Starting phenix.real_space_refine
on Fri Sep 11 09:38:09 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6e9f_9014/09_2026/6e9f_9014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e9f_9014/09_2026/6e9f_9014.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6e9f_9014/09_2026/6e9f_9014.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6e9f_9014/09_2026/6e9f_9014.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e9f_9014/09_2026/6e9f_9014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e9f_9014/09_2026/6e9f_9014.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e9f_9014/09_2026/6e9f_9014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e9f_9014/09_2026/6e9f_9014.cif"
  }
  resolution = 3.3
  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=   0.030
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: 6
    Type Number    sf(0)   Gaussians
     P      79      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    5245      2.51       5
     N    1491      2.21       5
     O    1899      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 8745
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 864, 7065
          Classifications: {'peptide': 864}
          Link IDs: {'PTRANS': 13, 'TRANS': 850}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 1110
          Classifications: {'RNAv2': 52}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 7, 'rna3p': 44}
    Chain: "C"
      Number of atoms: 569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 569
          Classifications: {'RNAv2': 27}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 15}
          Link IDs: {'rna2p': 1, 'rna3p': 25}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.91, per 1000 atoms: 0.22
  Number of scatterers: 8745
  At special positions: 0
  Unit cell: (106.65, 80.58, 97.17, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P      79     15.00
     Mg      1     11.99
     O    1899      8.00
     N    1491      7.00
     C    5245      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: 0.85
  Conformation dependent library (CDL) restraints added in 268.1 milliseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 5 sheets defined
      57.5% alpha, 3.0% beta
      23 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 65
    Processing helix  chain 'A' and resid 159 through 168
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 183 through 188
      removed outlier: 4.053A  pdb=" N   ASP A 186 " --> pdb=" O   ASN A 183 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A 187 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 229 through 233
    Processing helix  chain 'A' and resid 239 through 252
      removed outlier: 3.525A  pdb=" N   ASP A 243 " --> pdb=" O   ARG A 239 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 258
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 280 through 298
      removed outlier: 3.556A  pdb=" N   TYR A 285 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 286 " --> pdb=" O   LYS A 282 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LEU A 290 " --> pdb=" O   SER A 286 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
      removed outlier: 3.902A  pdb=" N   LEU A 313 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ASP A 314 " --> pdb=" O   TYR A 311 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLU A 315 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A 316 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 328
      removed outlier: 3.695A  pdb=" N   LYS A 321 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL A 326 " --> pdb=" O   ASN A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 333
      removed outlier: 3.583A  pdb=" N   VAL A 332 " --> pdb=" O   TYR A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 343 through 355
      removed outlier: 3.581A  pdb=" N   GLN A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ILE A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 371
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 4.531A  pdb=" N   GLU A 387 " --> pdb=" O   LYS A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 402
      removed outlier: 3.729A  pdb=" N   ASP A 401 " --> pdb=" O   LYS A 398 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   SER A 402 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 398 through 402'
    Processing helix  chain 'A' and resid 403 through 422
      removed outlier: 4.135A  pdb=" N   GLN A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 3.634A  pdb=" N   ALA A 427 " --> pdb=" O   ASP A 423 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASP A 428 " --> pdb=" O   SER A 424 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ASP A 429 " --> pdb=" O   ASP A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 445
    Processing helix  chain 'A' and resid 446 through 467
      removed outlier: 4.517A  pdb=" N   LYS A 456 " --> pdb=" O   ASP A 452 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LYS A 457 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   GLU A 460 " --> pdb=" O   LYS A 456 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   SER A 461 " --> pdb=" O   LYS A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 478
    Processing helix  chain 'A' and resid 489 through 493
      removed outlier: 3.852A  pdb=" N   PHE A 493 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 511
      removed outlier: 3.513A  pdb=" N   THR A 511 " --> pdb=" O   ILE A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 520
      removed outlier: 3.941A  pdb=" N   ASN A 520 " --> pdb=" O   GLY A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 535
      removed outlier: 3.533A  pdb=" N   LYS A 529 " --> pdb=" O   THR A 525 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE A 530 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 539
    Processing helix  chain 'A' and resid 558 through 571
      removed outlier: 3.636A  pdb=" N   ALA A 564 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLU A 568 " --> pdb=" O   ALA A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 595
      removed outlier: 3.693A  pdb=" N   LEU A 591 " --> pdb=" O   TYR A 587 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASP A 592 " --> pdb=" O   ARG A 588 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ILE A 593 " --> pdb=" O   ASP A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 604
    Processing helix  chain 'A' and resid 605 through 614
    Processing helix  chain 'A' and resid 628 through 640
      removed outlier: 3.686A  pdb=" N   ILE A 633 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ALA A 634 " --> pdb=" O   ARG A 630 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL A 637 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ILE A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ASP A 639 " --> pdb=" O   SER A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 647
      removed outlier: 3.544A  pdb=" N   LYS A 644 " --> pdb=" O   SER A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 655
      removed outlier: 3.895A  pdb=" N   LYS A 654 " --> pdb=" O   ASN A 651 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE A 655 " --> pdb=" O   PRO A 652 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 651 through 655'
    Processing helix  chain 'A' and resid 661 through 669
    Processing helix  chain 'A' and resid 673 through 682
      removed outlier: 3.565A  pdb=" N   ARG A 679 " --> pdb=" O   ALA A 675 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU A 682 " --> pdb=" O   GLU A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 706
      removed outlier: 3.602A  pdb=" N   ARG A 698 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU A 699 " --> pdb=" O   ASN A 695 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 701 " --> pdb=" O   ARG A 697 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP A 703 " --> pdb=" O   GLU A 699 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   MET A 704 " --> pdb=" O   LYS A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 739
      removed outlier: 4.406A  pdb=" N   LYS A 734 " --> pdb=" O   GLU A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 758
      removed outlier: 3.971A  pdb=" N   TYR A 749 " --> pdb=" O   LEU A 745 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU A 752 " --> pdb=" O   MET A 748 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   VAL A 756 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 777
      removed outlier: 3.837A  pdb=" N   TYR A 762 " --> pdb=" O   VAL A 758 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLU A 770 " --> pdb=" O   PHE A 766 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ASP A 772 " --> pdb=" O   CYS A 768 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LYS A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 797
    Processing helix  chain 'A' and resid 826 through 838
      removed outlier: 3.790A  pdb=" N   ILE A 833 " --> pdb=" O   TRP A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 853
      removed outlier: 3.929A  pdb=" N   VAL A 845 " --> pdb=" O   GLU A 841 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN A 850 " --> pdb=" O   ASN A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 890
      removed outlier: 4.169A  pdb=" N   HIS A 885 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 909
      removed outlier: 4.097A  pdb=" N   PHE A 902 " --> pdb=" O   ASP A 898 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ILE A 903 " --> pdb=" O   THR A 899 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER A 904 " --> pdb=" O   GLY A 900 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS A 909 " --> pdb=" O   LYS A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 920
      removed outlier: 3.557A  pdb=" N   TYR A 920 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 921 through 926
      removed outlier: 3.600A  pdb=" N   PHE A 924 " --> pdb=" O   CYS A 921 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   TYR A 926 " --> pdb=" O   PRO A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 934
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 73
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82
      removed outlier: 3.521A  pdb=" N   VAL A  89 " --> pdb=" O   SER A  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95
      removed outlier: 3.628A  pdb=" N   VAL A  95 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 114
      removed outlier: 6.807A  pdb=" N   SER A 120 " --> pdb=" O   ASN A 112 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   VAL A 114 " --> pdb=" O   GLY A 118 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   GLY A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265

    252 hydrogen bonds defined for protein.
    714 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      54 hydrogen bonds
      106 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 1.12 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: 2309
        1.33 -     1.45: 2182
        1.45 -     1.57: 4364
        1.57 -     1.69: 156
        1.69 -     1.81: 47
  Bond restraints: 9058
  Sorted by residual:
  bond pdb=" N   LYS A 160 "
       pdb=" CA  LYS A 160 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.04e-02 9.25e+03 8.19e+00
  bond pdb=" N   LEU A 159 "
       pdb=" CA  LEU A 159 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.19e-02 7.06e+03 8.11e+00
  bond pdb=" N   LYS A 165 "
       pdb=" CA  LYS A 165 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.23e-02 6.61e+03 7.23e+00
  bond pdb=" N   THR A 922 "
       pdb=" CA  THR A 922 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.04e-02 9.25e+03 7.19e+00
  bond pdb=" CB  PRO A 923 "
       pdb=" CG  PRO A 923 "
    ideal  model  delta    sigma   weight residual
    1.492  1.368  0.124 5.00e-02 4.00e+02 6.19e+00
  ... (remaining 9053 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.79: 12094
        2.79 -     5.59: 423
        5.59 -     8.38: 40
        8.38 -    11.18: 12
       11.18 -    13.97: 2
  Bond angle restraints: 12571
  Sorted by residual:
  angle pdb=" N   CYS A 921 "
        pdb=" CA  CYS A 921 "
        pdb=" C   CYS A 921 "
      ideal   model   delta    sigma   weight residual
     113.17  105.61    7.56 1.26e+00 6.30e-01 3.60e+01
  angle pdb=" C   THR A 922 "
        pdb=" N   PRO A 923 "
        pdb=" CA  PRO A 923 "
      ideal   model   delta    sigma   weight residual
     119.84  112.63    7.21 1.25e+00 6.40e-01 3.33e+01
  angle pdb=" N   LEU A 111 "
        pdb=" CA  LEU A 111 "
        pdb=" C   LEU A 111 "
      ideal   model   delta    sigma   weight residual
     109.24  118.32   -9.08 1.63e+00 3.76e-01 3.11e+01
  angle pdb=" N   VAL A 523 "
        pdb=" CA  VAL A 523 "
        pdb=" C   VAL A 523 "
      ideal   model   delta    sigma   weight residual
     111.91  107.19    4.72 8.90e-01 1.26e+00 2.81e+01
  angle pdb=" N   ILE A 882 "
        pdb=" CA  ILE A 882 "
        pdb=" C   ILE A 882 "
      ideal   model   delta    sigma   weight residual
     113.53  109.01    4.52 9.80e-01 1.04e+00 2.12e+01
  ... (remaining 12566 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4826
       17.85 -    35.69: 357
       35.69 -    53.54: 107
       53.54 -    71.39: 38
       71.39 -    89.24: 8
  Dihedral angle restraints: 5336
    sinusoidal: 2767
      harmonic: 2569
  Sorted by residual:
  dihedral pdb=" C4'   A B  12 "
           pdb=" C3'   A B  12 "
           pdb=" C2'   A B  12 "
           pdb=" C1'   A B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.65   75.00     1      3.10e+00 1.04e-01 7.40e+02
  dihedral pdb=" C4'   G B  22 "
           pdb=" C3'   G B  22 "
           pdb=" C2'   G B  22 "
           pdb=" C1'   G B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.80   73.15     1      3.10e+00 1.04e-01 7.09e+02
  dihedral pdb=" C4'   U B  25 "
           pdb=" C3'   U B  25 "
           pdb=" C2'   U B  25 "
           pdb=" C1'   U B  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.03   72.37     1      3.10e+00 1.04e-01 6.96e+02
  ... (remaining 5333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1106
       0.088 -    0.175: 221
       0.175 -    0.263: 119
       0.263 -    0.350: 10
       0.350 -    0.438: 3
  Chirality restraints: 1459
  Sorted by residual:
  chirality pdb=" C2'   G C  23 "
            pdb=" C3'   G C  23 "
            pdb=" O2'   G C  23 "
            pdb=" C1'   G C  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.35   -0.44 2.00e-01 2.50e+01 4.79e+00
  chirality pdb=" C2'   A B  38 "
            pdb=" C3'   A B  38 "
            pdb=" O2'   A B  38 "
            pdb=" C1'   A B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.36   -0.43 2.00e-01 2.50e+01 4.66e+00
  chirality pdb=" C2'   A B  32 "
            pdb=" C3'   A B  32 "
            pdb=" O2'   A B  32 "
            pdb=" C1'   A B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.42   -0.37 2.00e-01 2.50e+01 3.44e+00
  ... (remaining 1456 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 330 "    0.051 5.00e-02 4.00e+02   7.67e-02 9.42e+00
        pdb=" N   PRO A 331 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  38 "    0.032 2.00e-02 2.50e+03   1.70e-02 7.91e+00
        pdb=" N9    A B  38 "   -0.045 2.00e-02 2.50e+03
        pdb=" C8    A B  38 "    0.005 2.00e-02 2.50e+03
        pdb=" N7    A B  38 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A B  38 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A B  38 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A B  38 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A B  38 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    A B  38 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A B  38 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A B  38 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 916 "    0.023 2.00e-02 2.50e+03   2.06e-02 7.43e+00
        pdb=" CG  PHE A 916 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 916 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 916 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 916 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 916 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 916 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 72
        2.48 -     3.08: 5891
        3.08 -     3.69: 14370
        3.69 -     4.29: 20924
        4.29 -     4.90: 32380
  Nonbonded interactions: 73637
  Sorted by model distance:
  nonbonded pdb=" O4    U C   4 "
            pdb=" N3    U C   5 "
     model   vdw
     1.872 3.120
  nonbonded pdb=" O2'   A B  32 "
            pdb=" O5'   C B  33 "
     model   vdw
     2.091 3.040
  nonbonded pdb=" OP1   U B  23 "
            pdb="MG    MG B 101 "
     model   vdw
     2.102 2.170
  nonbonded pdb=" N1    G B  22 "
            pdb=" N6    A B  28 "
     model   vdw
     2.169 3.200
  nonbonded pdb=" C4    U C   4 "
            pdb=" N3    U C   5 "
     model   vdw
     2.178 3.340
  ... (remaining 73632 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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.580
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
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      :  0.011   0.124   9058  Z= 0.508
  Angle     :  1.199  13.972  12571  Z= 0.616
  Chirality :  0.090   0.438   1459
  Planarity :  0.006   0.077   1316
  Dihedral  : 14.542  89.236   3672
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  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: -5.59 (0.20), residues: 852
  helix: -4.18 (0.13), residues: 473
  sheet: -4.08 (0.83), residues: 25
  loop : -2.73 (0.27), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.002   ARG A 930 
 TYR   0.028   0.004   TYR A 912 
 PHE   0.048   0.004   PHE A 916 
 TRP   0.019   0.004   TRP A 829 
 HIS   0.011   0.002   HIS A 885 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01143 /  0.51 ( 9058)
  covalent geometry    : angle       1.19858 /  0.62 (12571)
  hydrogen bonds       : bond        0.29594 / 19.49 (  306)
  hydrogen bonds       : angle      10.97877 /  7.64 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  223 ASP cc_start: 0.8178 (t70) cc_final: 0.7925 (t0)
REVERT: A  241 LYS cc_start: 0.7553 (tttp) cc_final: 0.7239 (tptp)
REVERT: A  338 ARG cc_start: 0.7152 (mtm110) cc_final: 0.6853 (mmp80)
REVERT: A  375 TYR cc_start: 0.7400 (m-10) cc_final: 0.7167 (m-10)
REVERT: A  479 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7356 (ttpp)
REVERT: A  541 ASP cc_start: 0.7579 (t0) cc_final: 0.7297 (t0)
REVERT: A  768 CYS cc_start: 0.7385 (m) cc_final: 0.6969 (m)
REVERT: A  888 ASN cc_start: 0.7821 (t0) cc_final: 0.7558 (m-40)
REVERT: A  896 GLU cc_start: 0.6622 (pm20) cc_final: 0.6219 (tp30)
REVERT: A  926 TYR cc_start: 0.7934 (p90) cc_final: 0.7694 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1302
  time to fit residues: 38.3726
Evaluate side-chains
  118 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0170
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0970
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.4816

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  92 GLN
A 348 GLN
** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 885 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.143721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.126876 restraints weight = 13373.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.03
r_work: 0.3373 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9058  Z= 0.147
  Angle     :  0.831  11.917  12571  Z= 0.385
  Chirality :  0.062   0.649   1459
  Planarity :  0.005   0.046   1316
  Dihedral  : 12.814 142.789   1893
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.98 %
    Favored  : 85.31 %
  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: -4.22 (0.24), residues: 852
  helix: -2.89 (0.18), residues: 502
  sheet: -3.89 (0.86), residues: 25
  loop : -2.23 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 584 
 TYR   0.011   0.001   TYR A 453 
 PHE   0.018   0.002   PHE A 848 
 TRP   0.007   0.002   TRP A 309 
 HIS   0.004   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.15 ( 9058)
  covalent geometry    : angle       0.83137 /  0.38 (12571)
  hydrogen bonds       : bond        0.04642 /  2.87 (  306)
  hydrogen bonds       : angle       5.00277 /  3.53 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  167 PHE cc_start: 0.7341 (m-10) cc_final: 0.7050 (m-80)
REVERT: A  223 ASP cc_start: 0.8659 (t70) cc_final: 0.8418 (t0)
REVERT: A  241 LYS cc_start: 0.7633 (tttp) cc_final: 0.7214 (tptp)
REVERT: A  261 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7367 (t0)
REVERT: A  479 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7515 (ttpp)
REVERT: A  491 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7938 (pttm)
REVERT: A  538 GLU cc_start: 0.7788 (tp30) cc_final: 0.7545 (tp30)
REVERT: A  541 ASP cc_start: 0.7894 (t0) cc_final: 0.7640 (t0)
REVERT: A  579 ASP cc_start: 0.7138 (p0) cc_final: 0.6826 (p0)
REVERT: A  602 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6876 (tm-30)
REVERT: A  682 GLU cc_start: 0.8343 (tp30) cc_final: 0.8021 (tp30)
REVERT: A  704 MET cc_start: 0.8233 (mtp) cc_final: 0.8012 (mtp)
REVERT: A  768 CYS cc_start: 0.8586 (m) cc_final: 0.8230 (m)
REVERT: A  832 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7141 (mt)
REVERT: A  841 GLU cc_start: 0.8377 (pt0) cc_final: 0.8061 (pt0)
REVERT: A  888 ASN cc_start: 0.7991 (t0) cc_final: 0.7340 (m-40)
REVERT: A  896 GLU cc_start: 0.6671 (pm20) cc_final: 0.5946 (tp30)
  outliers start: 21
  outliers final: 13
  residues processed: 174
  average time/residue: 0.1002
  time to fit residues: 24.0051
Evaluate side-chains
  146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  794 THR
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  853 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 86 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 91 optimal weight:    8.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    2.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  92 GLN
A 103 ASN
A 346 ASN
A 481 ASN
A 581 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.115835 restraints weight = 13415.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.79
r_work: 0.3232 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9058  Z= 0.231
  Angle     :  0.823   9.307  12571  Z= 0.388
  Chirality :  0.060   0.590   1459
  Planarity :  0.004   0.043   1316
  Dihedral  : 12.841 172.033   1893
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 14.69 %
    Favored  : 80.67 %
  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: -3.29 (0.26), residues: 852
  helix: -2.15 (0.21), residues: 498
  sheet: -3.71 (0.84), residues: 25
  loop : -1.82 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 404 
 TYR   0.031   0.002   TYR A 762 
 PHE   0.023   0.003   PHE A 916 
 TRP   0.013   0.002   TRP A 297 
 HIS   0.005   0.002   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00512 /  0.23 ( 9058)
  covalent geometry    : angle       0.82263 /  0.39 (12571)
  hydrogen bonds       : bond        0.04457 /  2.84 (  306)
  hydrogen bonds       : angle       4.48670 /  3.17 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ASP cc_start: 0.8912 (t70) cc_final: 0.8710 (t0)
REVERT: A  241 LYS cc_start: 0.7936 (tttp) cc_final: 0.7309 (tptp)
REVERT: A  311 TYR cc_start: 0.8808 (m-10) cc_final: 0.8519 (m-10)
REVERT: A  479 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8050 (ttpp)
REVERT: A  538 GLU cc_start: 0.8049 (tp30) cc_final: 0.7771 (tp30)
REVERT: A  579 ASP cc_start: 0.7563 (p0) cc_final: 0.7349 (p0)
REVERT: A  602 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6943 (tm-30)
REVERT: A  645 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.7481 (m-80)
REVERT: A  682 GLU cc_start: 0.8602 (tp30) cc_final: 0.8273 (tp30)
REVERT: A  707 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8070 (pm20)
REVERT: A  832 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7326 (mt)
REVERT: A  847 GLU cc_start: 0.7557 (tp30) cc_final: 0.7128 (tm-30)
REVERT: A  867 GLU cc_start: 0.7085 (mp0) cc_final: 0.6693 (mt-10)
REVERT: A  868 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8561 (mt)
REVERT: A  888 ASN cc_start: 0.8210 (t0) cc_final: 0.7451 (m-40)
REVERT: A  894 LYS cc_start: 0.6873 (tptp) cc_final: 0.6636 (tptp)
REVERT: A  897 ARG cc_start: 0.7287 (ttp80) cc_final: 0.6996 (ttp80)
  outliers start: 36
  outliers final: 22
  residues processed: 150
  average time/residue: 0.0919
  time to fit residues: 19.4153
Evaluate side-chains
  134 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  610 ASP
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  645 TYR
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  853 CYS
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  935 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 73 optimal weight:    4.9990
   chunk 76 optimal weight:    0.4980
   chunk 47 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 ASN
A 346 ASN
A 581 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.133119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.117654 restraints weight = 13431.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.75
r_work: 0.3251 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9058  Z= 0.154
  Angle     :  0.715   9.246  12571  Z= 0.333
  Chirality :  0.054   0.541   1459
  Planarity :  0.004   0.038   1316
  Dihedral  : 12.567 164.659   1893
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 16.62 %
    Favored  : 78.48 %
  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: -2.69 (0.27), residues: 852
  helix: -1.64 (0.22), residues: 500
  sheet: -3.65 (0.87), residues: 25
  loop : -1.59 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 404 
 TYR   0.018   0.002   TYR A 762 
 PHE   0.017   0.002   PHE A 308 
 TRP   0.006   0.001   TRP A 297 
 HIS   0.005   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 ( 9058)
  covalent geometry    : angle       0.71489 /  0.33 (12571)
  hydrogen bonds       : bond        0.03678 /  2.34 (  306)
  hydrogen bonds       : angle       4.14593 /  2.93 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  241 LYS cc_start: 0.8058 (tttp) cc_final: 0.7437 (tptp)
REVERT: A  479 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8142 (ttpt)
REVERT: A  538 GLU cc_start: 0.7965 (tp30) cc_final: 0.7706 (tp30)
REVERT: A  546 ASP cc_start: 0.7829 (t0) cc_final: 0.7523 (m-30)
REVERT: A  579 ASP cc_start: 0.7409 (p0) cc_final: 0.7198 (p0)
REVERT: A  645 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.7335 (m-80)
REVERT: A  649 TYR cc_start: 0.8360 (t80) cc_final: 0.8085 (t80)
REVERT: A  682 GLU cc_start: 0.8549 (tp30) cc_final: 0.8131 (tp30)
REVERT: A  707 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8096 (pm20)
REVERT: A  832 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7352 (mt)
REVERT: A  841 GLU cc_start: 0.8328 (pt0) cc_final: 0.8079 (pt0)
REVERT: A  847 GLU cc_start: 0.7491 (tp30) cc_final: 0.7070 (tm-30)
REVERT: A  867 GLU cc_start: 0.7008 (mp0) cc_final: 0.6685 (mt-10)
REVERT: A  888 ASN cc_start: 0.8132 (t0) cc_final: 0.7408 (m-40)
REVERT: A  896 GLU cc_start: 0.6908 (pm20) cc_final: 0.6513 (tp30)
REVERT: A  897 ARG cc_start: 0.7336 (ttp80) cc_final: 0.7099 (ttp80)
  outliers start: 38
  outliers final: 20
  residues processed: 160
  average time/residue: 0.1008
  time to fit residues: 22.1743
Evaluate side-chains
  141 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  645 TYR
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  707 GLU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  853 CYS
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  911 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 87 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN
A 581 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.119364 restraints weight = 13228.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.71
r_work: 0.3280 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.4907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9058  Z= 0.131
  Angle     :  0.680   8.512  12571  Z= 0.317
  Chirality :  0.052   0.496   1459
  Planarity :  0.003   0.041   1316
  Dihedral  : 12.368 152.213   1893
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 17.01 %
    Favored  : 77.96 %
  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: -2.25 (0.27), residues: 852
  helix: -1.28 (0.23), residues: 495
  sheet: -3.49 (0.91), residues: 25
  loop : -1.42 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 255 
 TYR   0.014   0.001   TYR A 416 
 PHE   0.015   0.002   PHE A  71 
 TRP   0.006   0.001   TRP A 455 
 HIS   0.005   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 9058)
  covalent geometry    : angle       0.68042 /  0.32 (12571)
  hydrogen bonds       : bond        0.03403 /  2.17 (  306)
  hydrogen bonds       : angle       3.90001 /  2.76 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 132
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  241 LYS cc_start: 0.8054 (tttp) cc_final: 0.7384 (tptp)
REVERT: A  307 GLU cc_start: 0.6450 (tm-30) cc_final: 0.5892 (tm-30)
REVERT: A  479 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8149 (tmmt)
REVERT: A  538 GLU cc_start: 0.7968 (tp30) cc_final: 0.7696 (tp30)
REVERT: A  546 ASP cc_start: 0.7830 (t0) cc_final: 0.7542 (m-30)
REVERT: A  645 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7288 (m-10)
REVERT: A  682 GLU cc_start: 0.8536 (tp30) cc_final: 0.8144 (tp30)
REVERT: A  832 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7266 (mt)
REVERT: A  867 GLU cc_start: 0.6920 (mp0) cc_final: 0.6598 (mt-10)
REVERT: A  888 ASN cc_start: 0.8082 (t0) cc_final: 0.7340 (m110)
REVERT: A  896 GLU cc_start: 0.6827 (pm20) cc_final: 0.6467 (tp30)
  outliers start: 39
  outliers final: 23
  residues processed: 154
  average time/residue: 0.0907
  time to fit residues: 19.9406
Evaluate side-chains
  146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  645 TYR
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  794 THR
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  853 CYS
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 55 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 59 optimal weight:    0.4980
   chunk 3 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.133124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.117453 restraints weight = 13376.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.80
r_work: 0.3244 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.5134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9058  Z= 0.155
  Angle     :  0.697   8.243  12571  Z= 0.324
  Chirality :  0.053   0.489   1459
  Planarity :  0.003   0.041   1316
  Dihedral  : 12.247 139.151   1893
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 18.69 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.28), residues: 852
  helix: -1.10 (0.23), residues: 494
  sheet: -3.26 (0.81), residues: 33
  loop : -1.28 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 897 
 TYR   0.017   0.002   TYR A 416 
 PHE   0.013   0.002   PHE A 308 
 TRP   0.007   0.002   TRP A 297 
 HIS   0.005   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.15 ( 9058)
  covalent geometry    : angle       0.69653 /  0.32 (12571)
  hydrogen bonds       : bond        0.03495 /  2.21 (  306)
  hydrogen bonds       : angle       3.86530 /  2.74 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 126
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  127 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7396 (mp0)
REVERT: A  241 LYS cc_start: 0.8106 (tttp) cc_final: 0.7391 (tptp)
REVERT: A  307 GLU cc_start: 0.6507 (tm-30) cc_final: 0.5935 (tm-30)
REVERT: A  479 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8184 (tmmt)
REVERT: A  514 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8807 (pp)
REVERT: A  546 ASP cc_start: 0.8020 (t0) cc_final: 0.7686 (m-30)
REVERT: A  645 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7355 (m-80)
REVERT: A  682 GLU cc_start: 0.8598 (tp30) cc_final: 0.8225 (tp30)
REVERT: A  832 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7297 (mt)
REVERT: A  867 GLU cc_start: 0.6987 (mp0) cc_final: 0.6664 (mt-10)
  outliers start: 37
  outliers final: 29
  residues processed: 149
  average time/residue: 0.0970
  time to fit residues: 20.1230
Evaluate side-chains
  145 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  598 SER
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  645 TYR
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  794 THR
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  853 CYS
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  920 TYR
Chi-restraints excluded: chain A residue  935 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    0.2980
   chunk 61 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    0.1980
   chunk 40 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN
A 676 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.120100 restraints weight = 13273.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.70
r_work: 0.3292 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.5368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9058  Z= 0.126
  Angle     :  0.669   8.446  12571  Z= 0.310
  Chirality :  0.051   0.459   1459
  Planarity :  0.003   0.041   1316
  Dihedral  : 12.133 135.777   1893
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 18.94 %
    Favored  : 76.03 %
  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: -1.79 (0.28), residues: 852
  helix: -0.92 (0.23), residues: 497
  sheet: -3.20 (0.81), residues: 33
  loop : -1.14 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 255 
 TYR   0.016   0.001   TYR A 416 
 PHE   0.011   0.001   PHE A 848 
 TRP   0.007   0.001   TRP A 455 
 HIS   0.005   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 9058)
  covalent geometry    : angle       0.66893 /  0.31 (12571)
  hydrogen bonds       : bond        0.03296 /  2.10 (  306)
  hydrogen bonds       : angle       3.73489 /  2.62 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  127 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7432 (mp0)
REVERT: A  241 LYS cc_start: 0.8127 (tttp) cc_final: 0.7439 (tptp)
REVERT: A  307 GLU cc_start: 0.6492 (tm-30) cc_final: 0.6008 (tm-30)
REVERT: A  397 ASP cc_start: 0.8144 (t0) cc_final: 0.7752 (t0)
REVERT: A  479 LYS cc_start: 0.9008 (mtpp) cc_final: 0.8233 (tmmt)
REVERT: A  514 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8785 (pp)
REVERT: A  546 ASP cc_start: 0.7880 (t0) cc_final: 0.7599 (m-30)
REVERT: A  645 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7304 (m-10)
REVERT: A  682 GLU cc_start: 0.8533 (tp30) cc_final: 0.8189 (tp30)
REVERT: A  832 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7243 (mt)
REVERT: A  867 GLU cc_start: 0.6888 (mp0) cc_final: 0.6605 (mt-10)
  outliers start: 39
  outliers final: 27
  residues processed: 151
  average time/residue: 0.0948
  time to fit residues: 20.0249
Evaluate side-chains
  142 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  424 SER
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  598 SER
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  645 TYR
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  794 THR
Chi-restraints excluded: chain A residue  798 MET
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  853 CYS
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  920 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0010
   chunk 23 optimal weight:    0.4980
   chunk 74 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   overall best weight:    0.8788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.136719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.121351 restraints weight = 13245.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.72
r_work: 0.3303 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.5580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9058  Z= 0.122
  Angle     :  0.672   9.454  12571  Z= 0.309
  Chirality :  0.050   0.446   1459
  Planarity :  0.003   0.042   1316
  Dihedral  : 12.067 135.030   1893
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 19.85 %
    Favored  : 76.03 %
  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: 852
  helix: -0.72 (0.24), residues: 496
  sheet: -3.10 (0.81), residues: 33
  loop : -1.11 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 897 
 TYR   0.016   0.001   TYR A 416 
 PHE   0.016   0.002   PHE A 848 
 TRP   0.007   0.001   TRP A 297 
 HIS   0.005   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 ( 9058)
  covalent geometry    : angle       0.67205 /  0.31 (12571)
  hydrogen bonds       : bond        0.03219 /  2.02 (  306)
  hydrogen bonds       : angle       3.66141 /  2.56 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7449 (mp0)
REVERT: A  241 LYS cc_start: 0.8075 (tttp) cc_final: 0.7368 (tptp)
REVERT: A  307 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6063 (tm-30)
REVERT: A  397 ASP cc_start: 0.8057 (t0) cc_final: 0.7629 (t0)
REVERT: A  479 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8225 (tmmt)
REVERT: A  514 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8744 (pp)
REVERT: A  546 ASP cc_start: 0.7855 (t0) cc_final: 0.7562 (m-30)
REVERT: A  645 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7298 (m-10)
REVERT: A  832 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7208 (mt)
REVERT: A  867 GLU cc_start: 0.6875 (mp0) cc_final: 0.6596 (mt-10)
REVERT: A  894 LYS cc_start: 0.7015 (tptp) cc_final: 0.5994 (mmmm)
  outliers start: 32
  outliers final: 24
  residues processed: 144
  average time/residue: 0.0912
  time to fit residues: 18.6554
Evaluate side-chains
  149 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  424 SER
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  598 SER
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  645 TYR
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  798 MET
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  853 CYS
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  920 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0970
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0870
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    1.1960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.135942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.120553 restraints weight = 13202.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.74
r_work: 0.3293 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9058  Z= 0.136
  Angle     :  0.684   8.907  12571  Z= 0.315
  Chirality :  0.051   0.446   1459
  Planarity :  0.003   0.042   1316
  Dihedral  : 12.011 134.640   1893
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.62 %
    Favored  : 75.64 %
  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: 852
  helix: -0.66 (0.24), residues: 495
  sheet: -3.09 (0.94), residues: 24
  loop : -0.97 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 897 
 TYR   0.017   0.001   TYR A 416 
 PHE   0.011   0.001   PHE A 848 
 TRP   0.008   0.002   TRP A 297 
 HIS   0.005   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 ( 9058)
  covalent geometry    : angle       0.68390 /  0.31 (12571)
  hydrogen bonds       : bond        0.03303 /  2.08 (  306)
  hydrogen bonds       : angle       3.68542 /  2.58 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7283 (mp0)
REVERT: A  156 MET cc_start: 0.7952 (tpp) cc_final: 0.7741 (tpt)
REVERT: A  205 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8655 (mmm)
REVERT: A  241 LYS cc_start: 0.8081 (tttp) cc_final: 0.7371 (tptp)
REVERT: A  307 GLU cc_start: 0.6559 (tm-30) cc_final: 0.6033 (tm-30)
REVERT: A  380 PHE cc_start: 0.8651 (p90) cc_final: 0.8357 (p90)
REVERT: A  397 ASP cc_start: 0.8083 (t0) cc_final: 0.7648 (t0)
REVERT: A  479 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8248 (tmmt)
REVERT: A  546 ASP cc_start: 0.7783 (t0) cc_final: 0.7475 (m-30)
REVERT: A  645 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.7329 (m-10)
REVERT: A  682 GLU cc_start: 0.8318 (tp30) cc_final: 0.8110 (tp30)
REVERT: A  832 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7226 (mt)
REVERT: A  847 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7317 (tm-30)
REVERT: A  867 GLU cc_start: 0.6931 (mp0) cc_final: 0.6638 (mt-10)
REVERT: A  894 LYS cc_start: 0.7046 (tptp) cc_final: 0.6019 (mmmm)
  outliers start: 29
  outliers final: 22
  residues processed: 138
  average time/residue: 0.0942
  time to fit residues: 18.4329
Evaluate side-chains
  146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  424 SER
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  598 SER
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  645 TYR
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  798 MET
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  920 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.128033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.113002 restraints weight = 13543.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.69
r_work: 0.3199 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.5644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   9058  Z= 0.209
  Angle     :  0.749   8.345  12571  Z= 0.349
  Chirality :  0.055   0.455   1459
  Planarity :  0.004   0.042   1316
  Dihedral  : 12.073 135.239   1893
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.26 %
    Favored  : 75.52 %
  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: -1.52 (0.28), residues: 852
  helix: -0.72 (0.24), residues: 494
  sheet: -3.14 (0.93), residues: 25
  loop : -1.05 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 279 
 TYR   0.016   0.002   TYR A 416 
 PHE   0.014   0.002   PHE A 916 
 TRP   0.013   0.002   TRP A 297 
 HIS   0.005   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00479 /  0.21 ( 9058)
  covalent geometry    : angle       0.74903 /  0.35 (12571)
  hydrogen bonds       : bond        0.03806 /  2.39 (  306)
  hydrogen bonds       : angle       3.89278 /  2.72 (  820)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7381 (mp0)
REVERT: A  205 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8641 (mmm)
REVERT: A  275 LYS cc_start: 0.7234 (tptt) cc_final: 0.6649 (ttpt)
REVERT: A  307 GLU cc_start: 0.6480 (tm-30) cc_final: 0.5938 (tm-30)
REVERT: A  397 ASP cc_start: 0.8062 (t0) cc_final: 0.7650 (t0)
REVERT: A  479 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8319 (tmmt)
REVERT: A  546 ASP cc_start: 0.7919 (t0) cc_final: 0.7672 (m-30)
REVERT: A  645 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7740 (m-80)
REVERT: A  682 GLU cc_start: 0.8383 (tp30) cc_final: 0.8181 (tp30)
REVERT: A  790 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8808 (mmtm)
REVERT: A  832 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7414 (mt)
REVERT: A  867 GLU cc_start: 0.7032 (mp0) cc_final: 0.6697 (mt-10)
  outliers start: 25
  outliers final: 20
  residues processed: 134
  average time/residue: 0.0972
  time to fit residues: 18.3009
Evaluate side-chains
  136 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  424 SER
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  598 SER
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  645 TYR
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  832 LEU
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  920 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0670
   chunk 48 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.6922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.135357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.120446 restraints weight = 13461.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.70
r_work: 0.3297 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.5840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9058  Z= 0.117
  Angle     :  0.677   8.359  12571  Z= 0.312
  Chirality :  0.050   0.411   1459
  Planarity :  0.003   0.041   1316
  Dihedral  : 11.998 133.728   1893
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.39 %
    Favored  : 75.26 %
  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 (0.29), residues: 852
  helix: -0.52 (0.24), residues: 495
  sheet: -3.19 (0.92), residues: 24
  loop : -0.92 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 138 
 TYR   0.016   0.001   TYR A 416 
 PHE   0.011   0.001   PHE A 848 
 TRP   0.007   0.001   TRP A 455 
 HIS   0.004   0.001   HIS A 879 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 9058)
  covalent geometry    : angle       0.67724 /  0.31 (12571)
  hydrogen bonds       : bond        0.03211 /  2.02 (  306)
  hydrogen bonds       : angle       3.69926 /  2.58 (  820)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1973.30 seconds
wall clock time: 34 minutes 48.25 seconds (2088.25 seconds total)