Starting phenix.real_space_refine
on Sat Aug 23 03:15:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8woi_37690/08_2025/8woi_37690.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8woi_37690/08_2025/8woi_37690.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8woi_37690/08_2025/8woi_37690.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8woi_37690/08_2025/8woi_37690.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8woi_37690/08_2025/8woi_37690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8woi_37690/08_2025/8woi_37690.map"
  }
  resolution = 3.4
  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=   0.003 sd=   0.100
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    5965      2.51       5
     N    1587      2.21       5
     O    1734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9324
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1217, 9324
          Classifications: {'peptide': 1217}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 30, 'TRANS': 1186}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 1.83, per 1000 atoms: 0.20
  Number of scatterers: 9324
  At special positions: 0
  Unit cell: (72.6, 106.7, 144.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1734      8.00
     N    1587      7.00
     C    5965      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: 0.55
  Conformation dependent library (CDL) restraints added in 223.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2228

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 7 sheets defined
      47.7% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 53
      removed outlier: 3.564A  pdb=" N   VAL A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   SER A  45 " --> pdb=" O   MET A  41 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ALA A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 67
      removed outlier: 3.546A  pdb=" N   PHE A  59 " --> pdb=" O   MET A  55 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU A  60 " --> pdb=" O   PRO A  56 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL A  66 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 85
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.917A  pdb=" N   VAL A 116 " --> pdb=" O   GLY A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 127
      removed outlier: 3.664A  pdb=" N   GLU A 125 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 135
    Processing helix  chain 'A' and resid 143 through 148
    Processing helix  chain 'A' and resid 150 through 160
      removed outlier: 3.564A  pdb=" N   VAL A 155 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 176
      removed outlier: 3.689A  pdb=" N   TYR A 169 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR A 172 " --> pdb=" O   HIS A 168 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE A 173 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 184
      removed outlier: 3.524A  pdb=" N   VAL A 182 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER A 183 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA A 184 " --> pdb=" O   GLY A 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 178 through 184'
    Processing helix  chain 'A' and resid 186 through 191
      removed outlier: 3.766A  pdb=" N   LEU A 190 " --> pdb=" O   LYS A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 200
    Processing helix  chain 'A' and resid 204 through 221
      removed outlier: 4.174A  pdb=" N   THR A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LYS A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 221 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 233
      removed outlier: 3.500A  pdb=" N   ILE A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A 232 " --> pdb=" O   GLU A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 254 through 263
      removed outlier: 4.094A  pdb=" N   LYS A 259 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   LEU A 260 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LYS A 263 " --> pdb=" O   LYS A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 273
      removed outlier: 4.102A  pdb=" N   GLY A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 281
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.585A  pdb=" N   VAL A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 294
    Processing helix  chain 'A' and resid 302 through 311
      removed outlier: 3.575A  pdb=" N   THR A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA A 311 " --> pdb=" O   ALA A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 321 through 325
      removed outlier: 3.656A  pdb=" N   ASN A 324 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 325 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 321 through 325'
    Processing helix  chain 'A' and resid 326 through 342
      removed outlier: 3.639A  pdb=" N   LYS A 332 " --> pdb=" O   PHE A 328 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 338 " --> pdb=" O   ALA A 334 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ILE A 341 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 434
      removed outlier: 3.874A  pdb=" N   LEU A 434 " --> pdb=" O   ILE A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 464
    Processing helix  chain 'A' and resid 470 through 479
      removed outlier: 3.717A  pdb=" N   GLU A 474 " --> pdb=" O   MET A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 520
      removed outlier: 3.740A  pdb=" N   MET A 518 " --> pdb=" O   ILE A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 547
      removed outlier: 3.548A  pdb=" N   ILE A 541 " --> pdb=" O   SER A 537 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 565
      removed outlier: 3.699A  pdb=" N   THR A 564 " --> pdb=" O   ARG A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 605
    Processing helix  chain 'A' and resid 621 through 631
      removed outlier: 3.591A  pdb=" N   HIS A 625 " --> pdb=" O   THR A 621 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER A 628 " --> pdb=" O   SER A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 666
      removed outlier: 3.641A  pdb=" N   THR A 666 " --> pdb=" O   THR A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 680
      removed outlier: 3.777A  pdb=" N   LEU A 677 " --> pdb=" O   PHE A 673 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A 679 " --> pdb=" O   ARG A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 695
      removed outlier: 3.703A  pdb=" N   ILE A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 708
      removed outlier: 3.656A  pdb=" N   THR A 703 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 715
    Processing helix  chain 'A' and resid 731 through 737
    Processing helix  chain 'A' and resid 739 through 744
      removed outlier: 3.961A  pdb=" N   GLY A 743 " --> pdb=" O   LEU A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 751
      removed outlier: 3.504A  pdb=" N   HIS A 749 " --> pdb=" O   TYR A 745 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A 751 " --> pdb=" O   ILE A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 772
      removed outlier: 3.508A  pdb=" N   SER A 769 " --> pdb=" O   ARG A 765 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A 770 " --> pdb=" O   MET A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 774
      No H-bonds generated for 'chain 'A' and resid 773 through 774'
    Processing helix  chain 'A' and resid 775 through 779
    Processing helix  chain 'A' and resid 800 through 805
      removed outlier: 3.691A  pdb=" N   ILE A 804 " --> pdb=" O   VAL A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 821
      removed outlier: 3.981A  pdb=" N   ASN A 814 " --> pdb=" O   VAL A 810 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR A 820 " --> pdb=" O   THR A 816 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A 821 " --> pdb=" O   SER A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 829
      removed outlier: 3.871A  pdb=" N   GLU A 829 " --> pdb=" O   ALA A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 853
      removed outlier: 3.686A  pdb=" N   LEU A 835 " --> pdb=" O   ARG A 831 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 837 " --> pdb=" O   SER A 833 " (cutoff:3.500A)
      Proline residue:  A 841  - end of helix
      removed outlier: 4.050A  pdb=" N   ALA A 846 " --> pdb=" O   LEU A 842 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASN A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 865
      removed outlier: 4.067A  pdb=" N   ALA A 864 " --> pdb=" O   ASP A 860 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   HIS A 865 " --> pdb=" O   THR A 861 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 860 through 865'
    Processing helix  chain 'A' and resid 866 through 873
      removed outlier: 3.563A  pdb=" N   ILE A 871 " --> pdb=" O   LYS A 867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 884
      removed outlier: 3.620A  pdb=" N   ALA A 884 " --> pdb=" O   ARG A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 892
      removed outlier: 3.765A  pdb=" N   ILE A 891 " --> pdb=" O   ALA A 887 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LEU A 892 " --> pdb=" O   GLN A 888 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 887 through 892'
    Processing helix  chain 'A' and resid 892 through 897
    Processing helix  chain 'A' and resid 899 through 921
      removed outlier: 3.625A  pdb=" N   GLN A 903 " --> pdb=" O   LEU A 899 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER A 906 " --> pdb=" O   PRO A 902 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR A 912 " --> pdb=" O   TYR A 908 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE A 915 " --> pdb=" O   GLN A 911 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY A 918 " --> pdb=" O   GLY A 914 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN A 921 " --> pdb=" O   PHE A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 921 through 926
    Processing helix  chain 'A' and resid 927 through 939
      removed outlier: 3.779A  pdb=" N   ILE A 931 " --> pdb=" O   SER A 927 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 936 " --> pdb=" O   LEU A 932 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU A 938 " --> pdb=" O   TYR A 934 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL A 939 " --> pdb=" O   GLY A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 967
      removed outlier: 3.846A  pdb=" N   VAL A 952 " --> pdb=" O   LYS A 948 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ALA A 960 " --> pdb=" O   LEU A 956 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ASN A 961 " --> pdb=" O   VAL A 957 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER A 962 " --> pdb=" O   ILE A 958 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A 964 " --> pdb=" O   ALA A 960 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLU A 965 " --> pdb=" O   ASN A 961 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR A 966 " --> pdb=" O   SER A 962 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 967 " --> pdb=" O   VAL A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 975
      removed outlier: 3.744A  pdb=" N   ILE A 973 " --> pdb=" O   LEU A 969 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1079
      No H-bonds generated for 'chain 'A' and resid 1077 through 1079'
    Processing helix  chain 'A' and resid 1084 through 1088
      removed outlier: 3.619A  pdb=" N   ILE A1088 " --> pdb=" O   ARG A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1123
    Processing helix  chain 'A' and resid 1127 through 1133
    Processing helix  chain 'A' and resid 1150 through 1165
      removed outlier: 3.830A  pdb=" N   GLN A1155 " --> pdb=" O   GLY A1151 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ARG A1156 " --> pdb=" O   GLY A1152 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A1157 " --> pdb=" O   GLN A1153 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ALA A1160 " --> pdb=" O   ARG A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1187 through 1194
      removed outlier: 3.719A  pdb=" N   GLU A1192 " --> pdb=" O   GLN A1188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1240 through 1247
      removed outlier: 3.906A  pdb=" N   LEU A1244 " --> pdb=" O   ALA A1240 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 386 through 387
      removed outlier: 5.768A  pdb=" N   PHE A 367 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   LEU A 425 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   ASP A 369 " --> pdb=" O   GLN A 423 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   GLN A 423 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   SER A 421 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 559
      removed outlier: 6.489A  pdb=" N   VAL A 398 " --> pdb=" O   ALA A 559 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   VAL A 573 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 443 through 445
      removed outlier: 6.363A  pdb=" N   GLY A 444 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 645 through 647
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1028 through 1034
      removed outlier: 5.727A  pdb=" N   ARG A1029 " --> pdb=" O   PHE A1017 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   PHE A1017 " --> pdb=" O   ARG A1029 " (cutoff:3.500A)
      removed outlier: 5.708A  pdb=" N   LEU A1033 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ARG A1013 " --> pdb=" O   LEU A1033 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1169 through 1171
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1217 through 1220
      removed outlier: 7.104A  pdb=" N   VAL A1218 " --> pdb=" O   VAL A1225 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    705 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.11

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2928
        1.34 -     1.45: 1406
        1.45 -     1.57: 5096
        1.57 -     1.69: 0
        1.69 -     1.81: 67
  Bond restraints: 9497
  Sorted by residual:
  bond pdb=" CA  SER A 631 "
       pdb=" C   SER A 631 "
    ideal  model  delta    sigma   weight residual
    1.522  1.460  0.062 1.34e-02 5.57e+03 2.17e+01
  bond pdb=" CA  TYR A 336 "
       pdb=" CB  TYR A 336 "
    ideal  model  delta    sigma   weight residual
    1.530  1.457  0.073 1.63e-02 3.76e+03 2.01e+01
  bond pdb=" N   LEU A 632 "
       pdb=" CA  LEU A 632 "
    ideal  model  delta    sigma   weight residual
    1.453  1.403  0.050 1.37e-02 5.33e+03 1.35e+01
  bond pdb=" CA  ARG A 635 "
       pdb=" C   ARG A 635 "
    ideal  model  delta    sigma   weight residual
    1.522  1.478  0.043 1.25e-02 6.40e+03 1.21e+01
  bond pdb=" CA  TYR A 336 "
       pdb=" C   TYR A 336 "
    ideal  model  delta    sigma   weight residual
    1.524  1.490  0.035 1.29e-02 6.01e+03 7.18e+00
  ... (remaining 9492 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.26: 12818
        7.26 -    14.53: 24
       14.53 -    21.79: 4
       21.79 -    29.05: 2
       29.05 -    36.32: 2
  Bond angle restraints: 12850
  Sorted by residual:
  angle pdb=" N   ASP A1111 "
        pdb=" CA  ASP A1111 "
        pdb=" C   ASP A1111 "
      ideal   model   delta    sigma   weight residual
     109.95   73.63   36.32 1.44e+00 4.82e-01 6.36e+02
  angle pdb=" N   LYS A1110 "
        pdb=" CA  LYS A1110 "
        pdb=" C   LYS A1110 "
      ideal   model   delta    sigma   weight residual
     108.99   76.22   32.77 1.57e+00 4.06e-01 4.36e+02
  angle pdb=" N   LEU A 632 "
        pdb=" CA  LEU A 632 "
        pdb=" C   LEU A 632 "
      ideal   model   delta    sigma   weight residual
     110.41   91.21   19.20 1.23e+00 6.61e-01 2.44e+02
  angle pdb=" N   ARG A 635 "
        pdb=" CA  ARG A 635 "
        pdb=" C   ARG A 635 "
      ideal   model   delta    sigma   weight residual
     114.09   90.77   23.32 1.55e+00 4.16e-01 2.26e+02
  angle pdb=" C   ASP A1111 "
        pdb=" CA  ASP A1111 "
        pdb=" CB  ASP A1111 "
      ideal   model   delta    sigma   weight residual
     111.48  137.08  -25.60 1.91e+00 2.74e-01 1.80e+02
  ... (remaining 12845 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.13: 5302
       15.13 -    30.26: 260
       30.26 -    45.39: 67
       45.39 -    60.52: 2
       60.52 -    75.65: 9
  Dihedral angle restraints: 5640
    sinusoidal: 2152
      harmonic: 3488
  Sorted by residual:
  dihedral pdb=" N   ASP A1111 "
           pdb=" C   ASP A1111 "
           pdb=" CA  ASP A1111 "
           pdb=" CB  ASP A1111 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   86.85   35.95     0      2.50e+00 1.60e-01 2.07e+02
  dihedral pdb=" C   LEU A 634 "
           pdb=" N   LEU A 634 "
           pdb=" CA  LEU A 634 "
           pdb=" CB  LEU A 634 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -97.48  -25.12     0      2.50e+00 1.60e-01 1.01e+02
  dihedral pdb=" N   LEU A 634 "
           pdb=" C   LEU A 634 "
           pdb=" CA  LEU A 634 "
           pdb=" CB  LEU A 634 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   97.87   24.93     0      2.50e+00 1.60e-01 9.94e+01
  ... (remaining 5637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.149: 1459
       0.149 -    0.298: 16
       0.298 -    0.447: 1
       0.447 -    0.596: 1
       0.596 -    0.745: 2
  Chirality restraints: 1479
  Sorted by residual:
  chirality pdb=" CA  SER A 633 "
            pdb=" N   SER A 633 "
            pdb=" C   SER A 633 "
            pdb=" CB  SER A 633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.39e+01
  chirality pdb=" CA  LEU A 634 "
            pdb=" N   LEU A 634 "
            pdb=" C   LEU A 634 "
            pdb=" CB  LEU A 634 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.12   -0.61 2.00e-01 2.50e+01 9.42e+00
  chirality pdb=" CA  LYS A1110 "
            pdb=" N   LYS A1110 "
            pdb=" C   LYS A1110 "
            pdb=" CB  LYS A1110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.04   -0.52 2.00e-01 2.50e+01 6.89e+00
  ... (remaining 1476 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 681 "   -0.068 5.00e-02 4.00e+02   1.03e-01 1.71e+01
        pdb=" N   PRO A 682 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO A 682 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 682 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  55 "   -0.044 5.00e-02 4.00e+02   6.52e-02 6.79e+00
        pdb=" N   PRO A  56 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A  56 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  56 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 701 "    0.037 5.00e-02 4.00e+02   5.60e-02 5.01e+00
        pdb=" N   PRO A 702 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 702 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 702 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.43: 19
        2.43 -     3.05: 5078
        3.05 -     3.67: 13044
        3.67 -     4.28: 19500
        4.28 -     4.90: 32246
  Nonbonded interactions: 69887
  Sorted by model distance:
  nonbonded pdb=" N   ASP A1111 "
            pdb=" O   ASP A1111 "
     model   vdw
     1.818 2.496
  nonbonded pdb=" N   LYS A1110 "
            pdb=" O   LYS A1110 "
     model   vdw
     1.897 2.496
  nonbonded pdb=" N   ARG A 635 "
            pdb=" N   SER A 636 "
     model   vdw
     2.086 2.560
  nonbonded pdb=" N   LEU A 632 "
            pdb=" O   LEU A 632 "
     model   vdw
     2.168 2.496
  nonbonded pdb=" OE2 GLU A 829 "
            pdb=" OG  SER A 944 "
     model   vdw
     2.291 3.040
  ... (remaining 69882 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.770
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
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   0.073   9497  Z= 0.248
  Angle     :  1.204  36.318  12850  Z= 0.719
  Chirality :  0.062   0.745   1479
  Planarity :  0.007   0.103   1640
  Dihedral  : 10.494  75.652   3412
  Min Nonbonded Distance : 1.818

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.07 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.24 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.54 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.25 %

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 aren not related in a simple way.
  whole: -6.42 (0.16), residues: 1213
  helix: -4.82 (0.07), residues: 688
  sheet: -2.61 (0.65), residues: 71
  loop : -3.22 (0.24), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 516 
 TYR   0.017   0.002   TYR A 110 
 PHE   0.026   0.002   PHE A 752 
 TRP   0.020   0.002   TRP A 933 
 HIS   0.010   0.002   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 9497)
  covalent geometry    : angle       1.20369 (12850)
  hydrogen bonds       : bond        0.34753 (  251)
  hydrogen bonds       : angle      10.67663 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   87 SER cc_start: 0.9082 (p) cc_final: 0.8681 (m)
REVERT: A  398 VAL cc_start: 0.9076 (t) cc_final: 0.8860 (p)
REVERT: A  604 MET cc_start: 0.7160 (ptm) cc_final: 0.6586 (ttp)
REVERT: A  725 ARG cc_start: 0.8087 (ptp90) cc_final: 0.7857 (ptp90)
REVERT: A  815 MET cc_start: 0.7582 (mmp) cc_final: 0.7351 (mmp)
REVERT: A 1055 ILE cc_start: 0.8741 (pt) cc_final: 0.8305 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0975
  time to fit residues: 20.4896
Evaluate side-chains
  91 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0060
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0470
   chunk 51 optimal weight:   30.0000
   chunk 117 optimal weight:    9.9990
   overall best weight:    0.8896

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A 168 HIS
A 448 GLN
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 602 GLN
A 748 GLN
A 758 ASN
A 784 HIS
A1041 GLN
A1205 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.168414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.124370 restraints weight = 11296.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.22
r_work: 0.3021 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9497  Z= 0.143
  Angle     :  0.643  12.125  12850  Z= 0.346
  Chirality :  0.042   0.151   1479
  Planarity :  0.005   0.083   1640
  Dihedral  :  6.477  32.756   1323
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  7.02 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.17 %

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 aren not related in a simple way.
  whole: -5.15 (0.19), residues: 1213
  helix: -3.71 (0.13), residues: 672
  sheet: -2.22 (0.68), residues: 66
  loop : -2.87 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1013 
 TYR   0.014   0.001   TYR A 262 
 PHE   0.028   0.002   PHE A 134 
 TRP   0.009   0.001   TRP A 933 
 HIS   0.003   0.001   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9497)
  covalent geometry    : angle       0.64316 (12850)
  hydrogen bonds       : bond        0.04623 (  251)
  hydrogen bonds       : angle       5.63410 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.8930 (tt) cc_final: 0.8696 (tp)
REVERT: A  270 LEU cc_start: 0.8353 (mt) cc_final: 0.8138 (mt)
REVERT: A  339 MET cc_start: 0.8914 (mmm) cc_final: 0.8598 (mmm)
REVERT: A  384 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8284 (ptp90)
REVERT: A  488 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8705 (mt)
REVERT: A  604 MET cc_start: 0.8015 (ptm) cc_final: 0.7390 (ttp)
REVERT: A  653 ARG cc_start: 0.5770 (ptp-170) cc_final: 0.5435 (ttp-170)
REVERT: A  815 MET cc_start: 0.8489 (mmp) cc_final: 0.8246 (mmp)
REVERT: A  904 LYS cc_start: 0.8118 (mttt) cc_final: 0.7771 (ttpp)
REVERT: A 1026 MET cc_start: 0.7596 (tpp) cc_final: 0.7390 (tpp)
  outliers start: 15
  outliers final: 5
  residues processed: 121
  average time/residue: 0.0903
  time to fit residues: 14.8676
Evaluate side-chains
  89 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue 1087 LYS
Chi-restraints excluded: chain A residue 1200 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9980
   chunk 114 optimal weight:    9.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1188 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.165418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.120702 restraints weight = 11337.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.55
r_work: 0.3024 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9497  Z= 0.132
  Angle     :  0.598  12.538  12850  Z= 0.320
  Chirality :  0.042   0.143   1479
  Planarity :  0.004   0.073   1640
  Dihedral  :  5.948  34.363   1323
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.56 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.08 %

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 aren not related in a simple way.
  whole: -4.39 (0.20), residues: 1213
  helix: -2.98 (0.16), residues: 679
  sheet: -1.95 (0.71), residues: 66
  loop : -2.68 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1029 
 TYR   0.009   0.001   TYR A1062 
 PHE   0.021   0.002   PHE A 134 
 TRP   0.007   0.001   TRP A 933 
 HIS   0.004   0.001   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9497)
  covalent geometry    : angle       0.59786 (12850)
  hydrogen bonds       : bond        0.04192 (  251)
  hydrogen bonds       : angle       4.94564 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.8953 (tt) cc_final: 0.8715 (tp)
REVERT: A  305 PHE cc_start: 0.8405 (t80) cc_final: 0.8176 (t80)
REVERT: A  384 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8182 (ptp90)
REVERT: A  472 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7846 (mt-10)
REVERT: A  488 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8695 (mt)
REVERT: A  548 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7587 (mtm180)
REVERT: A  550 MET cc_start: 0.8275 (mtp) cc_final: 0.8016 (mtp)
REVERT: A  604 MET cc_start: 0.7966 (ptm) cc_final: 0.7438 (ttm)
REVERT: A  653 ARG cc_start: 0.5754 (ptp-170) cc_final: 0.5428 (ttp-170)
REVERT: A  904 LYS cc_start: 0.8201 (mttt) cc_final: 0.7881 (ttpp)
REVERT: A 1026 MET cc_start: 0.7537 (tpp) cc_final: 0.7272 (tpp)
REVERT: A 1074 LYS cc_start: 0.7360 (mtpp) cc_final: 0.6828 (mtmm)
  outliers start: 10
  outliers final: 5
  residues processed: 100
  average time/residue: 0.0808
  time to fit residues: 11.1169
Evaluate side-chains
  86 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue 1087 LYS
Chi-restraints excluded: chain A residue 1200 THR
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 120 optimal weight:    0.0040
   chunk 34 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0030
   chunk 21 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.7404

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

Flipped N/Q/H residues before XYZ refinement:
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.166038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119630 restraints weight = 11442.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.38
r_work: 0.3047 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9497  Z= 0.117
  Angle     :  0.558   9.956  12850  Z= 0.299
  Chirality :  0.041   0.148   1479
  Planarity :  0.004   0.073   1640
  Dihedral  :  5.587  32.356   1323
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.66 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.08 %

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 aren not related in a simple way.
  whole: -3.88 (0.22), residues: 1213
  helix: -2.49 (0.17), residues: 684
  sheet: -1.74 (0.72), residues: 64
  loop : -2.59 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1036 
 TYR   0.008   0.001   TYR A1241 
 PHE   0.018   0.001   PHE A 134 
 TRP   0.006   0.001   TRP A 933 
 HIS   0.002   0.000   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9497)
  covalent geometry    : angle       0.55756 (12850)
  hydrogen bonds       : bond        0.03469 (  251)
  hydrogen bonds       : angle       4.64298 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.8923 (tt) cc_final: 0.8703 (tp)
REVERT: A  384 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8169 (ptp90)
REVERT: A  472 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7782 (mt-10)
REVERT: A  488 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8664 (mt)
REVERT: A  548 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7586 (mtm180)
REVERT: A  550 MET cc_start: 0.8223 (mtp) cc_final: 0.7963 (mtp)
REVERT: A  604 MET cc_start: 0.7795 (ptm) cc_final: 0.7303 (ttm)
REVERT: A  653 ARG cc_start: 0.5735 (ptp-170) cc_final: 0.5389 (ttp-170)
REVERT: A  680 ASN cc_start: 0.9106 (t0) cc_final: 0.8898 (t0)
REVERT: A  904 LYS cc_start: 0.8131 (mttt) cc_final: 0.7849 (ttpp)
REVERT: A 1026 MET cc_start: 0.7545 (tpp) cc_final: 0.7172 (tpp)
REVERT: A 1074 LYS cc_start: 0.7352 (mtpp) cc_final: 0.6795 (mtmm)
  outliers start: 16
  outliers final: 8
  residues processed: 99
  average time/residue: 0.0928
  time to fit residues: 12.5257
Evaluate side-chains
  89 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  755 MET
Chi-restraints excluded: chain A residue 1087 LYS
Chi-restraints excluded: chain A residue 1200 THR
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.164251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.118408 restraints weight = 11334.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.33
r_work: 0.2960 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9497  Z= 0.162
  Angle     :  0.589   8.279  12850  Z= 0.314
  Chirality :  0.042   0.142   1479
  Planarity :  0.004   0.071   1640
  Dihedral  :  5.639  34.714   1323
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.99 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.08 %

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 aren not related in a simple way.
  whole: -3.74 (0.22), residues: 1213
  helix: -2.36 (0.18), residues: 682
  sheet: -2.06 (0.66), residues: 70
  loop : -2.51 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1029 
 TYR   0.011   0.001   TYR A 250 
 PHE   0.026   0.002   PHE A  69 
 TRP   0.008   0.001   TRP A 933 
 HIS   0.003   0.001   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9497)
  covalent geometry    : angle       0.58891 (12850)
  hydrogen bonds       : bond        0.04173 (  251)
  hydrogen bonds       : angle       4.60393 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8941 (tt) cc_final: 0.8734 (tp)
REVERT: A  305 PHE cc_start: 0.8446 (t80) cc_final: 0.8235 (t80)
REVERT: A  368 LYS cc_start: 0.7728 (mmmm) cc_final: 0.7448 (mmmm)
REVERT: A  472 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7877 (mt-10)
REVERT: A  488 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8874 (mt)
REVERT: A  544 GLU cc_start: 0.7534 (pp20) cc_final: 0.7271 (tm-30)
REVERT: A  548 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7005 (mtt180)
REVERT: A  604 MET cc_start: 0.7857 (ptm) cc_final: 0.7375 (ttm)
REVERT: A  653 ARG cc_start: 0.5849 (ptp-170) cc_final: 0.5507 (ttp-170)
REVERT: A  708 MET cc_start: 0.9224 (ttt) cc_final: 0.8967 (ttt)
REVERT: A 1026 MET cc_start: 0.7452 (tpp) cc_final: 0.7185 (tpp)
REVERT: A 1074 LYS cc_start: 0.7378 (mtpp) cc_final: 0.6898 (mtmm)
  outliers start: 18
  outliers final: 10
  residues processed: 106
  average time/residue: 0.0815
  time to fit residues: 11.7809
Evaluate side-chains
  94 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  755 MET
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1087 LYS
Chi-restraints excluded: chain A residue 1200 THR
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 48 optimal weight:    0.0670
   chunk 99 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0270
   chunk 12 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 58 optimal weight:   20.0000
   chunk 79 optimal weight:    0.0670
   chunk 33 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.2914

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

Flipped N/Q/H residues before XYZ refinement:
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1080 ASN
** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1248 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.168289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.123540 restraints weight = 11293.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.28
r_work: 0.3068 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9497  Z= 0.089
  Angle     :  0.514   7.296  12850  Z= 0.277
  Chirality :  0.040   0.143   1479
  Planarity :  0.003   0.070   1640
  Dihedral  :  5.120  31.301   1323
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.50 %
    Favored  : 87.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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 aren not related in a simple way.
  whole: -3.32 (0.23), residues: 1213
  helix: -1.98 (0.19), residues: 676
  sheet: -2.04 (0.65), residues: 70
  loop : -2.35 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1029 
 TYR   0.008   0.001   TYR A 220 
 PHE   0.019   0.001   PHE A 438 
 TRP   0.004   0.000   TRP A 933 
 HIS   0.001   0.000   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 9497)
  covalent geometry    : angle       0.51445 (12850)
  hydrogen bonds       : bond        0.02708 (  251)
  hydrogen bonds       : angle       4.32696 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8884 (tt) cc_final: 0.8607 (tp)
REVERT: A  438 PHE cc_start: 0.8568 (t80) cc_final: 0.8041 (t80)
REVERT: A  472 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7873 (mt-10)
REVERT: A  488 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8811 (mt)
REVERT: A  544 GLU cc_start: 0.7609 (pp20) cc_final: 0.7244 (tm-30)
REVERT: A  548 ARG cc_start: 0.7923 (mtm180) cc_final: 0.6897 (mtt180)
REVERT: A  604 MET cc_start: 0.7846 (ptm) cc_final: 0.7334 (ttm)
REVERT: A  653 ARG cc_start: 0.5679 (ptp-170) cc_final: 0.5342 (ttp-170)
REVERT: A  708 MET cc_start: 0.9184 (ttt) cc_final: 0.8963 (ttt)
REVERT: A  740 TYR cc_start: 0.8734 (t80) cc_final: 0.8490 (t80)
REVERT: A 1026 MET cc_start: 0.7490 (tpp) cc_final: 0.7281 (tpp)
REVERT: A 1074 LYS cc_start: 0.7277 (mtpp) cc_final: 0.6814 (mtmm)
  outliers start: 12
  outliers final: 7
  residues processed: 104
  average time/residue: 0.0795
  time to fit residues: 11.5482
Evaluate side-chains
  94 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1200 THR
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 118 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1080 ASN
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.166496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.120963 restraints weight = 11410.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.15
r_work: 0.2994 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9497  Z= 0.111
  Angle     :  0.525   6.455  12850  Z= 0.281
  Chirality :  0.041   0.141   1479
  Planarity :  0.003   0.063   1640
  Dihedral  :  5.085  32.987   1323
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.70 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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 aren not related in a simple way.
  whole: -3.13 (0.23), residues: 1213
  helix: -1.78 (0.19), residues: 675
  sheet: -2.18 (0.64), residues: 72
  loop : -2.30 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1029 
 TYR   0.008   0.001   TYR A 740 
 PHE   0.022   0.001   PHE A 305 
 TRP   0.004   0.001   TRP A 684 
 HIS   0.002   0.000   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9497)
  covalent geometry    : angle       0.52495 (12850)
  hydrogen bonds       : bond        0.03245 (  251)
  hydrogen bonds       : angle       4.27670 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8909 (tt) cc_final: 0.8610 (tp)
REVERT: A   74 MET cc_start: 0.8416 (mmp) cc_final: 0.8208 (mmt)
REVERT: A  368 LYS cc_start: 0.7744 (mmmm) cc_final: 0.7462 (mmmm)
REVERT: A  472 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7934 (mt-10)
REVERT: A  488 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8805 (mt)
REVERT: A  604 MET cc_start: 0.7871 (ptm) cc_final: 0.7345 (ttm)
REVERT: A  653 ARG cc_start: 0.5870 (ptp-170) cc_final: 0.5440 (ttp-170)
REVERT: A  708 MET cc_start: 0.9190 (ttt) cc_final: 0.8960 (ttt)
REVERT: A 1026 MET cc_start: 0.7474 (tpp) cc_final: 0.7248 (tpp)
REVERT: A 1074 LYS cc_start: 0.7239 (mtpp) cc_final: 0.6784 (mtmm)
  outliers start: 12
  outliers final: 8
  residues processed: 96
  average time/residue: 0.0780
  time to fit residues: 10.2427
Evaluate side-chains
  91 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1087 LYS
Chi-restraints excluded: chain A residue 1200 THR
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 73 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.166534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.121217 restraints weight = 11178.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.31
r_work: 0.2990 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9497  Z= 0.117
  Angle     :  0.546  15.572  12850  Z= 0.286
  Chirality :  0.041   0.139   1479
  Planarity :  0.003   0.065   1640
  Dihedral  :  5.070  32.620   1323
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.80 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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 aren not related in a simple way.
  whole: -3.03 (0.23), residues: 1213
  helix: -1.68 (0.19), residues: 677
  sheet: -2.21 (0.64), residues: 72
  loop : -2.28 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1029 
 TYR   0.008   0.001   TYR A 740 
 PHE   0.021   0.001   PHE A 305 
 TRP   0.005   0.001   TRP A 933 
 HIS   0.002   0.000   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9497)
  covalent geometry    : angle       0.54556 (12850)
  hydrogen bonds       : bond        0.03246 (  251)
  hydrogen bonds       : angle       4.26258 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8938 (tt) cc_final: 0.8714 (tp)
REVERT: A  368 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7604 (mmmm)
REVERT: A  472 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7970 (mt-10)
REVERT: A  488 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8631 (mt)
REVERT: A  604 MET cc_start: 0.7774 (ptm) cc_final: 0.7236 (ttm)
REVERT: A  653 ARG cc_start: 0.5790 (ptp-170) cc_final: 0.5449 (ttp-170)
REVERT: A  656 MET cc_start: 0.8764 (mtt) cc_final: 0.8553 (mtm)
REVERT: A  708 MET cc_start: 0.9191 (ttt) cc_final: 0.8964 (ttt)
REVERT: A 1026 MET cc_start: 0.7537 (tpp) cc_final: 0.7331 (tpp)
REVERT: A 1074 LYS cc_start: 0.7390 (mtpp) cc_final: 0.6927 (mtmm)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.0840
  time to fit residues: 11.6219
Evaluate side-chains
  96 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue 1010 ILE
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1087 LYS
Chi-restraints excluded: chain A residue 1200 THR
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 120 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 102 optimal weight:    0.1980
   chunk 113 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.4388

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

Flipped N/Q/H residues before XYZ refinement:
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 GLN
A 575 GLN
** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.166346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.122327 restraints weight = 11167.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.42
r_work: 0.2994 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9497  Z= 0.180
  Angle     :  0.607  14.474  12850  Z= 0.317
  Chirality :  0.043   0.139   1479
  Planarity :  0.004   0.066   1640
  Dihedral  :  5.383  34.634   1323
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.11 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.08 %

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 aren not related in a simple way.
  whole: -3.12 (0.23), residues: 1213
  helix: -1.81 (0.19), residues: 672
  sheet: -2.14 (0.66), residues: 70
  loop : -2.25 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1029 
 TYR   0.013   0.001   TYR A 250 
 PHE   0.028   0.002   PHE A  69 
 TRP   0.006   0.001   TRP A 933 
 HIS   0.003   0.001   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 9497)
  covalent geometry    : angle       0.60688 (12850)
  hydrogen bonds       : bond        0.04237 (  251)
  hydrogen bonds       : angle       4.47629 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   39 LEU cc_start: 0.8974 (tt) cc_final: 0.8768 (tp)
REVERT: A  368 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7717 (mmmm)
REVERT: A  472 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8003 (mt-10)
REVERT: A  488 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8744 (mt)
REVERT: A  604 MET cc_start: 0.7799 (ptm) cc_final: 0.7269 (ttm)
REVERT: A  653 ARG cc_start: 0.5880 (ptp-170) cc_final: 0.5577 (ttp-170)
REVERT: A  708 MET cc_start: 0.9208 (ttt) cc_final: 0.8962 (ttt)
REVERT: A  783 GLU cc_start: 0.7847 (pm20) cc_final: 0.7579 (pm20)
REVERT: A 1026 MET cc_start: 0.7552 (tpp) cc_final: 0.7314 (tpp)
REVERT: A 1074 LYS cc_start: 0.7407 (mtpp) cc_final: 0.6877 (mtmm)
  outliers start: 12
  outliers final: 10
  residues processed: 92
  average time/residue: 0.0910
  time to fit residues: 11.2423
Evaluate side-chains
  91 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue 1010 ILE
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1087 LYS
Chi-restraints excluded: chain A residue 1200 THR
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0270
   chunk 98 optimal weight:    0.8980
   chunk 111 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 40 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 92 optimal weight:    0.5980
   chunk 113 optimal weight:    0.9980
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.168008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.123604 restraints weight = 11245.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.38
r_work: 0.2990 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9497  Z= 0.098
  Angle     :  0.544  15.564  12850  Z= 0.285
  Chirality :  0.040   0.139   1479
  Planarity :  0.003   0.066   1640
  Dihedral  :  5.000  31.889   1323
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.11 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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 aren not related in a simple way.
  whole: -2.83 (0.23), residues: 1213
  helix: -1.53 (0.20), residues: 668
  sheet: -2.21 (0.65), residues: 72
  loop : -2.13 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1029 
 TYR   0.007   0.001   TYR A 740 
 PHE   0.025   0.001   PHE A 438 
 TRP   0.004   0.001   TRP A 933 
 HIS   0.001   0.000   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 9497)
  covalent geometry    : angle       0.54392 (12850)
  hydrogen bonds       : bond        0.02932 (  251)
  hydrogen bonds       : angle       4.23707 (  705)

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

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

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2426 Ramachandran restraints generated.
    1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7698 (mmmm)
REVERT: A  472 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7944 (mt-10)
REVERT: A  488 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8722 (mt)
REVERT: A  604 MET cc_start: 0.7794 (ptm) cc_final: 0.7211 (ttm)
REVERT: A  653 ARG cc_start: 0.5778 (ptp-170) cc_final: 0.5444 (ttp-170)
REVERT: A  708 MET cc_start: 0.9191 (ttt) cc_final: 0.8980 (ttt)
REVERT: A  783 GLU cc_start: 0.7845 (pm20) cc_final: 0.7583 (pm20)
REVERT: A 1074 LYS cc_start: 0.7344 (mtpp) cc_final: 0.6829 (mtmm)
  outliers start: 13
  outliers final: 10
  residues processed: 97
  average time/residue: 0.0974
  time to fit residues: 12.7632
Evaluate side-chains
  93 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue 1010 ILE
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1087 LYS
Chi-restraints excluded: chain A residue 1200 THR
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 83 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 38 optimal weight:    0.1980
   chunk 31 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0020
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1080 ASN
** A1093 GLN ** 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 = 0.3878 r_free = 0.3878 target = 0.168646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.124982 restraints weight = 11099.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.41
r_work: 0.3087 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9497  Z= 0.098
  Angle     :  0.533  14.510  12850  Z= 0.280
  Chirality :  0.040   0.150   1479
  Planarity :  0.003   0.064   1640
  Dihedral  :  4.845  31.714   1323
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 12.31 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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 aren not related in a simple way.
  whole: -2.61 (0.24), residues: 1213
  helix: -1.36 (0.20), residues: 667
  sheet: -2.06 (0.66), residues: 72
  loop : -2.05 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1029 
 TYR   0.007   0.001   TYR A 740 
 PHE   0.028   0.001   PHE A 438 
 TRP   0.004   0.001   TRP A 684 
 HIS   0.002   0.000   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 9497)
  covalent geometry    : angle       0.53347 (12850)
  hydrogen bonds       : bond        0.02874 (  251)
  hydrogen bonds       : angle       4.12470 (  705)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1864.54 seconds
wall clock time: 32 minutes 29.54 seconds (1949.54 seconds total)