Starting phenix.real_space_refine
on Fri Sep 11 20:30:10 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7way_32389/09_2026/7way_32389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7way_32389/09_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_32389/09_2026/7way_32389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7way_32389/09_2026/7way_32389.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7way_32389/09_2026/7way_32389.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7way_32389/09_2026/7way_32389.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7way_32389/09_2026/7way_32389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7way_32389/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.25, 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: 0.98
  Conformation dependent library (CDL) restraints added in 321.2 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: 1.00
  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: 2.85

  Time building geometry restraints manager: 1.30 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=" C3'  DT B   2 "
       pdb=" C2'  DT B   2 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.61e+00
  bond pdb=" C3'  DC C  24 "
       pdb=" C2'  DC C  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.59e+00
  bond pdb=" C3'  DA B  24 "
       pdb=" C2'  DA B  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.71e+00
  bond pdb=" C3'  DT B   3 "
       pdb=" C2'  DT B   3 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.31e+00
  bond pdb=" C1'  DC C  19 "
       pdb=" N1   DC C  19 "
    ideal  model  delta    sigma   weight residual
    1.468  1.502 -0.034 1.40e-02 5.10e+03 5.96e+00
  ... (remaining 12036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 16514
        2.10 -     4.20: 484
        4.20 -     6.30: 35
        6.30 -     8.40: 4
        8.40 -    10.50: 1
  Bond angle restraints: 17038
  Sorted by residual:
  angle pdb=" N3   DT B   8 "
        pdb=" C4   DT B   8 "
        pdb=" O4   DT B   8 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.87e+01
  angle pdb=" N3   DT B   2 "
        pdb=" C4   DT B   2 "
        pdb=" O4   DT B   2 "
      ideal   model   delta    sigma   weight residual
     119.90  122.43   -2.53 6.00e-01 2.78e+00 1.78e+01
  angle pdb=" N3   DT C  21 "
        pdb=" C4   DT C  21 "
        pdb=" O4   DT C  21 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.73e+01
  angle pdb=" N3   DT B  14 "
        pdb=" C4   DT B  14 "
        pdb=" O4   DT B  14 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT B  11 "
        pdb=" C4   DT B  11 "
        pdb=" O4   DT B  11 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.71e+01
  ... (remaining 17033 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.00: 6346
       32.00 -    64.00: 521
       64.00 -    96.01: 23
       96.01 -   128.01: 0
      128.01 -   160.01: 1
  Dihedral angle restraints: 6891
    sinusoidal: 4089
      harmonic: 2802
  Sorted by residual:
  dihedral pdb=" C4'   A D  42 "
           pdb=" C3'   A D  42 "
           pdb=" C2'   A D  42 "
           pdb=" C1'   A D  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.43   72.77     1      3.10e+00 1.04e-01 7.03e+02
  dihedral pdb=" C4'   A D  15 "
           pdb=" C3'   A D  15 "
           pdb=" C2'   A D  15 "
           pdb=" C1'   A D  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.43   72.77     1      3.10e+00 1.04e-01 7.03e+02
  dihedral pdb=" C4'   U D 103 "
           pdb=" C3'   U D 103 "
           pdb=" C2'   U D 103 "
           pdb=" C1'   U D 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -35.85   72.20     1      3.10e+00 1.04e-01 6.94e+02
  ... (remaining 6888 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1630
       0.063 -    0.126: 186
       0.126 -    0.190: 9
       0.190 -    0.253: 110
       0.253 -    0.316: 26
  Chirality restraints: 1961
  Sorted by residual:
  chirality pdb=" P     U D  41 "
            pdb=" OP1   U D  41 "
            pdb=" OP2   U D  41 "
            pdb=" O5'   U D  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.49   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" C3'   U D 103 "
            pdb=" C4'   U D 103 "
            pdb=" O3'   U D 103 "
            pdb=" C2'   U D 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.79    0.29 2.00e-01 2.50e+01 2.07e+00
  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
  ... (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:             0.880
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.930
  Find NCS groups from input model:        0.060
  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:7.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
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= 0.293
  Angle     :  0.715  10.496  17038  Z= 0.433
  Chirality :  0.073   0.316   1961
  Planarity :  0.004   0.043   1543
  Dihedral  : 18.458 160.010   5081
  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/Z
  covalent geometry    : bond        0.00424 /  0.29 (12041)
  covalent geometry    : angle       0.71513 /  0.43 (17038)
  hydrogen bonds       : bond        0.11559 / 12.34 (  571)
  hydrogen bonds       : angle       4.76739 /  6.63 ( 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  : 0.350 
Fit side-chains
  outliers start: 0
  outliers final: 1
  residues processed: 54
  average time/residue: 0.6955
  time to fit residues: 40.2265
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  : 0.346 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.4980
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    3.0988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN
A 907 GLN

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 = 0.111601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.076474 restraints weight = 22335.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 2.51
r_work: 0.2788 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  12041  Z= 0.258
  Angle     :  0.997  19.908  17038  Z= 0.439
  Chirality :  0.100   1.347   1961
  Planarity :  0.004   0.045   1543
  Dihedral  : 19.562 155.279   3073
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  5.13 %
    Favored  : 94.28 %
  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:  1.29 (0.28), residues: 954
  helix:  2.17 (0.25), residues: 438
  sheet: -0.14 (0.43), residues: 139
  loop : -0.29 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 764 
 TYR   0.020   0.002   TYR A 372 
 PHE   0.015   0.002   PHE A 588 
 TRP   0.014   0.002   TRP A 598 
 HIS   0.009   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00548 /  0.26 (12041)
  covalent geometry    : angle       0.99657 /  0.44 (17038)
  hydrogen bonds       : bond        0.06607 /  7.29 (  571)
  hydrogen bonds       : angle       4.11944 /  5.73 ( 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
  40 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.222 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 38
  average time/residue: 0.6719
  time to fit residues: 27.5740
Evaluate side-chains
  35 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  279 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 12 optimal weight:   30.0000
   chunk 74 optimal weight:    0.6980
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN
A 737 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.112493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.077127 restraints weight = 22629.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.63
r_work: 0.2811 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12041  Z= 0.187
  Angle     :  0.812  11.548  17038  Z= 0.371
  Chirality :  0.073   0.879   1961
  Planarity :  0.004   0.044   1543
  Dihedral  : 19.650 161.439   3073
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  5.72 %
    Favored  : 93.44 %
  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:  1.38 (0.28), residues: 954
  helix:  2.33 (0.25), residues: 434
  sheet: -0.12 (0.43), residues: 139
  loop : -0.32 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 824 
 TYR   0.016   0.001   TYR A  85 
 PHE   0.014   0.001   PHE A 196 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.009   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.19 (12041)
  covalent geometry    : angle       0.81222 /  0.37 (17038)
  hydrogen bonds       : bond        0.05930 /  6.56 (  571)
  hydrogen bonds       : angle       3.93870 /  5.48 ( 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
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 3
  residues processed: 40
  average time/residue: 0.6562
  time to fit residues: 28.2906
Evaluate side-chains
  36 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  780 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 69 optimal weight:    0.1980
   chunk 29 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 95 optimal weight:    0.0980
   chunk 43 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 GLN
A 340 ASN
A 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.112905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.077709 restraints weight = 22517.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.45
r_work: 0.2824 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.1132

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= 0.171
  Angle     :  0.761  10.216  17038  Z= 0.351
  Chirality :  0.065   0.747   1961
  Planarity :  0.004   0.049   1543
  Dihedral  : 19.702 165.344   3073
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  7.75 %
    Favored  : 91.66 %
  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:  1.41 (0.28), residues: 954
  helix:  2.33 (0.25), residues: 441
  sheet: -0.08 (0.43), residues: 138
  loop : -0.34 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 824 
 TYR   0.016   0.002   TYR A 853 
 PHE   0.009   0.001   PHE A 196 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.008   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.17 (12041)
  covalent geometry    : angle       0.76141 /  0.35 (17038)
  hydrogen bonds       : bond        0.05556 /  6.17 (  571)
  hydrogen bonds       : angle       3.83934 /  5.34 ( 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
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 42
  average time/residue: 0.5829
  time to fit residues: 26.7628
Evaluate side-chains
  41 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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  780 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 100 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.111901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.076906 restraints weight = 22426.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.53
r_work: 0.2792 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12041  Z= 0.205
  Angle     :  0.782  10.430  17038  Z= 0.361
  Chirality :  0.065   0.766   1961
  Planarity :  0.004   0.043   1543
  Dihedral  : 19.810 168.572   3073
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.30 %
    Favored  : 89.75 %
  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:  1.39 (0.28), residues: 954
  helix:  2.29 (0.25), residues: 442
  sheet: -0.09 (0.44), residues: 137
  loop : -0.30 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 824 
 TYR   0.022   0.002   TYR A 372 
 PHE   0.012   0.001   PHE A 588 
 TRP   0.014   0.001   TRP A  86 
 HIS   0.009   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00443 /  0.21 (12041)
  covalent geometry    : angle       0.78180 /  0.36 (17038)
  hydrogen bonds       : bond        0.06003 /  6.65 (  571)
  hydrogen bonds       : angle       3.88710 /  5.40 ( 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
  47 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  278 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8413 (mmmt)
  outliers start: 8
  outliers final: 5
  residues processed: 43
  average time/residue: 0.5645
  time to fit residues: 26.5495
Evaluate side-chains
  41 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  267 ASP
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:    3.9990
   chunk 111 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 99 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.113296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.078127 restraints weight = 22512.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.45
r_work: 0.2836 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.1275

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= 0.136
  Angle     :  0.750  17.406  17038  Z= 0.343
  Chirality :  0.061   0.697   1961
  Planarity :  0.004   0.040   1543
  Dihedral  : 19.729 170.125   3073
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.77 %
    Favored  : 89.39 %
  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:  2.48 (0.25), residues: 436
  sheet: -0.01 (0.44), residues: 136
  loop : -0.28 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 824 
 TYR   0.016   0.001   TYR A 853 
 PHE   0.014   0.001   PHE A 196 
 TRP   0.013   0.001   TRP A 782 
 HIS   0.004   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.14 (12041)
  covalent geometry    : angle       0.74961 /  0.34 (17038)
  hydrogen bonds       : bond        0.05288 /  5.88 (  571)
  hydrogen bonds       : angle       3.80464 /  5.25 ( 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
  44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  195 ASP cc_start: 0.8271 (t70) cc_final: 0.7988 (t70)
REVERT: A  292 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8292 (tt0)
  outliers start: 7
  outliers final: 4
  residues processed: 41
  average time/residue: 0.5768
  time to fit residues: 25.9015
Evaluate side-chains
  41 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.113665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.078385 restraints weight = 22508.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 2.49
r_work: 0.2842 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12041  Z= 0.142
  Angle     :  0.730  15.415  17038  Z= 0.336
  Chirality :  0.060   0.655   1961
  Planarity :  0.004   0.041   1543
  Dihedral  : 19.698 172.940   3071
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  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:  1.60 (0.28), residues: 954
  helix:  2.52 (0.25), residues: 437
  sheet:  0.02 (0.44), residues: 136
  loop : -0.25 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 824 
 TYR   0.022   0.001   TYR A 372 
 PHE   0.011   0.001   PHE A 196 
 TRP   0.012   0.001   TRP A  86 
 HIS   0.002   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.14 (12041)
  covalent geometry    : angle       0.72965 /  0.34 (17038)
  hydrogen bonds       : bond        0.05142 /  5.72 (  571)
  hydrogen bonds       : angle       3.76937 /  5.18 ( 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
  48 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A  195 ASP cc_start: 0.8284 (t70) cc_final: 0.8004 (t70)
  outliers start: 8
  outliers final: 5
  residues processed: 45
  average time/residue: 0.5451
  time to fit residues: 26.9400
Evaluate side-chains
  40 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  248 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 103 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 76 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.112839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.077753 restraints weight = 22363.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.44
r_work: 0.2826 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12041  Z= 0.168
  Angle     :  0.752  16.315  17038  Z= 0.345
  Chirality :  0.061   0.650   1961
  Planarity :  0.004   0.040   1543
  Dihedral  : 19.672 173.596   3071
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.25 %
    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:  1.58 (0.28), residues: 954
  helix:  2.55 (0.25), residues: 435
  sheet:  0.02 (0.44), residues: 136
  loop : -0.32 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 956 
 TYR   0.016   0.001   TYR A 853 
 PHE   0.010   0.001   PHE A 196 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.004   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.17 (12041)
  covalent geometry    : angle       0.75176 /  0.34 (17038)
  hydrogen bonds       : bond        0.05445 /  6.04 (  571)
  hydrogen bonds       : angle       3.79948 /  5.24 ( 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
  45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  195 ASP cc_start: 0.8317 (t70) cc_final: 0.7994 (t70)
  outliers start: 9
  outliers final: 4
  residues processed: 41
  average time/residue: 0.5653
  time to fit residues: 25.2881
Evaluate side-chains
  40 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  279 ILE
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:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 93 optimal weight:    0.2980
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.113619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.078615 restraints weight = 22317.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.44
r_work: 0.2843 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start:          0.1413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12041  Z= 0.130
  Angle     :  0.742  16.766  17038  Z= 0.339
  Chirality :  0.059   0.611   1961
  Planarity :  0.004   0.040   1543
  Dihedral  : 19.689 174.542   3071
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.97 %
    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:  1.58 (0.28), residues: 954
  helix:  2.46 (0.25), residues: 442
  sheet:  0.05 (0.44), residues: 136
  loop : -0.25 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 956 
 TYR   0.033   0.001   TYR A 372 
 PHE   0.011   0.001   PHE A 196 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.13 (12041)
  covalent geometry    : angle       0.74212 /  0.34 (17038)
  hydrogen bonds       : bond        0.05103 /  5.66 (  571)
  hydrogen bonds       : angle       3.76226 /  5.16 ( 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
  41 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.325 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 40
  average time/residue: 0.5973
  time to fit residues: 26.1233
Evaluate side-chains
  37 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
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:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 62 optimal weight:    0.3980
   chunk 43 optimal weight:    4.9990
   chunk 82 optimal weight:    0.3980
   chunk 95 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.112515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.077386 restraints weight = 22354.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.43
r_work: 0.2816 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12041  Z= 0.182
  Angle     :  0.763  16.502  17038  Z= 0.350
  Chirality :  0.061   0.655   1961
  Planarity :  0.004   0.040   1543
  Dihedral  : 19.641 173.958   3071
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.85 %
    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:  1.53 (0.28), residues: 954
  helix:  2.42 (0.25), residues: 441
  sheet: -0.02 (0.44), residues: 137
  loop : -0.26 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 824 
 TYR   0.017   0.002   TYR A 776 
 PHE   0.012   0.001   PHE A 588 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.005   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.18 (12041)
  covalent geometry    : angle       0.76270 /  0.35 (17038)
  hydrogen bonds       : bond        0.05605 /  6.21 (  571)
  hydrogen bonds       : angle       3.81846 /  5.26 ( 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
  43 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  486 TRP cc_start: 0.8101 (m-10) cc_final: 0.7798 (m-10)
  outliers start: 7
  outliers final: 4
  residues processed: 40
  average time/residue: 0.6181
  time to fit residues: 26.7949
Evaluate side-chains
  41 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  267 ASP
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 70 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0980
   chunk 101 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0020
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.1992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.113291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.077783 restraints weight = 22449.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.50
r_work: 0.2836 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.1467

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= 0.139
  Angle     :  0.745  16.575  17038  Z= 0.341
  Chirality :  0.059   0.619   1961
  Planarity :  0.004   0.040   1543
  Dihedral  : 19.657 174.967   3071
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 11.44 %
    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:  1.55 (0.28), residues: 954
  helix:  2.45 (0.25), residues: 441
  sheet:  0.03 (0.44), residues: 136
  loop : -0.27 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 824 
 TYR   0.027   0.001   TYR A 372 
 PHE   0.010   0.001   PHE A 196 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.003   0.001   HIS A 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.14 (12041)
  covalent geometry    : angle       0.74500 /  0.34 (17038)
  hydrogen bonds       : bond        0.05237 /  5.80 (  571)
  hydrogen bonds       : angle       3.77780 /  5.19 ( 1556)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2934.54 seconds
wall clock time: 50 minutes 52.82 seconds (3052.82 seconds total)