Starting phenix.real_space_refine
on Fri Aug  7 03:28:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hm5_52286/08_2026/9hm5_52286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hm5_52286/08_2026/9hm5_52286.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hm5_52286/08_2026/9hm5_52286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hm5_52286/08_2026/9hm5_52286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hm5_52286/08_2026/9hm5_52286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hm5_52286/08_2026/9hm5_52286.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 7
    Type Number    sf(0)   Gaussians
     P      85      5.49       5
     Mg      2      5.21       5
     S      20      5.16       5
     C    5809      2.51       5
     N    1656      2.21       5
     O    2073      1.98       5
     H    8834      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 18479
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 15760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 958, 15760
          Classifications: {'peptide': 958}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 938}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 1504
          Classifications: {'RNA': 47}
          Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 22, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 3, 'rna3p': 43}
    Chain: "C"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 1085
          Classifications: {'RNA': 34}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 17}
          Link IDs: {'rna2p': 4, 'rna3p': 29}
    Chain: "D"
      Number of atoms: 128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 128
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 1, 'rna3p': 2}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.36, per 1000 atoms: 0.18
  Number of scatterers: 18479
  At special positions: 0
  Unit cell: (99.19, 110.11, 128.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      20     16.00
     P      85     15.00
     Mg      2     11.99
     O    2073      8.00
     N    1656      7.00
     C    5809      6.00
     H    8834      1.00
    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: 1.84
  Conformation dependent library (CDL) restraints added in 456.3 milliseconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1832

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 9 sheets defined
      50.7% alpha, 13.2% beta
      32 base pairs and 51 stacking pairs defined.
    Time for finding SS restraints: 2.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 228 through 240
      removed outlier: 3.630A  pdb=" N   GLU A 236 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   SER A 237 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 250
      removed outlier: 3.558A  pdb=" N   LYS A 248 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   THR A 250 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 270
      removed outlier: 3.736A  pdb=" N   GLU A 269 " --> pdb=" O   ASP A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 314
      removed outlier: 3.559A  pdb=" N   GLN A 303 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER A 308 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASP A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLY A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 322
    Processing helix  chain 'A' and resid 332 through 355
      removed outlier: 3.789A  pdb=" N   LYS A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A 351 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLN A 355 " --> pdb=" O   VAL A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 370
      removed outlier: 3.604A  pdb=" N   LYS A 363 " --> pdb=" O   ASP A 359 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 365 " --> pdb=" O   GLN A 361 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A 366 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A 367 " --> pdb=" O   LYS A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 384
      removed outlier: 3.546A  pdb=" N   GLN A 375 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   PHE A 384 " --> pdb=" O   MET A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 418
      removed outlier: 3.766A  pdb=" N   ILE A 404 " --> pdb=" O   GLU A 400 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 408 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ARG A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   THR A 416 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   SER A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 453
      removed outlier: 4.272A  pdb=" N   ALA A 445 " --> pdb=" O   ARG A 441 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   SER A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   SER A 453 " --> pdb=" O   GLN A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 481
      removed outlier: 3.621A  pdb=" N   GLN A 476 " --> pdb=" O   TYR A 472 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LYS A 477 " --> pdb=" O   ARG A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 509 through 514
      removed outlier: 3.544A  pdb=" N   PHE A 513 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 530
    Processing helix  chain 'A' and resid 532 through 537
      removed outlier: 3.594A  pdb=" N   VAL A 536 " --> pdb=" O   TYR A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 548
    Processing helix  chain 'A' and resid 555 through 568
    Processing helix  chain 'A' and resid 579 through 586
      removed outlier: 3.634A  pdb=" N   LEU A 583 " --> pdb=" O   GLU A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 599
    Processing helix  chain 'A' and resid 607 through 617
      removed outlier: 3.939A  pdb=" N   TRP A 613 " --> pdb=" O   HIS A 609 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   TRP A 617 " --> pdb=" O   TRP A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 624
    Processing helix  chain 'A' and resid 642 through 649
      removed outlier: 4.097A  pdb=" N   LYS A 648 " --> pdb=" O   SER A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 697
      removed outlier: 3.983A  pdb=" N   LYS A 690 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER A 691 " --> pdb=" O   ASP A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 700
      No H-bonds generated for 'chain 'A' and resid 698 through 700'
    Processing helix  chain 'A' and resid 725 through 729
    Processing helix  chain 'A' and resid 732 through 742
      removed outlier: 3.521A  pdb=" N   ALA A 738 " --> pdb=" O   LYS A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 747
      removed outlier: 3.603A  pdb=" N   TYR A 746 " --> pdb=" O   LYS A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 774 through 779
      removed outlier: 3.839A  pdb=" N   LYS A 779 " --> pdb=" O   SER A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 787
    Processing helix  chain 'A' and resid 790 through 801
    Processing helix  chain 'A' and resid 827 through 846
      removed outlier: 3.604A  pdb=" N   LEU A 831 " --> pdb=" O   ASP A 827 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ALA A 839 " --> pdb=" O   TRP A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 878
    Processing helix  chain 'A' and resid 889 through 900
      removed outlier: 3.987A  pdb=" N   LYS A 893 " --> pdb=" O   ASP A 889 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A 895 " --> pdb=" O   LYS A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 914
    Processing helix  chain 'A' and resid 968 through 970
      No H-bonds generated for 'chain 'A' and resid 968 through 970'
    Processing helix  chain 'A' and resid 971 through 977
      removed outlier: 3.796A  pdb=" N   LEU A 975 " --> pdb=" O   GLU A 971 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ASP A 977 " --> pdb=" O   LYS A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1024
      removed outlier: 4.266A  pdb=" N   LEU A1004 " --> pdb=" O   THR A1000 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   VAL A1005 " --> pdb=" O   LYS A1001 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLY A1010 " --> pdb=" O   ALA A1006 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A1011 " --> pdb=" O   ASN A1007 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ARG A1022 " --> pdb=" O   HIS A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1046
      removed outlier: 3.718A  pdb=" N   GLU A1040 " --> pdb=" O   THR A1036 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP A1041 " --> pdb=" O   GLY A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1050 through 1064
      removed outlier: 4.481A  pdb=" N   ASN A1064 " --> pdb=" O   GLN A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1078
      removed outlier: 3.861A  pdb=" N   VAL A1077 " --> pdb=" O   SER A1073 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG A1078 " --> pdb=" O   LEU A1074 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1073 through 1078'
    Processing helix  chain 'A' and resid 1128 through 1132
      removed outlier: 4.386A  pdb=" N   ARG A1131 " --> pdb=" O   ASN A1128 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE A1132 " --> pdb=" O   SER A1129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1128 through 1132'
    Processing helix  chain 'A' and resid 1135 through 1137
      No H-bonds generated for 'chain 'A' and resid 1135 through 1137'
    Processing helix  chain 'A' and resid 1138 through 1157
    Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464
      removed outlier: 3.910A  pdb=" N   LEU A 428 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   HIS A 434 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE A 593 " --> pdb=" O   HIS A 434 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ILE A 590 " --> pdb=" O   GLN A  17 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   TYR A 664 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   THR A 669 " --> pdb=" O   GLU A 633 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   GLU A 633 " --> pdb=" O   THR A 669 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   SER A 671 " --> pdb=" O   ASN A 631 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ASN A 631 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA A 212 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   TYR A 638 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   TYR A 423 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A 215 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ALA A 425 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 277
    Processing sheet with id=AA3, first strand: chain 'A' and resid 467 through 468
    Processing sheet with id=AA4, first strand: chain 'A' and resid 720 through 724
      removed outlier: 7.073A  pdb=" N   PHE A 707 " --> pdb=" O   LEU A1028 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ILE A1030 " --> pdb=" O   PHE A 707 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   PHE A 709 " --> pdb=" O   ILE A1030 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   GLU A1032 " --> pdb=" O   PHE A 709 " (cutoff:3.500A)
      removed outlier: 8.799A  pdb=" N   ILE A 711 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   GLY A1096 " --> pdb=" O   GLY A1027 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE A1029 " --> pdb=" O   GLY A1096 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE A1098 " --> pdb=" O   ILE A1029 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   LYS A1031 " --> pdb=" O   ILE A1098 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 748 through 753
    Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 761
    Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 818
    Processing sheet with id=AA8, first strand: chain 'A' and resid 857 through 861
      removed outlier: 6.483A  pdb=" N   ALA A 936 " --> pdb=" O   HIS A 955 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   HIS A 955 " --> pdb=" O   ALA A 936 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   CYS A 938 " --> pdb=" O   VAL A 953 " (cutoff:3.500A)
      removed outlier: 5.766A  pdb=" N   VAL A 953 " --> pdb=" O   CYS A 938 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1106 through 1107
      removed outlier: 3.797A  pdb=" N   CYS A1107 " --> pdb=" O   ILE A1111 " (cutoff:3.500A)

    334 hydrogen bonds defined for protein.
    921 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      81 hydrogen bonds
      162 hydrogen bond angles
      0 basepair planarities
      32 basepair parallelities
      51 stacking parallelities
  Total time for adding SS restraints: 4.63

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8516
        1.03 -     1.23: 347
        1.23 -     1.42: 4348
        1.42 -     1.61: 5582
        1.61 -     1.81: 31
  Bond restraints: 18824
  Sorted by residual:
  bond pdb=" C6    A B  55 "
       pdb=" N6    A B  55 "
    ideal  model  delta    sigma   weight residual
    1.335  1.231  0.104 8.00e-03 1.56e+04 1.71e+02
  bond pdb=" C6    A B  56 "
       pdb=" N6    A B  56 "
    ideal  model  delta    sigma   weight residual
    1.335  1.232  0.103 8.00e-03 1.56e+04 1.67e+02
  bond pdb=" CG  PRO A 210 "
       pdb=" CD  PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.503  1.099  0.404 3.40e-02 8.65e+02 1.41e+02
  bond pdb=" C5'   U C  17 "
       pdb=" C4'   U C  17 "
    ideal  model  delta    sigma   weight residual
    1.508  1.435  0.073 7.00e-03 2.04e+04 1.08e+02
  bond pdb=" C5'   U C  16 "
       pdb=" C4'   U C  16 "
    ideal  model  delta    sigma   weight residual
    1.508  1.439  0.069 7.00e-03 2.04e+04 9.79e+01
  ... (remaining 18819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.77: 33655
        3.77 -     7.54: 302
        7.54 -    11.32: 43
       11.32 -    15.09: 3
       15.09 -    18.86: 2
  Bond angle restraints: 34005
  Sorted by residual:
  angle pdb=" N   PRO A 210 "
        pdb=" CD  PRO A 210 "
        pdb=" CG  PRO A 210 "
      ideal   model   delta    sigma   weight residual
     103.20   84.34   18.86 1.50e+00 4.44e-01 1.58e+02
  angle pdb=" N1    A B  55 "
        pdb=" C2    A B  55 "
        pdb=" N3    A B  55 "
      ideal   model   delta    sigma   weight residual
     129.30  135.29   -5.99 5.00e-01 4.00e+00 1.44e+02
  angle pdb=" N1    A B  56 "
        pdb=" C2    A B  56 "
        pdb=" N3    A B  56 "
      ideal   model   delta    sigma   weight residual
     129.30  135.06   -5.76 5.00e-01 4.00e+00 1.33e+02
  angle pdb=" CA  PRO A 210 "
        pdb=" N   PRO A 210 "
        pdb=" CD  PRO A 210 "
      ideal   model   delta    sigma   weight residual
     112.00   95.94   16.06 1.40e+00 5.10e-01 1.32e+02
  angle pdb=" N9    A B  55 "
        pdb=" C8    A B  55 "
        pdb=" N7    A B  55 "
      ideal   model   delta    sigma   weight residual
     113.80  119.39   -5.59 5.00e-01 4.00e+00 1.25e+02
  ... (remaining 34000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.62: 8504
       35.62 -    71.24: 340
       71.24 -   106.86: 35
      106.86 -   142.49: 1
      142.49 -   178.11: 1
  Dihedral angle restraints: 8881
    sinusoidal: 5538
      harmonic: 3343
  Sorted by residual:
  dihedral pdb=" C4'   C D  75 "
           pdb=" C3'   C D  75 "
           pdb=" C2'   C D  75 "
           pdb=" C1'   C D  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.20  -70.20     1      8.00e+00 1.56e-02 9.92e+01
  dihedral pdb=" C5'   C D  75 "
           pdb=" C4'   C D  75 "
           pdb=" C3'   C D  75 "
           pdb=" O3'   C D  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   79.60   67.40     1      8.00e+00 1.56e-02 9.24e+01
  dihedral pdb=" O4'   C D  75 "
           pdb=" C2'   C D  75 "
           pdb=" C1'   C D  75 "
           pdb=" C3'   C D  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   24.13  -59.13     1      8.00e+00 1.56e-02 7.30e+01
  ... (remaining 8878 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.147: 1532
       0.147 -    0.295: 26
       0.295 -    0.442: 13
       0.442 -    0.590: 20
       0.590 -    0.737: 5
  Chirality restraints: 1596
  Sorted by residual:
  chirality pdb=" CG  LEU A 365 "
            pdb=" CB  LEU A 365 "
            pdb=" CD1 LEU A 365 "
            pdb=" CD2 LEU A 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.36e+01
  chirality pdb=" CG  LEU A 346 "
            pdb=" CB  LEU A 346 "
            pdb=" CD1 LEU A 346 "
            pdb=" CD2 LEU A 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.86   -0.73 2.00e-01 2.50e+01 1.35e+01
  chirality pdb=" CB  ILE A 353 "
            pdb=" CA  ILE A 353 "
            pdb=" CG1 ILE A 353 "
            pdb=" CG2 ILE A 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.96    0.69 2.00e-01 2.50e+01 1.18e+01
  ... (remaining 1593 not shown)

  Planarity restraints: 2457
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  10 "    0.230 2.00e-02 2.50e+03   8.70e-02 2.46e+02
        pdb=" N9    A C  10 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    A C  10 "   -0.066 2.00e-02 2.50e+03
        pdb=" N7    A C  10 "   -0.033 2.00e-02 2.50e+03
        pdb=" C5    A C  10 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    A C  10 "    0.042 2.00e-02 2.50e+03
        pdb=" N6    A C  10 "    0.123 2.00e-02 2.50e+03
        pdb=" N1    A C  10 "    0.022 2.00e-02 2.50e+03
        pdb=" C2    A C  10 "   -0.045 2.00e-02 2.50e+03
        pdb=" N3    A C  10 "   -0.067 2.00e-02 2.50e+03
        pdb=" C4    A C  10 "   -0.038 2.00e-02 2.50e+03
        pdb=" H8    A C  10 "   -0.103 2.00e-02 2.50e+03
        pdb=" H2    A C  10 "   -0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  59 "    0.202 2.00e-02 2.50e+03   7.75e-02 1.80e+02
        pdb=" N1    U B  59 "   -0.031 2.00e-02 2.50e+03
        pdb=" C2    U B  59 "   -0.065 2.00e-02 2.50e+03
        pdb=" O2    U B  59 "   -0.106 2.00e-02 2.50e+03
        pdb=" N3    U B  59 "   -0.014 2.00e-02 2.50e+03
        pdb=" C4    U B  59 "    0.020 2.00e-02 2.50e+03
        pdb=" O4    U B  59 "    0.081 2.00e-02 2.50e+03
        pdb=" C5    U B  59 "   -0.017 2.00e-02 2.50e+03
        pdb=" C6    U B  59 "   -0.041 2.00e-02 2.50e+03
        pdb=" H5    U B  59 "   -0.016 2.00e-02 2.50e+03
        pdb=" H3    U B  59 "    0.045 2.00e-02 2.50e+03
        pdb=" H6    U B  59 "   -0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  60 "    0.165 2.00e-02 2.50e+03   6.25e-02 1.37e+02
        pdb=" N9    G B  60 "   -0.004 2.00e-02 2.50e+03
        pdb=" C8    G B  60 "   -0.065 2.00e-02 2.50e+03
        pdb=" N7    G B  60 "   -0.028 2.00e-02 2.50e+03
        pdb=" C5    G B  60 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    G B  60 "    0.023 2.00e-02 2.50e+03
        pdb=" O6    G B  60 "    0.084 2.00e-02 2.50e+03
        pdb=" N1    G B  60 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G B  60 "   -0.007 2.00e-02 2.50e+03
        pdb=" N2    G B  60 "   -0.092 2.00e-02 2.50e+03
        pdb=" N3    G B  60 "   -0.013 2.00e-02 2.50e+03
        pdb=" C4    G B  60 "   -0.013 2.00e-02 2.50e+03
        pdb=" H8    G B  60 "   -0.074 2.00e-02 2.50e+03
        pdb=" H1    G B  60 "    0.029 2.00e-02 2.50e+03
  ... (remaining 2454 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 904
        2.19 -     2.79: 35301
        2.79 -     3.39: 46869
        3.39 -     4.00: 61569
        4.00 -     4.60: 96456
  Nonbonded interactions: 241099
  Sorted by model distance:
  nonbonded pdb=" HZ2 LYS A 600 "
            pdb=" O   LYS A 605 "
     model   vdw
     1.584 2.450
  nonbonded pdb=" HE  ARG A 841 "
            pdb=" O   LEU A 995 "
     model   vdw
     1.590 2.450
  nonbonded pdb=" HZ2 LYS A 766 "
            pdb=" OP2   G B  28 "
     model   vdw
     1.594 2.450
  nonbonded pdb=" OD1 ASN A 887 "
            pdb=" H   ASP A 889 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OD1 ASN A 316 "
            pdb=" H   TYR A 317 "
     model   vdw
     1.619 2.450
  ... (remaining 241094 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.910
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     20.900
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.404   9990  Z= 0.688
  Angle     :  1.002  18.860  13839  Z= 0.868
  Chirality :  0.094   0.737   1596
  Planarity :  0.006   0.125   1459
  Dihedral  : 18.256 178.108   4350
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.16 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 14.22 %
    Favored  : 85.66 %
  Cbeta Deviations :  1.20 %
  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: -1.28 (0.27), residues: 950
  helix: -0.56 (0.26), residues: 404
  sheet: -0.93 (0.44), residues: 123
  loop : -0.96 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1131 
 TYR   0.013   0.001   TYR A 664 
 PHE   0.011   0.001   PHE A 957 
 TRP   0.009   0.001   TRP A 424 
 HIS   0.003   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01076 /  0.69 ( 9990)
  covalent geometry    : angle       1.00191 /  0.87 (13839)
  hydrogen bonds       : bond        0.16939 / 10.77 (  415)
  hydrogen bonds       : angle       6.35013 /  4.25 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 GLU cc_start: 0.7608 (tp30) cc_final: 0.7307 (tp30)
  outliers start: 1
  outliers final: 1
  residues processed: 65
  average time/residue: 0.2329
  time to fit residues: 21.3110
Evaluate side-chains
  62 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  979 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.2980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1123 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.157540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.130391 restraints weight = 43482.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 2.42
r_work: 0.3884 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.0543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9990  Z= 0.153
  Angle     :  0.573   6.582  13839  Z= 0.337
  Chirality :  0.040   0.383   1596
  Planarity :  0.004   0.044   1459
  Dihedral  : 17.346 179.109   2323
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.58 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.41 %
    Favored  : 85.43 %
  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: -1.01 (0.27), residues: 950
  helix: -0.17 (0.26), residues: 411
  sheet: -0.81 (0.45), residues: 123
  loop : -1.01 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 441 
 TYR   0.014   0.001   TYR A 664 
 PHE   0.011   0.001   PHE A 228 
 TRP   0.008   0.001   TRP A 466 
 HIS   0.002   0.001   HIS A 838 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 9990)
  covalent geometry    : angle       0.57257 /  0.34 (13839)
  hydrogen bonds       : bond        0.06660 /  4.41 (  415)
  hydrogen bonds       : angle       4.96822 /  3.37 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 GLU cc_start: 0.7931 (tp30) cc_final: 0.7632 (tp30)
REVERT: A  417 GLU cc_start: 0.7778 (tp30) cc_final: 0.7474 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 74
  average time/residue: 0.1875
  time to fit residues: 19.9647
Evaluate side-chains
  71 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  865 ASP
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1099 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    2.1990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.150090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.124788 restraints weight = 44057.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 2.42
r_work: 0.3835 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9990  Z= 0.242
  Angle     :  0.617   7.922  13839  Z= 0.358
  Chirality :  0.042   0.427   1596
  Planarity :  0.004   0.032   1459
  Dihedral  : 17.232 177.357   2321
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.42 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.14 %
    Favored  : 82.89 %
  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: -1.30 (0.27), residues: 950
  helix: -0.30 (0.25), residues: 413
  sheet: -1.04 (0.44), residues: 123
  loop : -1.27 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 441 
 TYR   0.020   0.001   TYR A 664 
 PHE   0.017   0.002   PHE A 957 
 TRP   0.011   0.002   TRP A 466 
 HIS   0.004   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00541 /  0.24 ( 9990)
  covalent geometry    : angle       0.61666 /  0.36 (13839)
  hydrogen bonds       : bond        0.06828 /  4.46 (  415)
  hydrogen bonds       : angle       4.94686 /  3.34 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6227 (mp)
REVERT: A 1044 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8347 (tt0)
  outliers start: 17
  outliers final: 14
  residues processed: 80
  average time/residue: 0.2249
  time to fit residues: 25.2531
Evaluate side-chains
  74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  865 ASP
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1099 ASP
Chi-restraints excluded: chain A residue 1112 GLU
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1007 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 = 0.4226 r_free = 0.4226 target = 0.157692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.130507 restraints weight = 43222.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 2.38
r_work: 0.3880 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9990  Z= 0.129
  Angle     :  0.511   6.233  13839  Z= 0.301
  Chirality :  0.038   0.405   1596
  Planarity :  0.003   0.036   1459
  Dihedral  : 17.000 173.146   2321
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.42 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.61 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.27), residues: 950
  helix: -0.01 (0.26), residues: 413
  sheet: -1.07 (0.44), residues: 125
  loop : -1.20 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 441 
 TYR   0.014   0.001   TYR A 664 
 PHE   0.008   0.001   PHE A 957 
 TRP   0.010   0.001   TRP A 424 
 HIS   0.003   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 ( 9990)
  covalent geometry    : angle       0.51105 /  0.30 (13839)
  hydrogen bonds       : bond        0.05331 /  3.51 (  415)
  hydrogen bonds       : angle       4.60649 /  3.12 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6170 (mp)
REVERT: A  417 GLU cc_start: 0.7711 (tp30) cc_final: 0.7398 (tp30)
  outliers start: 20
  outliers final: 13
  residues processed: 86
  average time/residue: 0.2317
  time to fit residues: 28.1104
Evaluate side-chains
  78 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  865 ASP
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1099 ASP
Chi-restraints excluded: chain A residue 1112 GLU
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 85 optimal weight:    0.4980
   chunk 101 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1143 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.158215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.131144 restraints weight = 44756.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 2.52
r_work: 0.3876 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3755 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9990  Z= 0.198
  Angle     :  0.540   5.594  13839  Z= 0.312
  Chirality :  0.039   0.411   1596
  Planarity :  0.003   0.036   1459
  Dihedral  : 16.710 169.873   2321
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.53 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.72 %
    Favored  : 81.62 %
  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: -1.13 (0.27), residues: 950
  helix: -0.12 (0.26), residues: 419
  sheet: -0.96 (0.45), residues: 123
  loop : -1.24 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 441 
 TYR   0.017   0.001   TYR A 664 
 PHE   0.012   0.002   PHE A 957 
 TRP   0.009   0.001   TRP A 466 
 HIS   0.004   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00447 /  0.20 ( 9990)
  covalent geometry    : angle       0.54037 /  0.31 (13839)
  hydrogen bonds       : bond        0.05876 /  3.83 (  415)
  hydrogen bonds       : angle       4.63118 /  3.13 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6184 (mp)
REVERT: A  417 GLU cc_start: 0.7808 (tp30) cc_final: 0.7489 (tp30)
  outliers start: 23
  outliers final: 20
  residues processed: 82
  average time/residue: 0.2407
  time to fit residues: 27.5688
Evaluate side-chains
  82 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  846 MET
Chi-restraints excluded: chain A residue  865 ASP
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1043 ILE
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1099 ASP
Chi-restraints excluded: chain A residue 1112 GLU
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0870
   chunk 34 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    1.1162

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1007 ASN
A1064 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.160073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.132888 restraints weight = 44457.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.52
r_work: 0.3905 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3788 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9990  Z= 0.131
  Angle     :  0.492   5.221  13839  Z= 0.284
  Chirality :  0.037   0.385   1596
  Planarity :  0.003   0.064   1459
  Dihedral  : 16.663 166.869   2321
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.26 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.65 %
    Favored  : 81.16 %
  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: -1.04 (0.28), residues: 950
  helix:  0.01 (0.26), residues: 419
  sheet: -1.02 (0.44), residues: 131
  loop : -1.22 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1131 
 TYR   0.014   0.001   TYR A 664 
 PHE   0.008   0.001   PHE A 591 
 TRP   0.009   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 9990)
  covalent geometry    : angle       0.49181 /  0.28 (13839)
  hydrogen bonds       : bond        0.05026 /  3.30 (  415)
  hydrogen bonds       : angle       4.45435 /  3.01 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6219 (mp)
REVERT: A  417 GLU cc_start: 0.7768 (tp30) cc_final: 0.7456 (tp30)
  outliers start: 19
  outliers final: 17
  residues processed: 79
  average time/residue: 0.2090
  time to fit residues: 23.1183
Evaluate side-chains
  77 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  865 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1043 ILE
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1099 ASP
Chi-restraints excluded: chain A residue 1112 GLU
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1155 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 73 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.2186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.158860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.132315 restraints weight = 43586.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 2.30
r_work: 0.3910 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3794 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9990  Z= 0.149
  Angle     :  0.501   6.101  13839  Z= 0.287
  Chirality :  0.037   0.371   1596
  Planarity :  0.003   0.040   1459
  Dihedral  : 16.585 160.643   2321
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.42 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.53 %
    Favored  : 80.58 %
  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: -1.03 (0.28), residues: 950
  helix:  0.05 (0.27), residues: 419
  sheet: -1.08 (0.44), residues: 133
  loop : -1.23 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 441 
 TYR   0.015   0.001   TYR A 664 
 PHE   0.010   0.001   PHE A 591 
 TRP   0.009   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 9990)
  covalent geometry    : angle       0.50050 /  0.29 (13839)
  hydrogen bonds       : bond        0.05067 /  3.32 (  415)
  hydrogen bonds       : angle       4.41250 /  2.99 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 62
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6127 (mp)
REVERT: A  417 GLU cc_start: 0.7718 (tp30) cc_final: 0.7410 (tp30)
  outliers start: 25
  outliers final: 19
  residues processed: 86
  average time/residue: 0.2398
  time to fit residues: 28.7293
Evaluate side-chains
  76 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  865 ASP
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1043 ILE
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1099 ASP
Chi-restraints excluded: chain A residue 1112 GLU
Chi-restraints excluded: chain A residue 1118 THR
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1155 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0000
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.7986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.160465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.133899 restraints weight = 43190.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 2.30
r_work: 0.3934 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3815 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9990  Z= 0.108
  Angle     :  0.472   5.458  13839  Z= 0.270
  Chirality :  0.036   0.311   1596
  Planarity :  0.004   0.093   1459
  Dihedral  : 16.538 155.065   2321
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.74 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.88 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.28), residues: 950
  helix:  0.28 (0.27), residues: 413
  sheet: -0.90 (0.45), residues: 123
  loop : -1.02 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1131 
 TYR   0.012   0.001   TYR A 664 
 PHE   0.008   0.001   PHE A 963 
 TRP   0.008   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 9990)
  covalent geometry    : angle       0.47231 /  0.27 (13839)
  hydrogen bonds       : bond        0.04504 /  2.97 (  415)
  hydrogen bonds       : angle       4.25252 /  2.87 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6023 (mp)
REVERT: A  417 GLU cc_start: 0.7651 (tp30) cc_final: 0.7346 (tp30)
REVERT: A 1131 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7828 (tpp80)
  outliers start: 19
  outliers final: 13
  residues processed: 80
  average time/residue: 0.2510
  time to fit residues: 27.7160
Evaluate side-chains
  73 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1099 ASP
Chi-restraints excluded: chain A residue 1118 THR
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1155 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0970
   chunk 80 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1007 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.160063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.132906 restraints weight = 44518.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 2.51
r_work: 0.3908 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3785 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9990  Z= 0.151
  Angle     :  0.493   6.256  13839  Z= 0.280
  Chirality :  0.037   0.320   1596
  Planarity :  0.004   0.061   1459
  Dihedral  : 16.506 153.118   2321
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.11 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.99 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.28), residues: 950
  helix:  0.15 (0.27), residues: 427
  sheet: -0.97 (0.44), residues: 133
  loop : -1.22 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1131 
 TYR   0.014   0.001   TYR A 664 
 PHE   0.010   0.001   PHE A 591 
 TRP   0.009   0.001   TRP A 466 
 HIS   0.002   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.15 ( 9990)
  covalent geometry    : angle       0.49331 /  0.28 (13839)
  hydrogen bonds       : bond        0.04827 /  3.17 (  415)
  hydrogen bonds       : angle       4.29930 /  2.91 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6015 (mp)
REVERT: A  417 GLU cc_start: 0.7706 (tp30) cc_final: 0.7389 (tp30)
REVERT: A 1131 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7947 (tpp80)
  outliers start: 17
  outliers final: 15
  residues processed: 74
  average time/residue: 0.2263
  time to fit residues: 23.6414
Evaluate side-chains
  74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1043 ILE
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1099 ASP
Chi-restraints excluded: chain A residue 1118 THR
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1155 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0170
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 98 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.4024

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.159737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.132503 restraints weight = 44922.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.50
r_work: 0.3900 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3779 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9990  Z= 0.158
  Angle     :  0.504   6.355  13839  Z= 0.286
  Chirality :  0.037   0.308   1596
  Planarity :  0.004   0.061   1459
  Dihedral  : 16.518 150.424   2321
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.74 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.99 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.28), residues: 950
  helix:  0.13 (0.27), residues: 427
  sheet: -0.97 (0.44), residues: 133
  loop : -1.28 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1131 
 TYR   0.015   0.001   TYR A 664 
 PHE   0.011   0.001   PHE A 957 
 TRP   0.009   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.16 ( 9990)
  covalent geometry    : angle       0.50372 /  0.29 (13839)
  hydrogen bonds       : bond        0.04984 /  3.26 (  415)
  hydrogen bonds       : angle       4.31928 /  2.92 ( 1083)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6051 (mp)
REVERT: A  417 GLU cc_start: 0.7741 (tp30) cc_final: 0.7414 (tp30)
REVERT: A 1131 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7978 (tpp80)
  outliers start: 18
  outliers final: 16
  residues processed: 74
  average time/residue: 0.2360
  time to fit residues: 24.6115
Evaluate side-chains
  74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 THR
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1043 ILE
Chi-restraints excluded: chain A residue 1047 SER
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1099 ASP
Chi-restraints excluded: chain A residue 1118 THR
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1155 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 93 optimal weight:    3.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1007 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.159965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.133599 restraints weight = 43393.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 2.28
r_work: 0.3935 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3819 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9990  Z= 0.116
  Angle     :  0.475   5.877  13839  Z= 0.270
  Chirality :  0.036   0.280   1596
  Planarity :  0.004   0.064   1459
  Dihedral  : 16.494 148.412   2321
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.68 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.23 %
    Favored  : 80.81 %
  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: -0.71 (0.28), residues: 950
  helix:  0.30 (0.27), residues: 421
  sheet: -0.85 (0.46), residues: 125
  loop : -1.08 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 441 
 TYR   0.013   0.001   TYR A 664 
 PHE   0.007   0.001   PHE A 963 
 TRP   0.008   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A 986 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 ( 9990)
  covalent geometry    : angle       0.47463 /  0.27 (13839)
  hydrogen bonds       : bond        0.04455 /  2.94 (  415)
  hydrogen bonds       : angle       4.20042 /  2.84 ( 1083)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4650.76 seconds
wall clock time: 79 minutes 35.98 seconds (4775.98 seconds total)