Starting phenix.real_space_refine
on Wed Mar  4 03:20:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6iv6_9742/03_2026/6iv6_9742.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6iv6_9742/03_2026/6iv6_9742.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6iv6_9742/03_2026/6iv6_9742.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6iv6_9742/03_2026/6iv6_9742.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6iv6_9742/03_2026/6iv6_9742.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6iv6_9742/03_2026/6iv6_9742.map"
  }
  resolution = 3.6
  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=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      26      5.49       5
     S      21      5.16       5
     C    6406      2.51       5
     N    1722      2.21       5
     O    1983      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 10158
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1209, 9611
          Classifications: {'peptide': 1209}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'CIS': 4, 'PTRANS': 35, 'TRANS': 1169}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 267
          Unresolved non-hydrogen angles: 338
          Unresolved non-hydrogen dihedrals: 229
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ALY:plan-2': 4, 'ASP:plan': 5, 'GLU:plan': 9, 'GLN:plan1': 7, 'ASN:plan1': 4, 'TYR:plan': 5, 'PHE:plan': 2, 'HIS:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 178
    Chain: "G"
      Number of atoms: 547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 547
          Classifications: {'RNA': 26}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 8, 'rna3p': 17}
  Time building chain proxies: 2.52, per 1000 atoms: 0.25
  Number of scatterers: 10158
  At special positions: 0
  Unit cell: (110.39, 101.26, 113.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P      26     15.00
     O    1983      8.00
     N    1722      7.00
     C    6406      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 472.8 milliseconds
  

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2278

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      42.0% alpha, 7.9% beta
      6 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 34
    Processing helix  chain 'A' and resid 34 through 65
      removed outlier: 4.460A  pdb=" N   GLN A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LYS A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
      removed outlier: 3.616A  pdb=" N   LEU A  81 " --> pdb=" O   TYR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 109
      removed outlier: 4.212A  pdb=" N   GLU A 106 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL A 108 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 146
    Processing helix  chain 'A' and resid 163 through 168
      removed outlier: 3.864A  pdb=" N   TYR A 166 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE A 167 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A 168 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 163 through 168'
    Processing helix  chain 'A' and resid 169 through 175
      removed outlier: 3.949A  pdb=" N   ASN A 173 " --> pdb=" O   GLY A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 193
      removed outlier: 3.794A  pdb=" N   ARG A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.676A  pdb=" N   ARG A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 206 " --> pdb=" O   ASN A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 225
      removed outlier: 3.838A  pdb=" N   ILE A 221 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN A 222 " --> pdb=" O   ASP A 218 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 234
      removed outlier: 3.699A  pdb=" N   LEU A 233 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 244
      removed outlier: 3.891A  pdb=" N   LEU A 244 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 258
      removed outlier: 3.654A  pdb=" N   ALA A 251 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.503A  pdb=" N   ASN A 276 " --> pdb=" O   ASN A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 326
      removed outlier: 3.934A  pdb=" N   VAL A 319 " --> pdb=" O   ASP A 315 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   CYS A 320 " --> pdb=" O   ASP A 316 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN A 324 " --> pdb=" O   CYS A 320 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLU A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 343
      removed outlier: 3.664A  pdb=" N   GLY A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 357
      No H-bonds generated for 'chain 'A' and resid 355 through 357'
    Processing helix  chain 'A' and resid 358 through 366
    Processing helix  chain 'A' and resid 371 through 380
    Processing helix  chain 'A' and resid 381 through 385
      removed outlier: 3.850A  pdb=" N   VAL A 384 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 385 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 381 through 385'
    Processing helix  chain 'A' and resid 425 through 432
      removed outlier: 3.667A  pdb=" N   TYR A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   THR A 430 " --> pdb=" O   ILE A 426 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG A 432 " --> pdb=" O   HIS A 428 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 425 through 432'
    Processing helix  chain 'A' and resid 455 through 460
    Processing helix  chain 'A' and resid 464 through 469
    Processing helix  chain 'A' and resid 494 through 501
    Processing helix  chain 'A' and resid 501 through 511
      removed outlier: 3.656A  pdb=" N   LEU A 505 " --> pdb=" O   LEU A 501 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN A 506 " --> pdb=" O   ASP A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 539
      removed outlier: 4.002A  pdb=" N   GLU A 530 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ALA A 533 " --> pdb=" O   GLY A 529 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ASP A 536 " --> pdb=" O   GLY A 532 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU A 537 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 553
      removed outlier: 3.689A  pdb=" N   LEU A 544 " --> pdb=" O   LYS A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 584
      removed outlier: 3.981A  pdb=" N   ASN A 583 " --> pdb=" O   LYS A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 633
      removed outlier: 3.645A  pdb=" N   LEU A 633 " --> pdb=" O   PRO A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 657
    Processing helix  chain 'A' and resid 659 through 663
      removed outlier: 3.603A  pdb=" N   LYS A 662 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS A 663 " --> pdb=" O   THR A 660 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 659 through 663'
    Processing helix  chain 'A' and resid 669 through 686
      removed outlier: 3.848A  pdb=" N   ILE A 676 " --> pdb=" O   CYS A 672 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASP A 677 " --> pdb=" O   HIS A 673 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A 678 " --> pdb=" O   ALA A 674 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN A 684 " --> pdb=" O   LYS A 680 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS A 685 " --> pdb=" O   ALA A 681 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   HIS A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 716
      removed outlier: 3.554A  pdb=" N   VAL A 712 " --> pdb=" O   PHE A 708 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU A 713 " --> pdb=" O   TYR A 709 " (cutoff:3.500A)
      Proline residue:  A 714  - end of helix
    Processing helix  chain 'A' and resid 725 through 734
      removed outlier: 3.534A  pdb=" N   ILE A 729 " --> pdb=" O   ASN A 725 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU A 734 " --> pdb=" O   ASN A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 749
      removed outlier: 3.731A  pdb=" N   SER A 749 " --> pdb=" O   LYS A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 764
      removed outlier: 3.519A  pdb=" N   TYR A 762 " --> pdb=" O   LEU A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 772
      removed outlier: 3.514A  pdb=" N   LEU A 772 " --> pdb=" O   GLU A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 831
      removed outlier: 4.124A  pdb=" N   GLN A 831 " --> pdb=" O   LYS A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 854
    Processing helix  chain 'A' and resid 855 through 865
    Processing helix  chain 'A' and resid 915 through 926
      removed outlier: 3.538A  pdb=" N   ILE A 924 " --> pdb=" O   ASP A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 962
      removed outlier: 3.855A  pdb=" N   THR A 938 " --> pdb=" O   GLY A 934 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 939 " --> pdb=" O   GLU A 935 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS A 940 " --> pdb=" O   ILE A 936 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   SER A 948 " --> pdb=" O   SER A 944 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   HIS A 949 " --> pdb=" O   GLY A 945 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   HIS A 952 " --> pdb=" O   SER A 948 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A 959 " --> pdb=" O   SER A 955 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS A 960 " --> pdb=" O   GLN A 956 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR A 961 " --> pdb=" O   LEU A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 999
      removed outlier: 4.006A  pdb=" N   ASN A 988 " --> pdb=" O   GLN A 984 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ILE A 994 " --> pdb=" O   GLU A 990 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   HIS A 999 " --> pdb=" O   LYS A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1072
      removed outlier: 3.778A  pdb=" N   GLN A1068 " --> pdb=" O   ILE A1064 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   ALA A1069 " --> pdb=" O   ALA A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1138
    Processing helix  chain 'A' and resid 1154 through 1159
      removed outlier: 3.602A  pdb=" N   ILE A1158 " --> pdb=" O   LEU A1154 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   CYS A1159 " --> pdb=" O   VAL A1155 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1154 through 1159'
    Processing helix  chain 'A' and resid 1165 through 1179
      removed outlier: 3.667A  pdb=" N   LEU A1177 " --> pdb=" O   LEU A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1216 through 1238
      removed outlier: 3.579A  pdb=" N   GLY A1221 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A1222 " --> pdb=" O   ASP A1218 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE A1225 " --> pdb=" O   GLY A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1260
      removed outlier: 3.552A  pdb=" N   LEU A1255 " --> pdb=" O   ASN A1251 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLN A1259 " --> pdb=" O   LEU A1255 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASN A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 721 through 724
      removed outlier: 3.527A  pdb=" N   MET A 621 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ILE A 587 " --> pdb=" O   MET A 621 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   TYR A 594 " --> pdb=" O   ILE A 743 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 564
      removed outlier: 4.624A  pdb=" N   ILE A 785 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 624 through 625
    Processing sheet with id=AA4, first strand: chain 'A' and resid 892 through 897
      removed outlier: 6.879A  pdb=" N   VAL A 885 " --> pdb=" O   LEU A 893 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   GLN A 895 " --> pdb=" O   LEU A 883 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   LEU A 883 " --> pdb=" O   GLN A 895 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   SER A 897 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   LEU A 881 " --> pdb=" O   SER A 897 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   GLU A 968 " --> pdb=" O   ILE A 873 " (cutoff:3.500A)
      removed outlier: 9.244A  pdb=" N   ARG A 875 " --> pdb=" O   GLU A 968 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 900 through 905
      removed outlier: 3.755A  pdb=" N   ILE A 901 " --> pdb=" O   THR A 913 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR A 913 " --> pdb=" O   ILE A 901 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   THR A 903 " --> pdb=" O   MET A 911 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   MET A 911 " --> pdb=" O   THR A 903 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1077 through 1079
      removed outlier: 3.818A  pdb=" N   ILE A1090 " --> pdb=" O   TRP A1106 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TRP A1106 " --> pdb=" O   ILE A1090 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1181 through 1183

    294 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2749
        1.33 -     1.45: 2062
        1.45 -     1.57: 5529
        1.57 -     1.69: 52
        1.69 -     1.81: 35
  Bond restraints: 10427
  Sorted by residual:
  bond pdb=" C   ALY A 153 "
       pdb=" O   ALY A 153 "
    ideal  model  delta    sigma   weight residual
    1.231  1.363 -0.132 2.00e-02 2.50e+03 4.35e+01
  bond pdb=" C   ALY A 635 "
       pdb=" O   ALY A 635 "
    ideal  model  delta    sigma   weight residual
    1.231  1.360 -0.129 2.00e-02 2.50e+03 4.16e+01
  bond pdb=" C   ALY A 816 "
       pdb=" O   ALY A 816 "
    ideal  model  delta    sigma   weight residual
    1.231  1.359 -0.128 2.00e-02 2.50e+03 4.09e+01
  bond pdb=" N   GLN A 281 "
       pdb=" CA  GLN A 281 "
    ideal  model  delta    sigma   weight residual
    1.459  1.505 -0.046 1.20e-02 6.94e+03 1.44e+01
  bond pdb=" N   ASN A 280 "
       pdb=" CA  ASN A 280 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.20e-02 6.94e+03 9.44e+00
  ... (remaining 10422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.08: 13919
        3.08 -     6.17: 241
        6.17 -     9.25: 32
        9.25 -    12.33: 9
       12.33 -    15.41: 3
  Bond angle restraints: 14204
  Sorted by residual:
  angle pdb=" C   THR A 518 "
        pdb=" N   THR A 519 "
        pdb=" CA  THR A 519 "
      ideal   model   delta    sigma   weight residual
     121.70  136.98  -15.28 1.80e+00 3.09e-01 7.21e+01
  angle pdb=" O   ALY A 635 "
        pdb=" C   ALY A 635 "
        pdb=" N   VAL A 636 "
      ideal   model   delta    sigma   weight residual
     123.00  111.47   11.53 1.60e+00 3.91e-01 5.19e+01
  angle pdb=" CA  ALY A 153 "
        pdb=" C   ALY A 153 "
        pdb=" O   ALY A 153 "
      ideal   model   delta    sigma   weight residual
     120.80  109.97   10.83 1.70e+00 3.46e-01 4.06e+01
  angle pdb=" C   GLY A 120 "
        pdb=" N   TYR A 121 "
        pdb=" CA  TYR A 121 "
      ideal   model   delta    sigma   weight residual
     121.54  132.60  -11.06 1.91e+00 2.74e-01 3.35e+01
  angle pdb=" C   GLN A 281 "
        pdb=" N   HIS A 282 "
        pdb=" CA  HIS A 282 "
      ideal   model   delta    sigma   weight residual
     121.70  131.91  -10.21 1.80e+00 3.09e-01 3.22e+01
  ... (remaining 14199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 6061
       35.87 -    71.73: 183
       71.73 -   107.60: 17
      107.60 -   143.47: 1
      143.47 -   179.33: 3
  Dihedral angle restraints: 6265
    sinusoidal: 2725
      harmonic: 3540
  Sorted by residual:
  dihedral pdb=" O4'   C G  23 "
           pdb=" C1'   C G  23 "
           pdb=" N1    C G  23 "
           pdb=" C2    C G  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   51.91  148.09     1      1.50e+01 4.44e-03 7.89e+01
  dihedral pdb=" O4'   U G  16 "
           pdb=" C1'   U G  16 "
           pdb=" N1    U G  16 "
           pdb=" C2    U G  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.67  179.33     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U G  15 "
           pdb=" C1'   U G  15 "
           pdb=" N1    U G  15 "
           pdb=" C2    U G  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.81 -176.81     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 6262 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1338
       0.074 -    0.148: 199
       0.148 -    0.223: 21
       0.223 -    0.297: 5
       0.297 -    0.371: 1
  Chirality restraints: 1564
  Sorted by residual:
  chirality pdb=" CB  ILE A1029 "
            pdb=" CA  ILE A1029 "
            pdb=" CG1 ILE A1029 "
            pdb=" CG2 ILE A1029 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.44e+00
  chirality pdb=" CA  ASP A 665 "
            pdb=" N   ASP A 665 "
            pdb=" C   ASP A 665 "
            pdb=" CB  ASP A 665 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CB  THR A 516 "
            pdb=" CA  THR A 516 "
            pdb=" OG1 THR A 516 "
            pdb=" CG2 THR A 516 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 1561 not shown)

  Planarity restraints: 1754
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALY A 153 "    0.080 2.00e-02 2.50e+03   1.55e-01 2.41e+02
        pdb=" C   ALY A 153 "   -0.269 2.00e-02 2.50e+03
        pdb=" O   ALY A 153 "    0.090 2.00e-02 2.50e+03
        pdb=" N   LEU A 154 "    0.099 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALY A 635 "    0.083 2.00e-02 2.50e+03   1.53e-01 2.35e+02
        pdb=" C   ALY A 635 "   -0.265 2.00e-02 2.50e+03
        pdb=" O   ALY A 635 "    0.089 2.00e-02 2.50e+03
        pdb=" N   VAL A 636 "    0.094 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 112 "   -0.023 2.00e-02 2.50e+03   4.75e-02 2.25e+01
        pdb=" C   GLY A 112 "    0.082 2.00e-02 2.50e+03
        pdb=" O   GLY A 112 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   ASN A 113 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 1751 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2513
        2.79 -     3.32: 8624
        3.32 -     3.84: 15950
        3.84 -     4.37: 18856
        4.37 -     4.90: 31975
  Nonbonded interactions: 77918
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 623 "
            pdb=" O   LEU A 779 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR A  10 "
            pdb=" OD1 ASN A 998 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   THR A 208 "
            pdb=" OG  SER A 214 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   LYS A 512 "
            pdb=" OG1 THR A 515 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OH  TYR A 353 "
            pdb=" OD1 ASN A 522 "
     model   vdw
     2.342 3.040
  ... (remaining 77913 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 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.760
  Find NCS groups from input model:        0.050
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
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      :  0.005   0.132  10427  Z= 0.280
  Angle     :  1.041  15.413  14204  Z= 0.578
  Chirality :  0.053   0.371   1564
  Planarity :  0.008   0.155   1754
  Dihedral  : 17.648 179.332   3987
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.66 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.38 %
    Favored  : 91.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.17 (0.17), residues: 1187
  helix: -4.23 (0.11), residues: 426
  sheet: -2.75 (0.43), residues: 124
  loop : -3.01 (0.19), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 328 
 TYR   0.034   0.002   TYR A 327 
 PHE   0.020   0.002   PHE A  18 
 TRP   0.015   0.002   TRP A1042 
 HIS   0.006   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (10427)
  covalent geometry    : angle       1.04073 (14204)
  hydrogen bonds       : bond        0.27162 (  308)
  hydrogen bonds       : angle      10.00735 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7129 (t0) cc_final: 0.6854 (t0)
REVERT: A  162 LYS cc_start: 0.6627 (mttt) cc_final: 0.5393 (mmtt)
REVERT: A  293 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6771 (mtm180)
REVERT: A  380 TYR cc_start: 0.4658 (m-80) cc_final: 0.2956 (t80)
REVERT: A  498 LYS cc_start: 0.7230 (pptt) cc_final: 0.5648 (mmmm)
REVERT: A  560 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6464 (mt-10)
REVERT: A  894 GLU cc_start: 0.8383 (pt0) cc_final: 0.8165 (tt0)
REVERT: A  921 LYS cc_start: 0.5492 (ttpt) cc_final: 0.5243 (mtmt)
REVERT: A 1061 TYR cc_start: 0.7244 (t80) cc_final: 0.6788 (t80)
REVERT: A 1104 GLN cc_start: 0.7497 (mt0) cc_final: 0.7268 (mt0)
REVERT: A 1113 ASP cc_start: 0.7285 (t70) cc_final: 0.6657 (t70)
REVERT: A 1115 ARG cc_start: 0.7624 (mmt-90) cc_final: 0.7241 (mmt90)
REVERT: A 1243 ASN cc_start: 0.5276 (t0) cc_final: 0.5013 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 171
  average time/residue: 0.1132
  time to fit residues: 26.4751
Evaluate side-chains
  117 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue 1216 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.4980
   chunk 117 optimal weight:    3.9990
   overall best weight:    1.8988

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

Flipped N/Q/H residues before XYZ refinement:
A 159 HIS
A 204 GLN
A 219 GLN
A 236 HIS
A 269 GLN
A 279 HIS
A 296 HIS
A 324 ASN
A 506 ASN
A 526 ASN
A 612 ASN
A 642 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
A 742 GLN
A 843 ASN
A 859 ASN
A 869 ASN
A 910 GLN
A1018 GLN
A1043 ASN
A1089 HIS

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.185902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.181552 restraints weight = 12523.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.181276 restraints weight = 20291.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.166955 restraints weight = 18854.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.165281 restraints weight = 21533.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.165008 restraints weight = 21617.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10427  Z= 0.196
  Angle     :  0.704  12.156  14204  Z= 0.359
  Chirality :  0.044   0.194   1564
  Planarity :  0.005   0.048   1754
  Dihedral  : 15.082 174.843   1714
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.04 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.91 (0.19), residues: 1187
  helix: -2.46 (0.19), residues: 426
  sheet: -2.68 (0.46), residues: 121
  loop : -2.70 (0.20), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 104 
 TYR   0.023   0.002   TYR A 121 
 PHE   0.018   0.002   PHE A  18 
 TRP   0.010   0.002   TRP A1106 
 HIS   0.011   0.002   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (10427)
  covalent geometry    : angle       0.70370 (14204)
  hydrogen bonds       : bond        0.04664 (  308)
  hydrogen bonds       : angle       5.87351 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 MET cc_start: 0.7978 (ttm) cc_final: 0.7722 (ttt)
REVERT: A  162 LYS cc_start: 0.6926 (mttt) cc_final: 0.5850 (mmtt)
REVERT: A  293 ARG cc_start: 0.7372 (mtp180) cc_final: 0.7133 (mtt180)
REVERT: A  328 ARG cc_start: 0.5355 (mmm160) cc_final: 0.4927 (mtp-110)
REVERT: A  380 TYR cc_start: 0.4793 (m-80) cc_final: 0.3409 (t80)
REVERT: A  460 LYS cc_start: 0.4919 (mmtp) cc_final: 0.4614 (mmtt)
REVERT: A  498 LYS cc_start: 0.7905 (pptt) cc_final: 0.6738 (tptm)
REVERT: A  560 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6515 (mt-10)
REVERT: A  794 MET cc_start: 0.7793 (mmm) cc_final: 0.7581 (mmm)
REVERT: A  921 LYS cc_start: 0.6360 (ttpt) cc_final: 0.5869 (mttt)
REVERT: A 1113 ASP cc_start: 0.7036 (t70) cc_final: 0.6566 (t70)
REVERT: A 1115 ARG cc_start: 0.8049 (mmt-90) cc_final: 0.7735 (mmt90)
REVERT: A 1208 LEU cc_start: 0.7021 (tt) cc_final: 0.6700 (tp)
  outliers start: 26
  outliers final: 15
  residues processed: 139
  average time/residue: 0.1018
  time to fit residues: 20.2420
Evaluate side-chains
  116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 115 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 324 ASN
A 459 GLN
A 526 ASN
A 612 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 869 ASN
A 962 ASN
** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1198 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.179153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.173959 restraints weight = 12750.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.161986 restraints weight = 26390.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.159051 restraints weight = 24620.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.159087 restraints weight = 22714.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.159252 restraints weight = 17557.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  10427  Z= 0.271
  Angle     :  0.785  11.081  14204  Z= 0.399
  Chirality :  0.049   0.240   1564
  Planarity :  0.005   0.071   1754
  Dihedral  : 15.271 173.254   1712
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.77 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 18.16 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.51 (0.21), residues: 1187
  helix: -1.87 (0.21), residues: 444
  sheet: -2.63 (0.46), residues: 125
  loop : -2.64 (0.22), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 549 
 TYR   0.024   0.002   TYR A 327 
 PHE   0.019   0.002   PHE A  18 
 TRP   0.014   0.003   TRP A 575 
 HIS   0.007   0.002   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 (10427)
  covalent geometry    : angle       0.78548 (14204)
  hydrogen bonds       : bond        0.05306 (  308)
  hydrogen bonds       : angle       5.95464 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 106
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8420 (mtm180)
REVERT: A  293 ARG cc_start: 0.7457 (mtp180) cc_final: 0.7243 (mtt180)
REVERT: A  328 ARG cc_start: 0.5454 (mmm160) cc_final: 0.5130 (mtp180)
REVERT: A  498 LYS cc_start: 0.7963 (pptt) cc_final: 0.6660 (mmtp)
REVERT: A  921 LYS cc_start: 0.6261 (ttpt) cc_final: 0.6046 (mtmt)
REVERT: A 1068 GLN cc_start: 0.7909 (mp10) cc_final: 0.7475 (mp10)
REVERT: A 1115 ARG cc_start: 0.8197 (mmt-90) cc_final: 0.7924 (mmt90)
REVERT: A 1208 LEU cc_start: 0.7547 (tt) cc_final: 0.7288 (tp)
REVERT: A 1243 ASN cc_start: 0.6336 (t0) cc_final: 0.5932 (t0)
  outliers start: 54
  outliers final: 31
  residues processed: 148
  average time/residue: 0.0968
  time to fit residues: 20.5457
Evaluate side-chains
  133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   17 ARG
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  933 TRP
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1054 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.183558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.178350 restraints weight = 12554.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.177164 restraints weight = 25208.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.176582 restraints weight = 27360.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.166827 restraints weight = 26099.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.164604 restraints weight = 24064.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10427  Z= 0.178
  Angle     :  0.668  11.187  14204  Z= 0.337
  Chirality :  0.044   0.194   1564
  Planarity :  0.004   0.037   1754
  Dihedral  : 15.067 173.908   1712
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 18.47 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.21 (0.22), residues: 1187
  helix: -1.43 (0.23), residues: 440
  sheet: -2.73 (0.46), residues: 122
  loop : -2.56 (0.22), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 474 
 TYR   0.026   0.002   TYR A 356 
 PHE   0.029   0.002   PHE A 125 
 TRP   0.013   0.002   TRP A 575 
 HIS   0.005   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (10427)
  covalent geometry    : angle       0.66802 (14204)
  hydrogen bonds       : bond        0.04004 (  308)
  hydrogen bonds       : angle       5.46169 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 103
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8367 (mtm180)
REVERT: A  293 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7231 (mtt180)
REVERT: A  328 ARG cc_start: 0.5320 (mmm160) cc_final: 0.4924 (mtp180)
REVERT: A  495 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.5980 (tmm160)
REVERT: A  498 LYS cc_start: 0.7867 (pptt) cc_final: 0.6673 (mmtp)
REVERT: A 1115 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7789 (mmt90)
REVERT: A 1208 LEU cc_start: 0.7485 (tt) cc_final: 0.7239 (tp)
REVERT: A 1243 ASN cc_start: 0.6472 (t0) cc_final: 0.6181 (t0)
  outliers start: 57
  outliers final: 35
  residues processed: 153
  average time/residue: 0.0900
  time to fit residues: 19.7959
Evaluate side-chains
  133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 96
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   17 ARG
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue 1015 ASN
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1177 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 121 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1101 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 = 0.3930 r_free = 0.3930 target = 0.184433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.179536 restraints weight = 12584.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.169318 restraints weight = 22521.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.167472 restraints weight = 23900.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.167113 restraints weight = 24227.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.167217 restraints weight = 18968.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10427  Z= 0.148
  Angle     :  0.635  11.703  14204  Z= 0.317
  Chirality :  0.043   0.405   1564
  Planarity :  0.004   0.033   1754
  Dihedral  : 14.931 175.560   1712
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 19.78 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.23), residues: 1187
  helix: -0.93 (0.24), residues: 436
  sheet: -2.55 (0.47), residues: 122
  loop : -2.38 (0.22), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 474 
 TYR   0.029   0.002   TYR A 356 
 PHE   0.025   0.001   PHE A 125 
 TRP   0.013   0.001   TRP A 575 
 HIS   0.006   0.001   HIS A 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10427)
  covalent geometry    : angle       0.63501 (14204)
  hydrogen bonds       : bond        0.03609 (  308)
  hydrogen bonds       : angle       5.15623 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 101
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 LYS cc_start: 0.7820 (pptt) cc_final: 0.6758 (tptm)
REVERT: A 1048 ASP cc_start: 0.8867 (t0) cc_final: 0.8665 (t0)
REVERT: A 1208 LEU cc_start: 0.7407 (tt) cc_final: 0.7154 (tp)
  outliers start: 53
  outliers final: 44
  residues processed: 146
  average time/residue: 0.0940
  time to fit residues: 19.6098
Evaluate side-chains
  134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 90
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  162 LYS
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1015 ASN
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 102 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 85 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1101 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 = 0.3906 r_free = 0.3906 target = 0.181979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.180335 restraints weight = 12788.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.164780 restraints weight = 26047.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.163082 restraints weight = 33977.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.163182 restraints weight = 28679.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.163021 restraints weight = 25809.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.4298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10427  Z= 0.205
  Angle     :  0.691  11.948  14204  Z= 0.347
  Chirality :  0.046   0.360   1564
  Planarity :  0.004   0.076   1754
  Dihedral  : 15.015 172.559   1712
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  6.66 %
    Allowed  : 19.68 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.23), residues: 1187
  helix: -0.97 (0.24), residues: 442
  sheet: -2.50 (0.47), residues: 122
  loop : -2.39 (0.23), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  17 
 TYR   0.018   0.002   TYR A1116 
 PHE   0.026   0.002   PHE A 370 
 TRP   0.011   0.002   TRP A 689 
 HIS   0.007   0.001   HIS A 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (10427)
  covalent geometry    : angle       0.69137 (14204)
  hydrogen bonds       : bond        0.04119 (  308)
  hydrogen bonds       : angle       5.31056 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 96
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A  495 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6021 (tmm160)
REVERT: A  498 LYS cc_start: 0.7844 (pptt) cc_final: 0.6752 (tptm)
REVERT: A 1208 LEU cc_start: 0.7513 (tt) cc_final: 0.7266 (tp)
  outliers start: 66
  outliers final: 52
  residues processed: 151
  average time/residue: 0.0890
  time to fit residues: 19.5277
Evaluate side-chains
  144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 91
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  162 LYS
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  868 VAL
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1015 ASN
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1054 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1177 LEU
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 115 optimal weight:    0.0980
   chunk 95 optimal weight:    4.9990
   chunk 110 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 100 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 104 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1043 ASN
** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1251 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.187997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.183438 restraints weight = 12404.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.174576 restraints weight = 19535.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.173052 restraints weight = 23163.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.172908 restraints weight = 24820.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.172922 restraints weight = 19384.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10427  Z= 0.130
  Angle     :  0.614  11.244  14204  Z= 0.307
  Chirality :  0.043   0.441   1564
  Planarity :  0.004   0.052   1754
  Dihedral  : 14.803 176.227   1712
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 21.70 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.23), residues: 1187
  helix: -0.55 (0.25), residues: 435
  sheet: -2.30 (0.49), residues: 122
  loop : -2.25 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 474 
 TYR   0.015   0.001   TYR A 121 
 PHE   0.027   0.001   PHE A 125 
 TRP   0.013   0.001   TRP A 575 
 HIS   0.006   0.001   HIS A 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10427)
  covalent geometry    : angle       0.61394 (14204)
  hydrogen bonds       : bond        0.03345 (  308)
  hydrogen bonds       : angle       4.94559 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 99
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6190 (tmm)
REVERT: A  328 ARG cc_start: 0.4642 (tpp80) cc_final: 0.4223 (mtp180)
REVERT: A  495 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5987 (tmm160)
REVERT: A  498 LYS cc_start: 0.7713 (pptt) cc_final: 0.6525 (mmtp)
REVERT: A 1208 LEU cc_start: 0.7377 (tt) cc_final: 0.7126 (tp)
  outliers start: 49
  outliers final: 37
  residues processed: 142
  average time/residue: 0.0854
  time to fit residues: 17.7487
Evaluate side-chains
  130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 91
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  868 VAL
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 51 optimal weight:    0.1980
   chunk 77 optimal weight:    0.0670
   chunk 73 optimal weight:    2.9990
   chunk 85 optimal weight:    8.9990
   chunk 119 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.4322

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1101 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 = 0.3932 r_free = 0.3932 target = 0.184745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.183371 restraints weight = 12516.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 77)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.167721 restraints weight = 18876.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.166899 restraints weight = 26182.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.166523 restraints weight = 26300.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.166225 restraints weight = 22970.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10427  Z= 0.153
  Angle     :  0.634  11.680  14204  Z= 0.318
  Chirality :  0.044   0.468   1564
  Planarity :  0.004   0.056   1754
  Dihedral  : 14.772 174.501   1712
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 21.49 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.23), residues: 1187
  helix: -0.55 (0.25), residues: 434
  sheet: -2.22 (0.49), residues: 122
  loop : -2.25 (0.23), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 474 
 TYR   0.014   0.001   TYR A 121 
 PHE   0.024   0.002   PHE A 125 
 TRP   0.010   0.001   TRP A 689 
 HIS   0.010   0.001   HIS A 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (10427)
  covalent geometry    : angle       0.63354 (14204)
  hydrogen bonds       : bond        0.03525 (  308)
  hydrogen bonds       : angle       4.96833 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 92
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  328 ARG cc_start: 0.4785 (tpp80) cc_final: 0.4225 (mtp180)
REVERT: A  495 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6047 (tmm160)
REVERT: A  498 LYS cc_start: 0.7837 (pptt) cc_final: 0.6685 (tptm)
REVERT: A 1208 LEU cc_start: 0.7448 (tt) cc_final: 0.7198 (tp)
  outliers start: 50
  outliers final: 44
  residues processed: 136
  average time/residue: 0.0910
  time to fit residues: 18.3511
Evaluate side-chains
  133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 88
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  868 VAL
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 11 optimal weight:    0.0370
   chunk 87 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   overall best weight:    0.9260

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 276 ASN
A 526 ASN
A 686 HIS
** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.187793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.186285 restraints weight = 12530.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.169737 restraints weight = 24784.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.168652 restraints weight = 25508.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.168550 restraints weight = 22445.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.168245 restraints weight = 20785.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10427  Z= 0.121
  Angle     :  0.595  11.427  14204  Z= 0.299
  Chirality :  0.042   0.357   1564
  Planarity :  0.003   0.043   1754
  Dihedral  : 14.636 176.610   1712
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 22.50 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.24), residues: 1187
  helix: -0.29 (0.26), residues: 429
  sheet: -2.08 (0.50), residues: 122
  loop : -2.12 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 474 
 TYR   0.014   0.001   TYR A 121 
 PHE   0.027   0.001   PHE A 125 
 TRP   0.012   0.001   TRP A 575 
 HIS   0.011   0.001   HIS A 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10427)
  covalent geometry    : angle       0.59465 (14204)
  hydrogen bonds       : bond        0.03168 (  308)
  hydrogen bonds       : angle       4.76093 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 93
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6064 (tmm)
REVERT: A  328 ARG cc_start: 0.4682 (tpp80) cc_final: 0.4176 (mtp180)
REVERT: A  495 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.6018 (tmm160)
REVERT: A  498 LYS cc_start: 0.7796 (pptt) cc_final: 0.6471 (mmtp)
REVERT: A  510 PHE cc_start: 0.7337 (t80) cc_final: 0.7035 (t80)
REVERT: A 1208 LEU cc_start: 0.7431 (tt) cc_final: 0.7163 (tp)
  outliers start: 48
  outliers final: 39
  residues processed: 136
  average time/residue: 0.0843
  time to fit residues: 17.1076
Evaluate side-chains
  132 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 91
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  390 ASN
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  868 VAL
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 116 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1101 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 = 0.3933 r_free = 0.3933 target = 0.184910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.181224 restraints weight = 12398.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 97)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.175649 restraints weight = 20863.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.172082 restraints weight = 28154.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.171039 restraints weight = 21867.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.170285 restraints weight = 17469.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10427  Z= 0.168
  Angle     :  0.649  13.402  14204  Z= 0.325
  Chirality :  0.044   0.447   1564
  Planarity :  0.004   0.060   1754
  Dihedral  : 14.706 173.311   1712
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 21.90 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.28 (0.24), residues: 1187
  helix: -0.52 (0.25), residues: 444
  sheet: -2.07 (0.49), residues: 122
  loop : -2.18 (0.23), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 474 
 TYR   0.014   0.002   TYR A1116 
 PHE   0.025   0.002   PHE A 125 
 TRP   0.011   0.002   TRP A1042 
 HIS   0.007   0.001   HIS A 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (10427)
  covalent geometry    : angle       0.64876 (14204)
  hydrogen bonds       : bond        0.03619 (  308)
  hydrogen bonds       : angle       4.90566 (  867)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 91
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  328 ARG cc_start: 0.4708 (tpp80) cc_final: 0.4264 (mtp180)
REVERT: A  495 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.6095 (tmm160)
REVERT: A  498 LYS cc_start: 0.7868 (pptt) cc_final: 0.6723 (mmtp)
REVERT: A  817 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8079 (mtm180)
REVERT: A  972 PHE cc_start: 0.8101 (p90) cc_final: 0.7822 (p90)
REVERT: A 1208 LEU cc_start: 0.7411 (tt) cc_final: 0.7148 (tp)
  outliers start: 54
  outliers final: 45
  residues processed: 137
  average time/residue: 0.0905
  time to fit residues: 18.1058
Evaluate side-chains
  135 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 88
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  390 ASN
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  495 ARG
Chi-restraints excluded: chain A residue  543 THR
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  603 HIS
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  723 ASP
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  770 ASP
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  817 ARG
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  868 VAL
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue  911 MET
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  957 LEU
Chi-restraints excluded: chain A residue 1001 VAL
Chi-restraints excluded: chain A residue 1033 THR
Chi-restraints excluded: chain A residue 1054 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1154 LEU
Chi-restraints excluded: chain A residue 1155 VAL
Chi-restraints excluded: chain A residue 1227 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 121 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 89 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
A 276 ASN
A 526 ASN
** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 759 HIS
** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.187480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.186114 restraints weight = 12509.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.185765 restraints weight = 21117.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.169793 restraints weight = 22144.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.168858 restraints weight = 28242.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.168355 restraints weight = 24403.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.4643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10427  Z= 0.119
  Angle     :  0.602  12.345  14204  Z= 0.301
  Chirality :  0.042   0.380   1564
  Planarity :  0.003   0.043   1754
  Dihedral  : 14.599 176.231   1712
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 22.70 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.24), residues: 1187
  helix: -0.28 (0.26), residues: 436
  sheet: -1.91 (0.51), residues: 117
  loop : -2.10 (0.23), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 474 
 TYR   0.013   0.001   TYR A 121 
 PHE   0.028   0.001   PHE A 125 
 TRP   0.024   0.002   TRP A1042 
 HIS   0.007   0.001   HIS A 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10427)
  covalent geometry    : angle       0.60203 (14204)
  hydrogen bonds       : bond        0.03129 (  308)
  hydrogen bonds       : angle       4.69521 (  867)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1510.07 seconds
wall clock time: 26 minutes 50.57 seconds (1610.57 seconds total)