A 108 "
    ideal  model  delta    sigma   weight residual
    1.540  1.527  0.013 1.36e-02 5.41e+03 9.61e-01
  bond pdb=" N   TYR A 530 "
       pdb=" CA  TYR A 530 "
    ideal  model  delta    sigma   weight residual
    1.455  1.467 -0.012 1.29e-02 6.01e+03 9.27e-01
  bond pdb=" O4'  DA B  24 "
       pdb=" C1'  DA B  24 "
    ideal  model  delta    sigma   weight residual
    1.414  1.397  0.017 2.00e-02 2.50e+03 7.00e-01
  ... (remaining 12036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 16845
        2.10 -     4.20: 176
        4.20 -     6.30: 12
        6.30 -     8.40: 4
        8.40 -    10.50: 1
  Bond angle restraints: 17038
  Sorted by residual:
  angle pdb=" N   VAL A 524 "
        pdb=" CA  VAL A 524 "
        pdb=" C   VAL A 524 "
      ideal   model   delta    sigma   weight residual
     112.96  109.33    3.63 1.00e+00 1.00e+00 1.32e+01
  angle pdb=" N   ASN A 107 "
        pdb=" CA  ASN A 107 "
        pdb=" C   ASN A 107 "
      ideal   model   delta    sigma   weight residual
     114.75  110.90    3.85 1.26e+00 6.30e-01 9.34e+00
  angle pdb=" CA  LEU A 894 "
        pdb=" CB  LEU A 894 "
        pdb=" CG  LEU A 894 "
      ideal   model   delta    sigma   weight residual
     116.30  126.80  -10.50 3.50e+00 8.16e-02 8.99e+00
  angle pdb=" N   LEU A 529 "
        pdb=" CA  LEU A 529 "
        pdb=" C   LEU A 529 "
      ideal   model   delta    sigma   weight residual
     108.13  113.01   -4.88 1.72e+00 3.38e-01 8.03e+00
  angle pdb=" CA  TYR A 530 "
        pdb=" CB  TYR A 530 "
        pdb=" CG  TYR A 530 "
      ideal   model   delta    sigma   weight residual
     113.90  118.58   -4.68 1.80e+00 3.09e-01 6.76e+00
  ... (remaining 17033 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.00: 6651
       32.00 -    64.00: 557
       64.00 -    96.01: 57
       96.01 -   128.01: 0
      128.01 -   160.01: 2
  Dihedral angle restraints: 7267
    sinusoidal: 4465
      harmonic: 2802
  Sorted by residual:
  dihedral pdb=" O4'   U D  17 "
           pdb=" C1'   U D  17 "
           pdb=" N1    U D  17 "
           pdb=" C2    U D  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   90.82  141.18     1      1.70e+01 3.46e-03 5.91e+01
  dihedral pdb=" CA  ARG A 443 "
           pdb=" C   ARG A 443 "
           pdb=" N   SER A 444 "
           pdb=" CA  SER A 444 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.38  -25.62     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  LEU A 527 "
           pdb=" C   LEU A 527 "
           pdb=" N   ASN A 528 "
           pdb=" CA  ASN A 528 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 7264 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1760
       0.057 -    0.115: 179
       0.115 -    0.172: 21
       0.172 -    0.229: 0
       0.229 -    0.286: 1
  Chirality restraints: 1961
  Sorted by residual:
  chirality pdb=" CG  LEU A 529 "
            pdb=" CB  LEU A 529 "
            pdb=" CD1 LEU A 529 "
            pdb=" CD2 LEU A 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C3'   C D  40 "
            pdb=" C4'   C D  40 "
            pdb=" O3'   C D  40 "
            pdb=" C2'   C D  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.33   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" C1'   C D  19 "
            pdb=" O4'   C D  19 "
            pdb=" C2'   C D  19 "
            pdb=" N1    C D  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.33    0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 1958 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  56 "   -0.024 2.00e-02 2.50e+03   1.08e-02 3.18e+00
        pdb=" N9    A D  56 "    0.024 2.00e-02 2.50e+03
        pdb=" C8    A D  56 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  56 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    A D  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  56 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A D  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  56 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A D  56 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A D  56 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  38 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A  39 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  39 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  39 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 529 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.36e+00
        pdb=" C   LEU A 529 "    0.027 2.00e-02 2.50e+03
        pdb=" O   LEU A 529 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR A 530 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 592
        2.72 -     3.26: 10071
        3.26 -     3.81: 19637
        3.81 -     4.35: 24195
        4.35 -     4.90: 37246
  Nonbonded interactions: 91741
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 816 "
            pdb=" NE2 GLN A 963 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OG1 THR A  38 "
            pdb=" OD1 ASP A  40 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O2'   C D  40 "
            pdb=" OP1   U D  41 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   HIS A 173 "
            pdb=" OG1 THR A 183 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OD1 ASP A 865 "
            pdb=" OG  SER A 867 "
     model   vdw
     2.233 3.040
  ... (remaining 91736 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.870
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     11.690
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12041  Z= 0.164
  Angle     :  0.542  10.496  17038  Z= 0.297
  Chirality :  0.036   0.286   1961
  Planarity :  0.004   0.043   1543
  Dihedral  : 19.589 160.010   5457
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.28), residues: 954
  helix:  2.23 (0.25), residues: 430
  sheet: -0.08 (0.43), residues: 139
  loop : -0.28 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 956 
 TYR   0.019   0.001   TYR A 776 
 PHE   0.008   0.001   PHE A 543 
 TRP   0.012   0.001   TRP A 519 
 HIS   0.005   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (12041)
  covalent geometry    : angle       0.54240 (17038)
  hydrogen bonds       : bond        0.11559 (  571)
  hydrogen bonds       : angle       4.76739 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.302 
Fit side-chains
  outliers start: 0
  outliers final: 1
  residues processed: 54
  average time/residue: 0.6720
  time to fit residues: 38.9666
Evaluate side-chains
  35 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    4.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN
A 368 ASN
A 737 ASN
A 907 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.110427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.074925 restraints weight = 22386.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.53
r_work: 0.2766 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.0866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  12041  Z= 0.250
  Angle     :  0.599   7.277  17038  Z= 0.322
  Chirality :  0.039   0.220   1961
  Planarity :  0.004   0.045   1543
  Dihedral  : 21.740 161.791   3449
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.24 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.28), residues: 954
  helix:  2.15 (0.25), residues: 439
  sheet: -0.20 (0.43), residues: 139
  loop : -0.30 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 627 
 TYR   0.021   0.002   TYR A 776 
 PHE   0.012   0.002   PHE A 517 
 TRP   0.014   0.002   TRP A  86 
 HIS   0.015   0.002   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (12041)
  covalent geometry    : angle       0.59895 (17038)
  hydrogen bonds       : bond        0.06680 (  571)
  hydrogen bonds       : angle       4.09278 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 40
  average time/residue: 0.7436
  time to fit residues: 31.7874
Evaluate side-chains
  36 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0370
   chunk 2 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0970
   chunk 33 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 12 optimal weight:   30.0000
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.1660

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
A 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.112353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.077281 restraints weight = 22727.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.52
r_work: 0.2811 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12041  Z= 0.131
  Angle     :  0.509   6.698  17038  Z= 0.278
  Chirality :  0.035   0.175   1961
  Planarity :  0.004   0.044   1543
  Dihedral  : 21.758 158.698   3449
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  6.20 %
    Favored  : 92.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.28), residues: 954
  helix:  2.33 (0.25), residues: 441
  sheet: -0.10 (0.43), residues: 138
  loop : -0.27 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 956 
 TYR   0.015   0.001   TYR A  85 
 PHE   0.008   0.001   PHE A 509 
 TRP   0.012   0.001   TRP A 598 
 HIS   0.004   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12041)
  covalent geometry    : angle       0.50942 (17038)
  hydrogen bonds       : bond        0.05265 (  571)
  hydrogen bonds       : angle       3.82534 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.342 
Fit side-chains
  outliers start: 8
  outliers final: 4
  residues processed: 42
  average time/residue: 0.5840
  time to fit residues: 26.7944
Evaluate side-chains
  39 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    0.0670
   chunk 38 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9980
   chunk 43 optimal weight:    0.4980
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.8720

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.114315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.079757 restraints weight = 22780.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.50
r_work: 0.2860 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12041  Z= 0.109
  Angle     :  0.474   6.681  17038  Z= 0.258
  Chirality :  0.034   0.236   1961
  Planarity :  0.003   0.040   1543
  Dihedral  : 21.569 155.803   3449
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  7.75 %
    Favored  : 91.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.28), residues: 954
  helix:  2.60 (0.25), residues: 442
  sheet:  0.07 (0.41), residues: 155
  loop : -0.18 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 956 
 TYR   0.025   0.001   TYR A 372 
 PHE   0.008   0.001   PHE A 196 
 TRP   0.010   0.001   TRP A 598 
 HIS   0.005   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (12041)
  covalent geometry    : angle       0.47354 (17038)
  hydrogen bonds       : bond        0.04309 (  571)
  hydrogen bonds       : angle       3.59691 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7764 (t70) cc_final: 0.7298 (OUTLIER)
  outliers start: 4
  outliers final: 3
  residues processed: 48
  average time/residue: 0.5823
  time to fit residues: 30.2695
Evaluate side-chains
  39 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  279 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 6 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 100 optimal weight:   20.0000
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.112242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.077307 restraints weight = 22556.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.47
r_work: 0.2806 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12041  Z= 0.148
  Angle     :  0.506   9.413  17038  Z= 0.273
  Chirality :  0.035   0.208   1961
  Planarity :  0.003   0.039   1543
  Dihedral  : 21.547 156.053   3449
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.89 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.28), residues: 954
  helix:  2.54 (0.25), residues: 441
  sheet:  0.01 (0.43), residues: 136
  loop : -0.20 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 956 
 TYR   0.015   0.001   TYR A 853 
 PHE   0.008   0.001   PHE A 196 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.005   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12041)
  covalent geometry    : angle       0.50592 (17038)
  hydrogen bonds       : bond        0.05116 (  571)
  hydrogen bonds       : angle       3.68657 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7765 (t70) cc_final: 0.7344 (p0)
  outliers start: 7
  outliers final: 3
  residues processed: 44
  average time/residue: 0.6633
  time to fit residues: 31.6461
Evaluate side-chains
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 111 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 99 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 9 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.112603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.077726 restraints weight = 22619.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.46
r_work: 0.2814 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  12041  Z= 0.131
  Angle     :  0.507  10.242  17038  Z= 0.271
  Chirality :  0.034   0.186   1961
  Planarity :  0.003   0.040   1543
  Dihedral  : 21.547 155.897   3447
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 10.37 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.28), residues: 954
  helix:  2.58 (0.25), residues: 441
  sheet: -0.04 (0.41), residues: 153
  loop : -0.13 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 956 
 TYR   0.023   0.001   TYR A 372 
 PHE   0.008   0.001   PHE A 196 
 TRP   0.012   0.001   TRP A  86 
 HIS   0.004   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (12041)
  covalent geometry    : angle       0.50689 (17038)
  hydrogen bonds       : bond        0.04929 (  571)
  hydrogen bonds       : angle       3.65351 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7742 (t70) cc_final: 0.7318 (p0)
REVERT: A  486 TRP cc_start: 0.8076 (m-10) cc_final: 0.7751 (m-10)
  outliers start: 6
  outliers final: 4
  residues processed: 41
  average time/residue: 0.6235
  time to fit residues: 27.5960
Evaluate side-chains
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0870
   chunk 14 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.6164

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.112231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.077227 restraints weight = 22582.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.46
r_work: 0.2805 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12041  Z= 0.145
  Angle     :  0.517  10.751  17038  Z= 0.275
  Chirality :  0.035   0.187   1961
  Planarity :  0.003   0.040   1543
  Dihedral  : 21.525 155.703   3447
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.37 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.28), residues: 954
  helix:  2.55 (0.25), residues: 441
  sheet: -0.05 (0.41), residues: 153
  loop : -0.13 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 956 
 TYR   0.015   0.001   TYR A  85 
 PHE   0.007   0.001   PHE A 495 
 TRP   0.012   0.001   TRP A  86 
 HIS   0.005   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (12041)
  covalent geometry    : angle       0.51738 (17038)
  hydrogen bonds       : bond        0.05063 (  571)
  hydrogen bonds       : angle       3.66554 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  109 ASP cc_start: 0.7549 (t70) cc_final: 0.7163 (p0)
REVERT: A  486 TRP cc_start: 0.8104 (m-10) cc_final: 0.7832 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 48
  average time/residue: 0.6895
  time to fit residues: 35.8710
Evaluate side-chains
  45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.110428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.074875 restraints weight = 22213.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 2.48
r_work: 0.2766 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  12041  Z= 0.203
  Angle     :  0.572  13.381  17038  Z= 0.303
  Chirality :  0.037   0.197   1961
  Planarity :  0.004   0.041   1543
  Dihedral  : 21.539 155.446   3447
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.49 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.28), residues: 954
  helix:  2.46 (0.25), residues: 439
  sheet: -0.10 (0.44), residues: 137
  loop : -0.19 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 956 
 TYR   0.023   0.002   TYR A 372 
 PHE   0.010   0.001   PHE A 495 
 TRP   0.014   0.001   TRP A  86 
 HIS   0.008   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (12041)
  covalent geometry    : angle       0.57205 (17038)
  hydrogen bonds       : bond        0.06065 (  571)
  hydrogen bonds       : angle       3.85112 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.228 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 43
  average time/residue: 0.7301
  time to fit residues: 33.7410
Evaluate side-chains
  44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.112216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.076998 restraints weight = 22338.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.41
r_work: 0.2814 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12041  Z= 0.137
  Angle     :  0.542  14.990  17038  Z= 0.286
  Chirality :  0.035   0.185   1961
  Planarity :  0.004   0.041   1543
  Dihedral  : 21.553 155.417   3447
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.08 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.28), residues: 954
  helix:  2.48 (0.25), residues: 442
  sheet: -0.05 (0.44), residues: 136
  loop : -0.23 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG A 824 
 TYR   0.015   0.001   TYR A  85 
 PHE   0.007   0.001   PHE A 509 
 TRP   0.012   0.001   TRP A 598 
 HIS   0.004   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12041)
  covalent geometry    : angle       0.54223 (17038)
  hydrogen bonds       : bond        0.05198 (  571)
  hydrogen bonds       : angle       3.74062 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.331 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 43
  average time/residue: 0.6683
  time to fit residues: 30.9072
Evaluate side-chains
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 86 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0770
   chunk 19 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    2.2146

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.111162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.075989 restraints weight = 22319.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.39
r_work: 0.2788 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12041  Z= 0.179
  Angle     :  0.570  15.437  17038  Z= 0.300
  Chirality :  0.036   0.190   1961
  Planarity :  0.004   0.040   1543
  Dihedral  : 21.527 155.331   3447
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.85 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.28), residues: 954
  helix:  2.45 (0.25), residues: 441
  sheet: -0.05 (0.44), residues: 136
  loop : -0.26 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 824 
 TYR   0.024   0.002   TYR A 372 
 PHE   0.009   0.001   PHE A 495 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.003   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (12041)
  covalent geometry    : angle       0.56995 (17038)
  hydrogen bonds       : bond        0.05656 (  571)
  hydrogen bonds       : angle       3.79016 ( 1556)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.289 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 45
  average time/residue: 0.6329
  time to fit residues: 30.8871
Evaluate side-chains
  45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  158 ARG
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  780 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.109474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.074079 restraints weight = 22442.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 2.58
r_work: 0.2738 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12041  Z= 0.241
  Angle     :  0.623  15.271  17038  Z= 0.327
  Chirality :  0.039   0.205   1961
  Planarity :  0.004   0.041   1543
  Dihedral  : 21.583 155.369   3447
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 11.08 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.28), residues: 954
  helix:  2.37 (0.25), residues: 438
  sheet: -0.17 (0.44), residues: 137
  loop : -0.29 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 824 
 TYR   0.028   0.002   TYR A 776 
 PHE   0.010   0.002   PHE A 495 
 TRP   0.014   0.002   TRP A  86 
 HIS   0.003   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 (12041)
  covalent geometry    : angle       0.62312 (17038)
  hydrogen bonds       : bond        0.06576 (  571)
  hydrogen bonds       : angle       3.94888 ( 1556)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2855.62 seconds
wall clock time: 49 minutes 27.01 seconds (2967.01 seconds total)