Starting phenix.real_space_refine
on Wed Mar  4 11:13:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pty_13643/03_2026/7pty_13643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pty_13643/03_2026/7pty_13643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pty_13643/03_2026/7pty_13643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pty_13643/03_2026/7pty_13643.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pty_13643/03_2026/7pty_13643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pty_13643/03_2026/7pty_13643.map"
  }
  resolution = 4.63
  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
-------------------------------------------------------------------------------
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=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    8522      2.51       5
     N    2267      2.21       5
     O    2611      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13433
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 850, 6663
          Classifications: {'peptide': 850}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 25, 'TRANS': 824}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 6770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 865, 6770
          Classifications: {'peptide': 865}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 26, 'TRANS': 838}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 22
  Time building chain proxies: 3.15, per 1000 atoms: 0.23
  Number of scatterers: 13433
  At special positions: 0
  Unit cell: (142.2, 102.6, 137.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    2611      8.00
     N    2267      7.00
     C    8522      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 721.8 milliseconds
  

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3260

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 2 sheets defined
      64.7% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 64
      removed outlier: 3.709A  pdb=" N   ILE A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 90
      Proline residue:  A  80  - end of helix
    Processing helix  chain 'A' and resid 94 through 98
    Processing helix  chain 'A' and resid 107 through 122
    Processing helix  chain 'A' and resid 131 through 160
      removed outlier: 3.679A  pdb=" N   THR A 148 " --> pdb=" O   THR A 144 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLU A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ASN A 155 " --> pdb=" O   GLU A 151 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU A 160 " --> pdb=" O   PHE A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 190
      removed outlier: 3.615A  pdb=" N   LYS A 190 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 215
      removed outlier: 3.903A  pdb=" N   GLU A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN A 204 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   GLY A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE A 207 " --> pdb=" O   GLU A 203 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 236
    Processing helix  chain 'A' and resid 247 through 281
      removed outlier: 3.905A  pdb=" N   GLN A 281 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 307
    Processing helix  chain 'A' and resid 312 through 326
      removed outlier: 3.722A  pdb=" N   ASN A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 353
      removed outlier: 4.082A  pdb=" N   LYS A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 432
      removed outlier: 3.956A  pdb=" N   VAL A 431 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ASP A 432 " --> pdb=" O   VAL A 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 428 through 432'
    Processing helix  chain 'A' and resid 461 through 475
      removed outlier: 4.588A  pdb=" N   ILE A 465 " --> pdb=" O   ASN A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 492
      removed outlier: 3.606A  pdb=" N   ILE A 489 " --> pdb=" O   ALA A 485 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLU A 490 " --> pdb=" O   THR A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 513
      removed outlier: 4.992A  pdb=" N   VAL A 509 " --> pdb=" O   ALA A 505 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA A 510 " --> pdb=" O   MET A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 523
      removed outlier: 4.094A  pdb=" N   LEU A 519 " --> pdb=" O   ASN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 548
      removed outlier: 3.550A  pdb=" N   ILE A 543 " --> pdb=" O   THR A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 558
    Processing helix  chain 'A' and resid 573 through 582
    Processing helix  chain 'A' and resid 583 through 593
      removed outlier: 3.526A  pdb=" N   VAL A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER A 593 " --> pdb=" O   ASN A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 616
      removed outlier: 3.503A  pdb=" N   THR A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 626
      removed outlier: 3.955A  pdb=" N   LEU A 623 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 649
    Processing helix  chain 'A' and resid 650 through 661
    Processing helix  chain 'A' and resid 673 through 682
      removed outlier: 3.590A  pdb=" N   PHE A 677 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 694
      removed outlier: 3.600A  pdb=" N   LYS A 694 " --> pdb=" O   LEU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 718
    Processing helix  chain 'A' and resid 719 through 728
    Processing helix  chain 'A' and resid 738 through 742
    Processing helix  chain 'A' and resid 743 through 752
    Processing helix  chain 'A' and resid 753 through 764
    Processing helix  chain 'A' and resid 776 through 783
      removed outlier: 3.839A  pdb=" N   ILE A 780 " --> pdb=" O   THR A 776 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   MET A 783 " --> pdb=" O   HIS A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 797
    Processing helix  chain 'A' and resid 809 through 818
      removed outlier: 3.519A  pdb=" N   GLY A 818 " --> pdb=" O   ALA A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 829
      removed outlier: 3.620A  pdb=" N   VAL A 823 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 851
    Processing helix  chain 'A' and resid 852 through 862
    Processing helix  chain 'A' and resid 875 through 883
    Processing helix  chain 'A' and resid 885 through 894
      removed outlier: 3.552A  pdb=" N   VAL A 889 " --> pdb=" O   ASP A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 907
    Processing helix  chain 'A' and resid 908 through 916
    Processing helix  chain 'A' and resid 922 through 927
      removed outlier: 4.118A  pdb=" N   PHE A 926 " --> pdb=" O   LEU A 922 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 65
      removed outlier: 3.542A  pdb=" N   GLY B  65 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 89
      Proline residue:  B  80  - end of helix
    Processing helix  chain 'B' and resid 108 through 122
      removed outlier: 3.786A  pdb=" N   ILE B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'B' and resid 132 through 159
      removed outlier: 4.001A  pdb=" N   THR B 144 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL B 145 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLU B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 167 through 190
      removed outlier: 3.949A  pdb=" N   ILE B 171 " --> pdb=" O   GLU B 167 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN B 187 " --> pdb=" O   GLU B 183 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ARG B 188 " --> pdb=" O   LYS B 184 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE B 189 " --> pdb=" O   GLU B 185 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   LYS B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 213
      removed outlier: 4.237A  pdb=" N   GLU B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLN B 204 " --> pdb=" O   LYS B 200 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS B 205 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLY B 206 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ILE B 207 " --> pdb=" O   GLU B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 236
      removed outlier: 4.036A  pdb=" N   ASP B 231 " --> pdb=" O   ASN B 227 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   TYR B 236 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 281
      removed outlier: 4.108A  pdb=" N   TYR B 252 " --> pdb=" O   PHE B 248 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA B 253 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 327
      removed outlier: 4.076A  pdb=" N   ASN B 289 " --> pdb=" O   ASP B 285 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA B 290 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 351
    Processing helix  chain 'B' and resid 352 through 355
      removed outlier: 4.315A  pdb=" N   ILE B 355 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 352 through 355'
    Processing helix  chain 'B' and resid 428 through 432
      removed outlier: 3.628A  pdb=" N   VAL B 431 " --> pdb=" O   LYS B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 474
    Processing helix  chain 'B' and resid 477 through 490
    Processing helix  chain 'B' and resid 503 through 513
      removed outlier: 3.516A  pdb=" N   HIS B 507 " --> pdb=" O   ARG B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 522
    Processing helix  chain 'B' and resid 525 through 532
      removed outlier: 3.712A  pdb=" N   LEU B 532 " --> pdb=" O   ILE B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 546
      removed outlier: 4.240A  pdb=" N   GLU B 546 " --> pdb=" O   HIS B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 559
      removed outlier: 4.053A  pdb=" N   HIS B 559 " --> pdb=" O   LEU B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 580
      removed outlier: 4.317A  pdb=" N   ARG B 580 " --> pdb=" O   HIS B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 593
      removed outlier: 3.819A  pdb=" N   ARG B 588 " --> pdb=" O   SER B 584 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   ASN B 589 " --> pdb=" O   LYS B 585 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LEU B 590 " --> pdb=" O   THR B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 613
    Processing helix  chain 'B' and resid 617 through 626
      removed outlier: 3.935A  pdb=" N   ASP B 621 " --> pdb=" O   TYR B 617 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ASN B 625 " --> pdb=" O   ASP B 621 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   HIS B 626 " --> pdb=" O   ALA B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 649
    Processing helix  chain 'B' and resid 650 through 661
    Processing helix  chain 'B' and resid 673 through 682
      removed outlier: 4.268A  pdb=" N   PHE B 677 " --> pdb=" O   ALA B 673 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ALA B 678 " --> pdb=" O   PRO B 674 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA B 679 " --> pdb=" O   ILE B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 694
      removed outlier: 3.772A  pdb=" N   LYS B 694 " --> pdb=" O   LEU B 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 701
      removed outlier: 3.935A  pdb=" N   ILE B 699 " --> pdb=" O   LYS B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 717
      removed outlier: 3.772A  pdb=" N   PHE B 713 " --> pdb=" O   THR B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 728
    Processing helix  chain 'B' and resid 743 through 752
    Processing helix  chain 'B' and resid 753 through 763
    Processing helix  chain 'B' and resid 776 through 784
    Processing helix  chain 'B' and resid 787 through 796
      removed outlier: 3.935A  pdb=" N   VAL B 791 " --> pdb=" O   PRO B 787 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 818
    Processing helix  chain 'B' and resid 819 through 829
    Processing helix  chain 'B' and resid 842 through 851
      removed outlier: 3.543A  pdb=" N   LEU B 846 " --> pdb=" O   THR B 842 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 852 through 862
    Processing helix  chain 'B' and resid 875 through 884
    Processing helix  chain 'B' and resid 885 through 895
      removed outlier: 4.160A  pdb=" N   GLU B 894 " --> pdb=" O   ARG B 890 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LYS B 895 " --> pdb=" O   LEU B 891 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 904 through 906
      No H-bonds generated for 'chain 'B' and resid 904 through 906'
    Processing helix  chain 'B' and resid 907 through 916
      removed outlier: 3.647A  pdb=" N   ILE B 911 " --> pdb=" O   GLY B 907 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 920 through 927
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 401
    Processing sheet with id=AA2, first strand: chain 'B' and resid 406 through 408
      removed outlier: 3.954A  pdb=" N   ARG B 438 " --> pdb=" O   MET B 455 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET B 455 " --> pdb=" O   ARG B 438 " (cutoff:3.500A)

    695 hydrogen bonds defined for protein.
    2052 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.12

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4459
        1.34 -     1.46: 2794
        1.46 -     1.58: 6331
        1.58 -     1.70: 0
        1.70 -     1.82: 63
  Bond restraints: 13647
  Sorted by residual:
  bond pdb=" CA  ARG A 215 "
       pdb=" C   ARG A 215 "
    ideal  model  delta    sigma   weight residual
    1.523  1.569 -0.045 1.34e-02 5.57e+03 1.15e+01
  bond pdb=" C   CYS B 424 "
       pdb=" N   PRO B 425 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 2.34e-02 1.83e+03 2.12e+00
  bond pdb=" CD  GLU B 828 "
       pdb=" OE1 GLU B 828 "
    ideal  model  delta    sigma   weight residual
    1.249  1.223  0.026 1.90e-02 2.77e+03 1.88e+00
  bond pdb=" CG  GLU B 828 "
       pdb=" CD  GLU B 828 "
    ideal  model  delta    sigma   weight residual
    1.516  1.487  0.029 2.50e-02 1.60e+03 1.33e+00
  bond pdb=" C   VAL A 214 "
       pdb=" N   ARG A 215 "
    ideal  model  delta    sigma   weight residual
    1.332  1.317  0.015 1.40e-02 5.10e+03 1.16e+00
  ... (remaining 13642 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 17816
        1.61 -     3.23: 501
        3.23 -     4.84: 101
        4.84 -     6.46: 26
        6.46 -     8.07: 3
  Bond angle restraints: 18447
  Sorted by residual:
  angle pdb=" N   GLY B 191 "
        pdb=" CA  GLY B 191 "
        pdb=" C   GLY B 191 "
      ideal   model   delta    sigma   weight residual
     112.50  117.59   -5.09 1.16e+00 7.43e-01 1.93e+01
  angle pdb=" N   GLU B 828 "
        pdb=" CA  GLU B 828 "
        pdb=" CB  GLU B 828 "
      ideal   model   delta    sigma   weight residual
     110.28  116.53   -6.25 1.55e+00 4.16e-01 1.63e+01
  angle pdb=" C   LEU B 827 "
        pdb=" N   GLU B 828 "
        pdb=" CA  GLU B 828 "
      ideal   model   delta    sigma   weight residual
     120.31  114.88    5.43 1.52e+00 4.33e-01 1.28e+01
  angle pdb=" N   VAL A  77 "
        pdb=" CA  VAL A  77 "
        pdb=" C   VAL A  77 "
      ideal   model   delta    sigma   weight residual
     112.96  109.51    3.45 1.00e+00 1.00e+00 1.19e+01
  angle pdb=" C   LEU A 469 "
        pdb=" N   TYR A 470 "
        pdb=" CA  TYR A 470 "
      ideal   model   delta    sigma   weight residual
     120.31  115.39    4.92 1.52e+00 4.33e-01 1.05e+01
  ... (remaining 18442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7559
       17.96 -    35.91: 683
       35.91 -    53.87: 84
       53.87 -    71.83: 11
       71.83 -    89.78: 10
  Dihedral angle restraints: 8347
    sinusoidal: 3333
      harmonic: 5014
  Sorted by residual:
  dihedral pdb=" CA  GLU A 164 "
           pdb=" C   GLU A 164 "
           pdb=" N   SER A 165 "
           pdb=" CA  SER A 165 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.06   29.94     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  PHE A 444 "
           pdb=" C   PHE A 444 "
           pdb=" N   ASN A 445 "
           pdb=" CA  ASN A 445 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.87  -28.13     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  PHE B 156 "
           pdb=" C   PHE B 156 "
           pdb=" N   LYS B 157 "
           pdb=" CA  LYS B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.22   27.78     0      5.00e+00 4.00e-02 3.09e+01
  ... (remaining 8344 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1577
       0.043 -    0.086: 480
       0.086 -    0.129: 78
       0.129 -    0.172: 8
       0.172 -    0.216: 2
  Chirality restraints: 2145
  Sorted by residual:
  chirality pdb=" CB  ILE B 366 "
            pdb=" CA  ILE B 366 "
            pdb=" CG1 ILE B 366 "
            pdb=" CG2 ILE B 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CG  LEU A 254 "
            pdb=" CB  LEU A 254 "
            pdb=" CD1 LEU A 254 "
            pdb=" CD2 LEU A 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.25e-01
  chirality pdb=" CA  GLU B 114 "
            pdb=" N   GLU B 114 "
            pdb=" C   GLU B 114 "
            pdb=" CB  GLU B 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.19e-01
  ... (remaining 2142 not shown)

  Planarity restraints: 2382
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 448 "    0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO B 449 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 216 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.78e+00
        pdb=" N   PRO A 217 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 415 "   -0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO A 416 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 416 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 416 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 2379 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1407
        2.74 -     3.28: 16436
        3.28 -     3.82: 23587
        3.82 -     4.36: 28241
        4.36 -     4.90: 42335
  Nonbonded interactions: 112006
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 511 "
            pdb=" NE2 GLN B 549 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   GLU B 725 "
            pdb=" NE2 GLN B 729 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   PHE B 462 "
            pdb=" ND1 HIS B 466 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" OG  SER B 135 "
            pdb=" OG  SER B 273 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" NE2 HIS B 779 "
            pdb=" O   LEU B 808 "
     model   vdw
     2.219 3.120
  ... (remaining 112001 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 50 through 195 or (resid 196 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 197 through 578 or (resid 579 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 580 through 616 or (resid 6 \ 
17 and (name N or name CA or name C or name O or name CB )) or resid 618 through \ 
 928))
  selection = (chain 'B' and (resid 50 through 90 or resid 93 through 98 or resid 106 through  \ 
214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 216 through 219 or (resid 220 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 221 through 236 or resid 246 through 355 or resid 367 throug \ 
h 928))
}

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 group one per residue
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:             4.570
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.540
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13647  Z= 0.166
  Angle     :  0.681   8.072  18447  Z= 0.376
  Chirality :  0.041   0.216   2145
  Planarity :  0.005   0.060   2382
  Dihedral  : 13.762  89.785   5087
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 25.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.89 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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 (0.20), residues: 1699
  helix:  0.31 (0.17), residues: 971
  sheet: -3.98 (0.58), residues: 54
  loop : -2.57 (0.23), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 588 
 TYR   0.020   0.002   TYR A 716 
 PHE   0.033   0.002   PHE A 499 
 TRP   0.029   0.003   TRP A 389 
 HIS   0.004   0.001   HIS A 466 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (13647)
  covalent geometry    : angle       0.68056 (18447)
  hydrogen bonds       : bond        0.12899 (  695)
  hydrogen bonds       : angle       6.34213 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  424 CYS cc_start: 0.8001 (m) cc_final: 0.7772 (m)
REVERT: A  686 MET cc_start: 0.8863 (mmp) cc_final: 0.8549 (mmm)
REVERT: B  686 MET cc_start: 0.9148 (mpp) cc_final: 0.8614 (mpp)
REVERT: B  888 MET cc_start: 0.8923 (mtt) cc_final: 0.8367 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0934
  time to fit residues: 10.0895
Evaluate side-chains
  55 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 234 ASN
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 536 ASN
** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.044322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.036204 restraints weight = 171766.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.037021 restraints weight = 126224.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.037626 restraints weight = 100644.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.038087 restraints weight = 84346.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.038443 restraints weight = 73395.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13647  Z= 0.133
  Angle     :  0.598   6.515  18447  Z= 0.325
  Chirality :  0.040   0.227   2145
  Planarity :  0.004   0.056   2382
  Dihedral  :  5.823  27.603   1804
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.96 %
    Favored  : 93.84 %
  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 (0.20), residues: 1699
  helix:  0.41 (0.16), residues: 1001
  sheet: -3.93 (0.59), residues: 54
  loop : -2.61 (0.23), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 784 
 TYR   0.021   0.002   TYR B 261 
 PHE   0.025   0.001   PHE B 156 
 TRP   0.017   0.002   TRP A 389 
 HIS   0.004   0.001   HIS B 466 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13647)
  covalent geometry    : angle       0.59832 (18447)
  hydrogen bonds       : bond        0.04510 (  695)
  hydrogen bonds       : angle       5.27187 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ASN cc_start: 0.9326 (m110) cc_final: 0.9119 (m-40)
REVERT: A  686 MET cc_start: 0.9142 (mmp) cc_final: 0.8898 (mmm)
REVERT: B  455 MET cc_start: 0.8221 (pmm) cc_final: 0.8010 (pmm)
REVERT: B  869 TYR cc_start: 0.8566 (p90) cc_final: 0.8042 (p90)
REVERT: B  888 MET cc_start: 0.9053 (mtt) cc_final: 0.8359 (mtp)
REVERT: B  912 MET cc_start: 0.9617 (tpt) cc_final: 0.9388 (tpt)
  outliers start: 3
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0929
  time to fit residues: 10.2809
Evaluate side-chains
  55 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 142 optimal weight:    8.9990
   chunk 52 optimal weight:    0.5980
   chunk 111 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 85 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 169 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   chunk 24 optimal weight:   20.0000
   chunk 167 optimal weight:    6.9990
   chunk 165 optimal weight:   10.0000
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
A 388 ASN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN
** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.043395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.035364 restraints weight = 172808.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.036153 restraints weight = 128707.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.036727 restraints weight = 103327.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.037146 restraints weight = 87240.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.037480 restraints weight = 76608.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13647  Z= 0.173
  Angle     :  0.629   6.351  18447  Z= 0.342
  Chirality :  0.041   0.196   2145
  Planarity :  0.005   0.080   2382
  Dihedral  :  5.904  27.215   1804
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 19.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.69 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.20), residues: 1699
  helix:  0.39 (0.16), residues: 989
  sheet: -4.19 (0.58), residues: 55
  loop : -2.52 (0.23), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 430 
 TYR   0.017   0.002   TYR A 407 
 PHE   0.029   0.002   PHE B 156 
 TRP   0.006   0.001   TRP A 389 
 HIS   0.004   0.001   HIS B 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (13647)
  covalent geometry    : angle       0.62914 (18447)
  hydrogen bonds       : bond        0.04472 (  695)
  hydrogen bonds       : angle       5.30335 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ASN cc_start: 0.9343 (m110) cc_final: 0.9117 (m-40)
REVERT: A  686 MET cc_start: 0.9168 (mmp) cc_final: 0.8899 (mmm)
REVERT: B  455 MET cc_start: 0.8211 (pmm) cc_final: 0.7958 (pmm)
REVERT: B  869 TYR cc_start: 0.8688 (p90) cc_final: 0.8078 (p90)
REVERT: B  888 MET cc_start: 0.9084 (mtt) cc_final: 0.8366 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0938
  time to fit residues: 9.9843
Evaluate side-chains
  54 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 148 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0020
   chunk 55 optimal weight:    0.3980
   chunk 58 optimal weight:    4.9990
   chunk 121 optimal weight:    8.9990
   chunk 122 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 151 optimal weight:    5.9990
   overall best weight:    1.4392

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

Flipped N/Q/H residues before XYZ refinement:
A 450 GLN
A 526 GLN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN
** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.044657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.036444 restraints weight = 171418.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.037286 restraints weight = 126365.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.037923 restraints weight = 100311.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.038407 restraints weight = 83628.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.038758 restraints weight = 72416.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13647  Z= 0.129
  Angle     :  0.594   6.275  18447  Z= 0.319
  Chirality :  0.040   0.227   2145
  Planarity :  0.005   0.075   2382
  Dihedral  :  5.741  27.453   1804
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.13 %
    Favored  : 95.73 %
  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: -1.17 (0.20), residues: 1699
  helix:  0.53 (0.16), residues: 991
  sheet: -3.82 (0.64), residues: 48
  loop : -2.62 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 512 
 TYR   0.022   0.002   TYR B 261 
 PHE   0.023   0.001   PHE B 156 
 TRP   0.015   0.002   TRP B 413 
 HIS   0.004   0.001   HIS A 878 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (13647)
  covalent geometry    : angle       0.59380 (18447)
  hydrogen bonds       : bond        0.04154 (  695)
  hydrogen bonds       : angle       5.10300 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ASN cc_start: 0.9343 (m110) cc_final: 0.9139 (m-40)
REVERT: A  686 MET cc_start: 0.9147 (mmp) cc_final: 0.8883 (mmm)
REVERT: B  455 MET cc_start: 0.8006 (pmm) cc_final: 0.7741 (pmm)
REVERT: B  869 TYR cc_start: 0.8607 (p90) cc_final: 0.7860 (p90)
REVERT: B  888 MET cc_start: 0.8968 (mtt) cc_final: 0.8197 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0835
  time to fit residues: 9.7795
Evaluate side-chains
  54 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 163 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0470
   chunk 124 optimal weight:    0.4980
   chunk 119 optimal weight:    6.9990
   chunk 126 optimal weight:    0.9980
   chunk 165 optimal weight:    0.2980
   chunk 162 optimal weight:    5.9990
   chunk 111 optimal weight:    5.9990
   chunk 140 optimal weight:    6.9990
   overall best weight:    0.9680

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.045270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.036946 restraints weight = 171042.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.037818 restraints weight = 126007.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.038460 restraints weight = 99994.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.038946 restraints weight = 83563.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.039323 restraints weight = 72541.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13647  Z= 0.119
  Angle     :  0.588   6.418  18447  Z= 0.313
  Chirality :  0.039   0.218   2145
  Planarity :  0.004   0.057   2382
  Dihedral  :  5.564  26.896   1804
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.84 %
    Favored  : 97.02 %
  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: -1.06 (0.20), residues: 1699
  helix:  0.63 (0.16), residues: 991
  sheet: -3.83 (0.64), residues: 48
  loop : -2.62 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 430 
 TYR   0.025   0.002   TYR B 261 
 PHE   0.025   0.001   PHE B 462 
 TRP   0.007   0.001   TRP B 413 
 HIS   0.003   0.001   HIS B 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (13647)
  covalent geometry    : angle       0.58797 (18447)
  hydrogen bonds       : bond        0.04026 (  695)
  hydrogen bonds       : angle       4.94349 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ASN cc_start: 0.9350 (m110) cc_final: 0.9132 (m-40)
REVERT: A  686 MET cc_start: 0.9149 (mmp) cc_final: 0.8866 (mmm)
REVERT: B  265 MET cc_start: 0.8539 (mtt) cc_final: 0.8325 (mtp)
REVERT: B  618 MET cc_start: 0.7892 (mmp) cc_final: 0.7605 (mmp)
REVERT: B  869 TYR cc_start: 0.8495 (p90) cc_final: 0.7766 (p90)
REVERT: B  888 MET cc_start: 0.8963 (mtt) cc_final: 0.8126 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 71
  average time/residue: 0.0905
  time to fit residues: 10.7492
Evaluate side-chains
  53 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 154 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0000
   chunk 98 optimal weight:    4.9990
   chunk 121 optimal weight:    5.9990
   chunk 165 optimal weight:    0.2980
   chunk 131 optimal weight:    0.8980
   chunk 148 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 142 optimal weight:    0.8980
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 294 ASN
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.045816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.037850 restraints weight = 174401.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.038726 restraints weight = 127866.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.039376 restraints weight = 100837.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.039858 restraints weight = 83804.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.040247 restraints weight = 72389.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13647  Z= 0.118
  Angle     :  0.593   9.381  18447  Z= 0.313
  Chirality :  0.040   0.229   2145
  Planarity :  0.004   0.061   2382
  Dihedral  :  5.404  26.287   1804
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  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: -0.89 (0.20), residues: 1699
  helix:  0.79 (0.16), residues: 984
  sheet: -3.85 (0.63), residues: 48
  loop : -2.52 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 430 
 TYR   0.019   0.001   TYR B 261 
 PHE   0.022   0.001   PHE B 156 
 TRP   0.007   0.001   TRP B 413 
 HIS   0.007   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (13647)
  covalent geometry    : angle       0.59258 (18447)
  hydrogen bonds       : bond        0.03862 (  695)
  hydrogen bonds       : angle       4.86346 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ASN cc_start: 0.9398 (m110) cc_final: 0.9177 (m-40)
REVERT: A  686 MET cc_start: 0.9079 (mmp) cc_final: 0.8795 (mmm)
REVERT: B  869 TYR cc_start: 0.8406 (p90) cc_final: 0.7730 (p90)
REVERT: B  888 MET cc_start: 0.8941 (mtt) cc_final: 0.8075 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0898
  time to fit residues: 10.9739
Evaluate side-chains
  53 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 153 optimal weight:    0.7980
   chunk 10 optimal weight:    7.9990
   chunk 115 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 126 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0040
   overall best weight:    1.3194

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.045763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.037840 restraints weight = 173773.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.038721 restraints weight = 127356.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.039360 restraints weight = 100483.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.039852 restraints weight = 83509.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.040233 restraints weight = 72057.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13647  Z= 0.122
  Angle     :  0.590   7.641  18447  Z= 0.315
  Chirality :  0.040   0.209   2145
  Planarity :  0.004   0.052   2382
  Dihedral  :  5.383  26.401   1804
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  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: -0.84 (0.20), residues: 1699
  helix:  0.84 (0.16), residues: 982
  sheet: -3.86 (0.62), residues: 48
  loop : -2.51 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 908 
 TYR   0.032   0.002   TYR B 261 
 PHE   0.022   0.001   PHE B 156 
 TRP   0.005   0.001   TRP A 413 
 HIS   0.005   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13647)
  covalent geometry    : angle       0.59044 (18447)
  hydrogen bonds       : bond        0.03884 (  695)
  hydrogen bonds       : angle       4.88306 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ASN cc_start: 0.9392 (m110) cc_final: 0.9185 (m-40)
REVERT: A  686 MET cc_start: 0.9096 (mmp) cc_final: 0.8790 (mmm)
REVERT: B  869 TYR cc_start: 0.8438 (p90) cc_final: 0.7735 (p90)
REVERT: B  888 MET cc_start: 0.8977 (mtt) cc_final: 0.8098 (mtp)
REVERT: B  912 MET cc_start: 0.9566 (mmp) cc_final: 0.9267 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1090
  time to fit residues: 13.0517
Evaluate side-chains
  54 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 162 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 138 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 160 optimal weight:    3.9990
   chunk 158 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9990
   chunk 156 optimal weight:    7.9990
   chunk 155 optimal weight:    3.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 861 ASN
B 249 GLN
B 332 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.046325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.038225 restraints weight = 171879.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.039113 restraints weight = 125982.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.039774 restraints weight = 99246.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.040268 restraints weight = 82412.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.040641 restraints weight = 71136.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13647  Z= 0.119
  Angle     :  0.601   7.264  18447  Z= 0.319
  Chirality :  0.040   0.229   2145
  Planarity :  0.004   0.056   2382
  Dihedral  :  5.281  26.135   1804
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -0.84 (0.20), residues: 1699
  helix:  0.82 (0.16), residues: 994
  sheet: -3.97 (0.59), residues: 50
  loop : -2.52 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 430 
 TYR   0.026   0.002   TYR B 261 
 PHE   0.022   0.001   PHE B 156 
 TRP   0.004   0.001   TRP A 413 
 HIS   0.004   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (13647)
  covalent geometry    : angle       0.60086 (18447)
  hydrogen bonds       : bond        0.03850 (  695)
  hydrogen bonds       : angle       4.87186 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  686 MET cc_start: 0.9085 (mmp) cc_final: 0.8785 (mmm)
REVERT: B  265 MET cc_start: 0.8482 (mtt) cc_final: 0.8228 (mtp)
REVERT: B  869 TYR cc_start: 0.8351 (p90) cc_final: 0.7664 (p90)
REVERT: B  888 MET cc_start: 0.8943 (mtt) cc_final: 0.8063 (mtp)
REVERT: B  912 MET cc_start: 0.9566 (mmp) cc_final: 0.9215 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0983
  time to fit residues: 12.0830
Evaluate side-chains
  55 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 170 optimal weight:    8.9990
   chunk 150 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 126 optimal weight:   10.0000
   chunk 137 optimal weight:    4.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 526 GLN
A 861 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.044418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.036570 restraints weight = 179328.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.037431 restraints weight = 130663.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.038064 restraints weight = 102630.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.038544 restraints weight = 85118.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.038912 restraints weight = 73443.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13647  Z= 0.180
  Angle     :  0.656   7.270  18447  Z= 0.355
  Chirality :  0.041   0.199   2145
  Planarity :  0.005   0.054   2382
  Dihedral  :  5.550  26.378   1804
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  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: -0.98 (0.20), residues: 1699
  helix:  0.70 (0.16), residues: 981
  sheet: -4.15 (0.58), residues: 50
  loop : -2.49 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 438 
 TYR   0.021   0.002   TYR B 261 
 PHE   0.026   0.002   PHE B 156 
 TRP   0.015   0.002   TRP A 389 
 HIS   0.004   0.001   HIS B 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (13647)
  covalent geometry    : angle       0.65607 (18447)
  hydrogen bonds       : bond        0.04135 (  695)
  hydrogen bonds       : angle       5.11626 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 GLU cc_start: 0.9115 (mp0) cc_final: 0.8748 (mp0)
REVERT: A  686 MET cc_start: 0.9164 (mmp) cc_final: 0.8870 (mmm)
REVERT: B  265 MET cc_start: 0.8595 (mtt) cc_final: 0.8392 (mtp)
REVERT: B  869 TYR cc_start: 0.8584 (p90) cc_final: 0.7829 (p90)
REVERT: B  888 MET cc_start: 0.8980 (mtt) cc_final: 0.8117 (mtp)
REVERT: B  912 MET cc_start: 0.9624 (mmp) cc_final: 0.9254 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0942
  time to fit residues: 10.6372
Evaluate side-chains
  52 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 165 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0370
   chunk 114 optimal weight:    0.7980
   chunk 140 optimal weight:    7.9990
   chunk 128 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.9664

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.044977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.037076 restraints weight = 176740.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.037942 restraints weight = 128753.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.038589 restraints weight = 101084.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.039069 restraints weight = 83827.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.039439 restraints weight = 72428.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13647  Z= 0.140
  Angle     :  0.625   8.099  18447  Z= 0.334
  Chirality :  0.041   0.226   2145
  Planarity :  0.004   0.055   2382
  Dihedral  :  5.503  26.418   1804
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.20), residues: 1699
  helix:  0.71 (0.16), residues: 982
  sheet: -4.09 (0.58), residues: 50
  loop : -2.48 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 430 
 TYR   0.022   0.002   TYR B 261 
 PHE   0.023   0.002   PHE B 156 
 TRP   0.006   0.001   TRP A 708 
 HIS   0.006   0.001   HIS B 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (13647)
  covalent geometry    : angle       0.62494 (18447)
  hydrogen bonds       : bond        0.04023 (  695)
  hydrogen bonds       : angle       5.05708 ( 2052)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 GLU cc_start: 0.9119 (mp0) cc_final: 0.8809 (mp0)
REVERT: A  686 MET cc_start: 0.9104 (mmp) cc_final: 0.8813 (mmm)
REVERT: B  265 MET cc_start: 0.8531 (mtt) cc_final: 0.8293 (mtp)
REVERT: B  869 TYR cc_start: 0.8420 (p90) cc_final: 0.7722 (p90)
REVERT: B  888 MET cc_start: 0.8868 (mtt) cc_final: 0.7941 (mtp)
REVERT: B  912 MET cc_start: 0.9599 (mmp) cc_final: 0.9220 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0947
  time to fit residues: 10.4548
Evaluate side-chains
  55 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 156 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 140 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.043763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.035634 restraints weight = 171848.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.036418 restraints weight = 127592.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.036999 restraints weight = 102397.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.037432 restraints weight = 86385.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.037761 restraints weight = 75766.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13647  Z= 0.178
  Angle     :  0.661   8.265  18447  Z= 0.357
  Chirality :  0.041   0.192   2145
  Planarity :  0.005   0.053   2382
  Dihedral  :  5.726  28.192   1804
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 20.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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: -1.16 (0.20), residues: 1699
  helix:  0.51 (0.16), residues: 983
  sheet: -4.18 (0.59), residues: 45
  loop : -2.53 (0.22), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 430 
 TYR   0.024   0.003   TYR B 256 
 PHE   0.025   0.002   PHE B 156 
 TRP   0.012   0.002   TRP A 389 
 HIS   0.004   0.001   HIS B 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (13647)
  covalent geometry    : angle       0.66056 (18447)
  hydrogen bonds       : bond        0.04237 (  695)
  hydrogen bonds       : angle       5.23334 ( 2052)

===============================================================================
Job complete
usr+sys time: 1962.39 seconds
wall clock time: 35 minutes 6.31 seconds (2106.31 seconds total)