Starting phenix.real_space_refine
on Fri Oct 10 22:18:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wom_37692/10_2025/8wom_37692_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wom_37692/10_2025/8wom_37692.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wom_37692/10_2025/8wom_37692.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wom_37692/10_2025/8wom_37692.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wom_37692/10_2025/8wom_37692_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wom_37692/10_2025/8wom_37692_neut.cif"
  }
  resolution = 3.5
  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=   0.006 sd=   0.096
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    5987      2.51       5
     N    1583      2.21       5
     O    1740      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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9348
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1217, 9314
          Classifications: {'peptide': 1217}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 30, 'TRANS': 1186}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'BLD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.57, per 1000 atoms: 0.27
  Number of scatterers: 9348
  At special positions: 0
  Unit cell: (73.7, 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    1740      8.00
     N    1583      7.00
     C    5987      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: 0.89
  Conformation dependent library (CDL) restraints added in 386.7 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:
      68 helices and 6 sheets defined
      47.2% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 45
    Processing helix  chain 'A' and resid 46 through 51
      removed outlier: 3.504A  pdb=" N   VAL A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 71
      removed outlier: 4.165A  pdb=" N   LEU A  60 " --> pdb=" O   PRO A  56 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL A  66 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASN A  67 " --> pdb=" O   GLY A  63 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY A  68 " --> pdb=" O   GLN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 98
      removed outlier: 3.547A  pdb=" N   HIS A  81 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   TYR A  86 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE A  90 " --> pdb=" O   TYR A  86 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   VAL A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 131 through 135
    Processing helix  chain 'A' and resid 143 through 150
    Processing helix  chain 'A' and resid 150 through 160
      removed outlier: 3.565A  pdb=" N   VAL A 155 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLN A 156 " --> pdb=" O   THR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 176
      removed outlier: 3.617A  pdb=" N   TYR A 169 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A 170 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE A 173 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 184
    Processing helix  chain 'A' and resid 194 through 209
      removed outlier: 3.916A  pdb=" N   PHE A 200 " --> pdb=" O   PRO A 196 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ALA A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   ALA A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 221
      removed outlier: 4.392A  pdb=" N   LYS A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU A 218 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA A 221 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 233
      removed outlier: 4.670A  pdb=" N   ILE A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 254 through 263
      removed outlier: 3.745A  pdb=" N   LYS A 259 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   LEU A 260 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LYS A 263 " --> pdb=" O   LYS A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 270
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 289 through 294
    Processing helix  chain 'A' and resid 303 through 314
      removed outlier: 3.867A  pdb=" N   ALA A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE A 309 " --> pdb=" O   PHE A 305 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA A 311 " --> pdb=" O   ALA A 307 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 319
      removed outlier: 3.811A  pdb=" N   LEU A 318 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 324
    Processing helix  chain 'A' and resid 326 through 339
      removed outlier: 3.803A  pdb=" N   LYS A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LYS A 332 " --> pdb=" O   PHE A 328 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   TYR A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU A 338 " --> pdb=" O   ALA A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 414
      removed outlier: 4.033A  pdb=" N   GLU A 414 " --> pdb=" O   VAL A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 434
      No H-bonds generated for 'chain 'A' and resid 432 through 434'
    Processing helix  chain 'A' and resid 439 through 441
      No H-bonds generated for 'chain 'A' and resid 439 through 441'
    Processing helix  chain 'A' and resid 460 through 464
    Processing helix  chain 'A' and resid 470 through 477
    Processing helix  chain 'A' and resid 511 through 520
      removed outlier: 3.660A  pdb=" N   ALA A 515 " --> pdb=" O   ARG A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 550
      removed outlier: 3.994A  pdb=" N   VAL A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN A 543 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLU A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA A 545 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL A 549 " --> pdb=" O   ALA A 545 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   MET A 550 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 605
    Processing helix  chain 'A' and resid 621 through 632
      removed outlier: 3.606A  pdb=" N   HIS A 625 " --> pdb=" O   THR A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 679
      removed outlier: 3.556A  pdb=" N   ARG A 675 " --> pdb=" O   ASN A 671 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU A 677 " --> pdb=" O   PHE A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 700
      removed outlier: 3.847A  pdb=" N   ILE A 700 " --> pdb=" O   SER A 697 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 697 through 700'
    Processing helix  chain 'A' and resid 701 through 715
      removed outlier: 3.695A  pdb=" N   ALA A 705 " --> pdb=" O   GLY A 701 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   VAL A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER A 709 " --> pdb=" O   ALA A 705 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET A 711 " --> pdb=" O   VAL A 707 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE A 712 " --> pdb=" O   MET A 708 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLU A 713 " --> pdb=" O   SER A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 728
    Processing helix  chain 'A' and resid 728 through 737
      removed outlier: 4.592A  pdb=" N   TYR A 734 " --> pdb=" O   TYR A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 751
      removed outlier: 3.544A  pdb=" N   TYR A 750 " --> pdb=" O   LEU A 746 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   PHE A 751 " --> pdb=" O   ILE A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 772
      removed outlier: 3.993A  pdb=" N   ALA A 770 " --> pdb=" O   MET A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 780
      removed outlier: 4.157A  pdb=" N   PHE A 779 " --> pdb=" O   GLU A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 785
      removed outlier: 3.707A  pdb=" N   ASN A 785 " --> pdb=" O   ASP A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 808 through 813
    Processing helix  chain 'A' and resid 813 through 818
    Processing helix  chain 'A' and resid 820 through 829
      removed outlier: 3.799A  pdb=" N   VAL A 824 " --> pdb=" O   THR A 820 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA A 825 " --> pdb=" O   SER A 821 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   PHE A 826 " --> pdb=" O   PHE A 822 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLU A 829 " --> pdb=" O   ALA A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 853
      Proline residue:  A 841  - end of helix
      removed outlier: 3.575A  pdb=" N   LEU A 845 " --> pdb=" O   PRO A 841 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   PHE A 848 " --> pdb=" O   VAL A 844 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLN A 850 " --> pdb=" O   ALA A 846 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   GLN A 851 " --> pdb=" O   ASN A 847 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 852 " --> pdb=" O   PHE A 848 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER A 853 " --> pdb=" O   ALA A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 856
      No H-bonds generated for 'chain 'A' and resid 854 through 856'
    Processing helix  chain 'A' and resid 860 through 865
      removed outlier: 4.186A  pdb=" N   ALA A 864 " --> pdb=" O   ASP A 860 " (cutoff:3.500A)
      removed outlier: 4.164A  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 875
      removed outlier: 3.835A  pdb=" N   ILE A 871 " --> pdb=" O   LYS A 867 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 872 " --> pdb=" O   THR A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 883
    Processing helix  chain 'A' and resid 884 through 887
      removed outlier: 4.043A  pdb=" N   ALA A 887 " --> pdb=" O   ALA A 884 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 884 through 887'
    Processing helix  chain 'A' and resid 891 through 895
    Processing helix  chain 'A' and resid 900 through 905
    Processing helix  chain 'A' and resid 908 through 921
      removed outlier: 3.772A  pdb=" N   GLY A 914 " --> pdb=" O   SER A 910 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE A 915 " --> pdb=" O   GLN A 911 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN A 921 " --> pdb=" O   PHE A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 921 through 926
      removed outlier: 3.663A  pdb=" N   TYR A 925 " --> pdb=" O   GLN A 921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 939
      removed outlier: 3.701A  pdb=" N   ILE A 931 " --> pdb=" O   SER A 927 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 938 " --> pdb=" O   TYR A 934 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A 939 " --> pdb=" O   GLY A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 959
      removed outlier: 3.528A  pdb=" N   VAL A 955 " --> pdb=" O   LYS A 951 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 956 " --> pdb=" O   VAL A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 964
      removed outlier: 4.023A  pdb=" N   ALA A 964 " --> pdb=" O   ALA A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 975
      removed outlier: 4.002A  pdb=" N   ILE A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1059
      removed outlier: 4.425A  pdb=" N   GLU A1059 " --> pdb=" O   ILE A1055 " (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 1080 through 1086
      removed outlier: 3.980A  pdb=" N   LEU A1086 " --> pdb=" O   LYS A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1115 through 1123
      removed outlier: 3.950A  pdb=" N   ILE A1119 " --> pdb=" O   GLU A1115 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ASP A1120 " --> pdb=" O   SER A1116 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A1121 " --> pdb=" O   GLU A1117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1133
    Processing helix  chain 'A' and resid 1150 through 1166
      removed outlier: 3.780A  pdb=" N   GLN A1155 " --> pdb=" O   GLY A1151 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ARG A1156 " --> pdb=" O   GLY A1152 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A1157 " --> pdb=" O   GLN A1153 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA A1158 " --> pdb=" O   LYS A1154 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA A1160 " --> pdb=" O   ARG A1156 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA A1162 " --> pdb=" O   ALA A1158 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A1164 " --> pdb=" O   ALA A1160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1189 through 1194
    Processing helix  chain 'A' and resid 1240 through 1246
      removed outlier: 3.901A  pdb=" N   LEU A1244 " --> pdb=" O   ALA A1240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1249
      No H-bonds generated for 'chain 'A' and resid 1247 through 1249'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 371
      removed outlier: 5.812A  pdb=" N   PHE A 367 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   LEU A 425 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   ASP A 369 " --> pdb=" O   GLN A 423 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   GLN A 423 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER A 421 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 443 through 446
      removed outlier: 5.627A  pdb=" N   GLY A 444 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU A 525 " --> pdb=" O   VAL A 556 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   ALA A 572 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   ALA A 397 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE A 574 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   VAL A 573 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 645 through 646
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1028 through 1034
      removed outlier: 5.864A  pdb=" N   ARG A1029 " --> pdb=" O   PHE A1017 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   PHE A1017 " --> pdb=" O   ARG A1029 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A1015 " --> pdb=" O   PHE A1031 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   LEU A1033 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   ARG A1013 " --> pdb=" O   LEU A1033 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1041
      removed outlier: 7.109A  pdb=" N   GLY A1089 " --> pdb=" O   LEU A1171 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1216 through 1220
      removed outlier: 6.657A  pdb=" N   ILE A1216 " --> pdb=" O   GLN A1227 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLN A1227 " --> pdb=" O   ILE A1216 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   VAL A1218 " --> pdb=" O   VAL A1225 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    642 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: 1.58

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1549
        1.32 -     1.44: 2513
        1.44 -     1.56: 5394
        1.56 -     1.69: 1
        1.69 -     1.81: 67
  Bond restraints: 9524
  Sorted by residual:
  bond pdb=" CA  ILE A 195 "
       pdb=" C   ILE A 195 "
    ideal  model  delta    sigma   weight residual
    1.520  1.536 -0.016 8.80e-03 1.29e+04 3.27e+00
  bond pdb=" C   ALA A 668 "
       pdb=" N   PRO A 669 "
    ideal  model  delta    sigma   weight residual
    1.332  1.351 -0.019 1.30e-02 5.92e+03 2.19e+00
  bond pdb=" C   ILE A 195 "
       pdb=" N   PRO A 196 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.012 8.40e-03 1.42e+04 1.98e+00
  bond pdb=" CB  PRO A  56 "
       pdb=" CG  PRO A  56 "
    ideal  model  delta    sigma   weight residual
    1.492  1.429  0.063 5.00e-02 4.00e+02 1.59e+00
  bond pdb=" N   VAL A 605 "
       pdb=" CA  VAL A 605 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.90e-02 2.77e+03 1.56e+00
  ... (remaining 9519 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.23: 12813
        4.23 -     8.47: 74
        8.47 -    12.70: 4
       12.70 -    16.94: 1
       16.94 -    21.17: 6
  Bond angle restraints: 12898
  Sorted by residual:
  angle pdb=" C   ASN A1126 "
        pdb=" CA  ASN A1126 "
        pdb=" CB  ASN A1126 "
      ideal   model   delta    sigma   weight residual
     110.26   89.59   20.67 1.50e+00 4.44e-01 1.90e+02
  angle pdb=" N   ASN A1126 "
        pdb=" CA  ASN A1126 "
        pdb=" C   ASN A1126 "
      ideal   model   delta    sigma   weight residual
     109.59   91.32   18.27 1.47e+00 4.63e-01 1.54e+02
  angle pdb=" N   ARG A 653 "
        pdb=" CA  ARG A 653 "
        pdb=" CB  ARG A 653 "
      ideal   model   delta    sigma   weight residual
     110.39   90.68   19.71 1.59e+00 3.96e-01 1.54e+02
  angle pdb=" C   PHE A  69 "
        pdb=" CA  PHE A  69 "
        pdb=" CB  PHE A  69 "
      ideal   model   delta    sigma   weight residual
     110.70  131.83  -21.13 1.83e+00 2.99e-01 1.33e+02
  angle pdb=" N   GLY A 652 "
        pdb=" CA  GLY A 652 "
        pdb=" C   GLY A 652 "
      ideal   model   delta    sigma   weight residual
     113.18   92.01   21.17 2.37e+00 1.78e-01 7.98e+01
  ... (remaining 12893 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.44: 5603
       26.44 -    52.89: 97
       52.89 -    79.33: 13
       79.33 -   105.77: 2
      105.77 -   132.21: 1
  Dihedral angle restraints: 5716
    sinusoidal: 2228
      harmonic: 3488
  Sorted by residual:
  dihedral pdb=" C   ASN A1126 "
           pdb=" N   ASN A1126 "
           pdb=" CA  ASN A1126 "
           pdb=" CB  ASN A1126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -90.00  -32.60     0      2.50e+00 1.60e-01 1.70e+02
  dihedral pdb=" C   PHE A  69 "
           pdb=" N   PHE A  69 "
           pdb=" CA  PHE A  69 "
           pdb=" CB  PHE A  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -151.08   28.48     0      2.50e+00 1.60e-01 1.30e+02
  dihedral pdb=" N   ALA A1127 "
           pdb=" C   ALA A1127 "
           pdb=" CA  ALA A1127 "
           pdb=" CB  ALA A1127 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90   99.33   23.57     0      2.50e+00 1.60e-01 8.89e+01
  ... (remaining 5713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.208: 1481
       0.208 -    0.417: 7
       0.417 -    0.625: 1
       0.625 -    0.834: 2
       0.834 -    1.042: 1
  Chirality restraints: 1492
  Sorted by residual:
  chirality pdb=" CA  PHE A  69 "
            pdb=" N   PHE A  69 "
            pdb=" C   PHE A  69 "
            pdb=" CB  PHE A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.47    1.04 2.00e-01 2.50e+01 2.71e+01
  chirality pdb=" CA  ASN A1126 "
            pdb=" N   ASN A1126 "
            pdb=" C   ASN A1126 "
            pdb=" CB  ASN A1126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.26   -0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" CA  ALA A1127 "
            pdb=" N   ALA A1127 "
            pdb=" C   ALA A1127 "
            pdb=" CB  ALA A1127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    3.14   -0.66 2.00e-01 2.50e+01 1.08e+01
  ... (remaining 1489 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 681 "   -0.072 5.00e-02 4.00e+02   1.09e-01 1.92e+01
        pdb=" N   PRO A 682 "    0.189 5.00e-02 4.00e+02
        pdb=" CA  PRO A 682 "   -0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A 682 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 701 "   -0.045 5.00e-02 4.00e+02   6.73e-02 7.24e+00
        pdb=" N   PRO A 702 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 702 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 702 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 195 "    0.042 5.00e-02 4.00e+02   6.28e-02 6.30e+00
        pdb=" N   PRO A 196 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 196 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 196 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        1.00 -     1.78: 2
        1.78 -     2.56: 55
        2.56 -     3.34: 10734
        3.34 -     4.12: 20304
        4.12 -     4.90: 38073
  Nonbonded interactions: 69168
  Sorted by model distance:
  nonbonded pdb=" O   ASN A1126 "
            pdb=" OD1 ASN A1126 "
     model   vdw
     1.004 3.040
  nonbonded pdb=" O   ASN A1126 "
            pdb=" CG  ASN A1126 "
     model   vdw
     1.707 3.270
  nonbonded pdb=" C   ASN A1126 "
            pdb=" OD1 ASN A1126 "
     model   vdw
     2.081 3.270
  nonbonded pdb=" OG  SER A 697 "
            pdb=" O   ALA A 744 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OE2 GLU A 829 "
            pdb=" OG  SER A 944 "
     model   vdw
     2.335 3.040
  ... (remaining 69163 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     10.850
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
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   0.063   9524  Z= 0.219
  Angle     :  1.036  21.171  12898  Z= 0.592
  Chirality :  0.067   1.042   1492
  Planarity :  0.007   0.109   1640
  Dihedral  : 11.185 132.215   3488
  Min Nonbonded Distance : 1.004

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.45 %
  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: -6.42 (0.15), residues: 1213
  helix: -4.87 (0.07), residues: 634
  sheet: -3.52 (0.50), residues: 72
  loop : -3.31 (0.22), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 295 
 TYR   0.016   0.002   TYR A 730 
 PHE   0.026   0.002   PHE A  69 
 TRP   0.014   0.002   TRP A 933 
 HIS   0.010   0.002   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 9524)
  covalent geometry    : angle       1.03649 (12898)
  hydrogen bonds       : bond        0.34459 (  229)
  hydrogen bonds       : angle      11.39008 (  642)

*********************** 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
  190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.8607 (m-30) cc_final: 0.8382 (m-30)
REVERT: A  218 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7624 (tm-30)
REVERT: A  543 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8467 (tp-100)
REVERT: A  708 MET cc_start: 0.8645 (tmm) cc_final: 0.8406 (tmm)
REVERT: A 1006 ILE cc_start: 0.8354 (mm) cc_final: 0.8063 (tp)
REVERT: A 1026 MET cc_start: 0.6611 (mmm) cc_final: 0.6287 (mmm)
REVERT: A 1156 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.7493 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1420
  time to fit residues: 34.6954
Evaluate side-chains
  107 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 117 optimal weight:    0.0870
   overall best weight:    1.8962

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

Flipped N/Q/H residues before XYZ refinement:
A  51 HIS
A 168 HIS
A 350 GLN
A 503 GLN
A 602 GLN
A 748 GLN
A 758 ASN
** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4016 r_free = 0.4016 target = 0.173177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125969 restraints weight = 12336.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.122320 restraints weight = 10147.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.123825 restraints weight = 12041.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.124116 restraints weight = 7363.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.124823 restraints weight = 6667.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9524  Z= 0.230
  Angle     :  0.693  10.029  12898  Z= 0.376
  Chirality :  0.045   0.162   1492
  Planarity :  0.006   0.091   1640
  Dihedral  :  7.255  63.113   1407
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  7.54 %
    Favored  : 90.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.55 (0.18), residues: 1213
  helix: -4.05 (0.11), residues: 647
  sheet: -3.07 (0.54), residues: 72
  loop : -3.01 (0.24), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 725 
 TYR   0.018   0.002   TYR A 740 
 PHE   0.027   0.002   PHE A1130 
 TRP   0.009   0.002   TRP A 283 
 HIS   0.005   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 9524)
  covalent geometry    : angle       0.69313 (12898)
  hydrogen bonds       : bond        0.04579 (  229)
  hydrogen bonds       : angle       6.35744 (  642)

*********************** 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
  128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A  218 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7543 (tm-30)
REVERT: A  457 ILE cc_start: 0.8811 (pt) cc_final: 0.8530 (mt)
REVERT: A 1006 ILE cc_start: 0.8224 (mm) cc_final: 0.7965 (tp)
  outliers start: 16
  outliers final: 4
  residues processed: 127
  average time/residue: 0.1067
  time to fit residues: 18.7290
Evaluate side-chains
  97 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1203 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 94 optimal weight:    0.3980
   chunk 106 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 784 HIS
A 865 HIS
A1128 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.175652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128691 restraints weight = 12245.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.124236 restraints weight = 9370.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.125823 restraints weight = 11902.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.126286 restraints weight = 7018.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.126967 restraints weight = 6184.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9524  Z= 0.138
  Angle     :  0.598  11.851  12898  Z= 0.320
  Chirality :  0.042   0.154   1492
  Planarity :  0.005   0.079   1640
  Dihedral  :  6.371  46.719   1407
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.68 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.71 (0.20), residues: 1213
  helix: -3.22 (0.15), residues: 650
  sheet: -2.96 (0.51), residues: 82
  loop : -2.76 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1078 
 TYR   0.013   0.001   TYR A 740 
 PHE   0.028   0.002   PHE A 438 
 TRP   0.006   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9524)
  covalent geometry    : angle       0.59840 (12898)
  hydrogen bonds       : bond        0.03479 (  229)
  hydrogen bonds       : angle       5.37980 (  642)

*********************** 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
  127 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: A  457 ILE cc_start: 0.8630 (pt) cc_final: 0.8220 (mt)
REVERT: A  604 MET cc_start: 0.3530 (ttt) cc_final: 0.3207 (ptm)
REVERT: A 1014 HIS cc_start: 0.7755 (m90) cc_final: 0.7318 (m-70)
REVERT: A 1022 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7227 (ttp-170)
  outliers start: 16
  outliers final: 10
  residues processed: 123
  average time/residue: 0.1057
  time to fit residues: 18.0042
Evaluate side-chains
  106 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  734 TYR
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1063 ASP
Chi-restraints excluded: chain A residue 1074 LYS
Chi-restraints excluded: chain A residue 1203 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 91 optimal weight:    0.1980
   chunk 42 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 71 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 115 optimal weight:    7.9990
   chunk 43 optimal weight:    0.1980
   chunk 65 optimal weight:    0.0970
   chunk 22 optimal weight:    0.0170
   chunk 28 optimal weight:    0.3980
   chunk 101 optimal weight:   10.0000
   overall best weight:    0.1816

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
A 503 GLN
A 680 ASN
A 748 GLN
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.181501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.135196 restraints weight = 12337.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.130019 restraints weight = 11228.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131387 restraints weight = 11135.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.132619 restraints weight = 6581.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.132900 restraints weight = 5624.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9524  Z= 0.086
  Angle     :  0.524   9.023  12898  Z= 0.282
  Chirality :  0.040   0.141   1492
  Planarity :  0.004   0.067   1640
  Dihedral  :  5.713  43.522   1407
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.31 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.99 (0.21), residues: 1213
  helix: -2.62 (0.18), residues: 632
  sheet: -2.47 (0.58), residues: 74
  loop : -2.54 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 384 
 TYR   0.014   0.001   TYR A 740 
 PHE   0.026   0.001   PHE A1130 
 TRP   0.004   0.001   TRP A 185 
 HIS   0.002   0.000   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 9524)
  covalent geometry    : angle       0.52412 (12898)
  hydrogen bonds       : bond        0.02405 (  229)
  hydrogen bonds       : angle       4.69031 (  642)

*********************** 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
  130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8038 (mttp) cc_final: 0.7650 (pttm)
REVERT: A  218 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7489 (tm-30)
REVERT: A  449 GLU cc_start: 0.7465 (pm20) cc_final: 0.7190 (tm-30)
REVERT: A  457 ILE cc_start: 0.8460 (pt) cc_final: 0.8196 (mt)
REVERT: A  470 MET cc_start: 0.7113 (tpt) cc_final: 0.6574 (tpt)
REVERT: A  604 MET cc_start: 0.3556 (ttt) cc_final: 0.3173 (ptm)
REVERT: A 1014 HIS cc_start: 0.7773 (m90) cc_final: 0.7289 (m-70)
REVERT: A 1022 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.7430 (ttp-170)
  outliers start: 13
  outliers final: 7
  residues processed: 127
  average time/residue: 0.1110
  time to fit residues: 19.2972
Evaluate side-chains
  102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1074 LYS
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1157 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 112 optimal weight:    0.7980
   chunk 120 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 118 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 350 GLN
A 483 HIS
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 748 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 = 0.3978 r_free = 0.3978 target = 0.169863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.124122 restraints weight = 12464.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.119841 restraints weight = 12036.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.121240 restraints weight = 13912.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.121781 restraints weight = 8457.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.122215 restraints weight = 7558.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048   9524  Z= 0.332
  Angle     :  0.721   8.121  12898  Z= 0.380
  Chirality :  0.048   0.152   1492
  Planarity :  0.005   0.076   1640
  Dihedral  :  6.565  53.819   1407
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.33 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.08 (0.21), residues: 1213
  helix: -2.67 (0.17), residues: 644
  sheet: -2.65 (0.53), residues: 83
  loop : -2.53 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 295 
 TYR   0.023   0.002   TYR A 740 
 PHE   0.022   0.002   PHE A1130 
 TRP   0.011   0.002   TRP A 283 
 HIS   0.004   0.001   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00784 ( 9524)
  covalent geometry    : angle       0.72134 (12898)
  hydrogen bonds       : bond        0.04550 (  229)
  hydrogen bonds       : angle       5.48525 (  642)

*********************** 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
  119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8049 (mttp) cc_final: 0.7721 (pttm)
REVERT: A  218 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7598 (tm-30)
REVERT: A  457 ILE cc_start: 0.8819 (pt) cc_final: 0.8363 (mt)
REVERT: A  576 GLN cc_start: 0.8134 (pm20) cc_final: 0.7580 (tm-30)
REVERT: A  604 MET cc_start: 0.3504 (ttt) cc_final: 0.3111 (ptm)
REVERT: A  870 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7678 (mpp)
REVERT: A 1014 HIS cc_start: 0.7589 (m90) cc_final: 0.7258 (m-70)
REVERT: A 1193 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7508 (mtp85)
  outliers start: 24
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1144
  time to fit residues: 17.3254
Evaluate side-chains
  103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue  912 THR
Chi-restraints excluded: chain A residue 1074 LYS
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1203 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 81 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0570
   chunk 84 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 98 optimal weight:    7.9990
   chunk 120 optimal weight:    8.9990
   chunk 69 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
A 543 GLN
A 680 ASN
A 748 GLN
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.170395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.116555 restraints weight = 12660.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.117812 restraints weight = 6566.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.117675 restraints weight = 4586.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.118069 restraints weight = 4777.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.118482 restraints weight = 4264.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   9524  Z= 0.107
  Angle     :  0.559   9.664  12898  Z= 0.296
  Chirality :  0.041   0.150   1492
  Planarity :  0.004   0.074   1640
  Dihedral  :  5.951  46.498   1407
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.46 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.62 (0.22), residues: 1213
  helix: -2.24 (0.19), residues: 638
  sheet: -2.51 (0.54), residues: 86
  loop : -2.40 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 725 
 TYR   0.007   0.001   TYR A1241 
 PHE   0.027   0.001   PHE A1130 
 TRP   0.007   0.001   TRP A 185 
 HIS   0.002   0.000   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9524)
  covalent geometry    : angle       0.55883 (12898)
  hydrogen bonds       : bond        0.02862 (  229)
  hydrogen bonds       : angle       4.79817 (  642)

*********************** 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
  118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8099 (mttp) cc_final: 0.7575 (pttm)
REVERT: A  218 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7713 (tm-30)
REVERT: A  238 TYR cc_start: 0.8639 (m-80) cc_final: 0.8248 (m-80)
REVERT: A  470 MET cc_start: 0.7355 (tpt) cc_final: 0.6675 (tpt)
REVERT: A  576 GLN cc_start: 0.8347 (pm20) cc_final: 0.7713 (tm-30)
REVERT: A 1014 HIS cc_start: 0.8313 (m90) cc_final: 0.7623 (m-70)
REVERT: A 1193 ARG cc_start: 0.8193 (mtm180) cc_final: 0.7948 (mtp85)
  outliers start: 20
  outliers final: 16
  residues processed: 109
  average time/residue: 0.1118
  time to fit residues: 16.6866
Evaluate side-chains
  107 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  543 GLN
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain A residue  734 TYR
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue 1063 ASP
Chi-restraints excluded: chain A residue 1074 LYS
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1157 ILE
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1203 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 65 optimal weight:    0.0980
   chunk 95 optimal weight:    1.9990
   chunk 120 optimal weight:    9.9990
   chunk 105 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 108 optimal weight:    8.9990
   chunk 64 optimal weight:    0.0870
   overall best weight:    0.9962

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

Flipped N/Q/H residues before XYZ refinement:
A 543 GLN
A 680 ASN
** A1250 HIS ** 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 = 0.4028 r_free = 0.4028 target = 0.175128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.128238 restraints weight = 12190.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.123619 restraints weight = 9686.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.125036 restraints weight = 10740.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.125561 restraints weight = 6965.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.125947 restraints weight = 6229.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9524  Z= 0.133
  Angle     :  0.560   9.182  12898  Z= 0.296
  Chirality :  0.042   0.158   1492
  Planarity :  0.004   0.068   1640
  Dihedral  :  5.837  47.204   1407
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.76 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.35 (0.23), residues: 1213
  helix: -2.00 (0.19), residues: 638
  sheet: -2.39 (0.55), residues: 86
  loop : -2.30 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1078 
 TYR   0.020   0.001   TYR A 740 
 PHE   0.022   0.001   PHE A 438 
 TRP   0.006   0.001   TRP A 185 
 HIS   0.002   0.000   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9524)
  covalent geometry    : angle       0.55954 (12898)
  hydrogen bonds       : bond        0.02964 (  229)
  hydrogen bonds       : angle       4.70676 (  642)

*********************** 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
  117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.7945 (mttp) cc_final: 0.7679 (pttm)
REVERT: A  218 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7678 (tm-30)
REVERT: A 1014 HIS cc_start: 0.7709 (m90) cc_final: 0.7248 (m-70)
  outliers start: 21
  outliers final: 18
  residues processed: 109
  average time/residue: 0.1123
  time to fit residues: 16.7217
Evaluate side-chains
  107 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  734 TYR
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue 1063 ASP
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1157 ILE
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1198 ARG
Chi-restraints excluded: chain A residue 1203 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 94 optimal weight:    0.0010
   chunk 84 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   overall best weight:    0.9390

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
** A1250 HIS ** 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 = 0.4336 r_free = 0.4336 target = 0.198397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.145544 restraints weight = 12468.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.143831 restraints weight = 8676.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.144274 restraints weight = 7091.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.145231 restraints weight = 5246.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.145263 restraints weight = 4418.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9524  Z= 0.126
  Angle     :  0.553   9.284  12898  Z= 0.292
  Chirality :  0.041   0.151   1492
  Planarity :  0.004   0.070   1640
  Dihedral  :  5.762  46.963   1407
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.86 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.23), residues: 1213
  helix: -1.83 (0.20), residues: 639
  sheet: -2.26 (0.56), residues: 86
  loop : -2.25 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1007 
 TYR   0.018   0.001   TYR A 740 
 PHE   0.031   0.001   PHE A1130 
 TRP   0.006   0.001   TRP A 185 
 HIS   0.002   0.000   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9524)
  covalent geometry    : angle       0.55345 (12898)
  hydrogen bonds       : bond        0.02917 (  229)
  hydrogen bonds       : angle       4.65117 (  642)

*********************** 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
  117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8011 (mttp) cc_final: 0.7661 (pttm)
REVERT: A  218 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7635 (tm-30)
REVERT: A  576 GLN cc_start: 0.8114 (pm20) cc_final: 0.7635 (tm-30)
REVERT: A 1014 HIS cc_start: 0.8028 (m90) cc_final: 0.7486 (m-70)
REVERT: A 1070 MET cc_start: 0.8383 (tpp) cc_final: 0.7953 (tpp)
  outliers start: 22
  outliers final: 18
  residues processed: 111
  average time/residue: 0.1115
  time to fit residues: 16.9094
Evaluate side-chains
  103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain A residue  734 TYR
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1149 LEU
Chi-restraints excluded: chain A residue 1157 ILE
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1198 ARG
Chi-restraints excluded: chain A residue 1203 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.192868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.144023 restraints weight = 12350.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.141939 restraints weight = 8341.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.142852 restraints weight = 7018.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.143629 restraints weight = 5010.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.143723 restraints weight = 4302.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9524  Z= 0.114
  Angle     :  0.536   8.845  12898  Z= 0.284
  Chirality :  0.041   0.138   1492
  Planarity :  0.004   0.067   1640
  Dihedral  :  5.633  46.507   1407
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.46 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.98 (0.24), residues: 1213
  helix: -1.66 (0.20), residues: 638
  sheet: -2.18 (0.57), residues: 87
  loop : -2.21 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1078 
 TYR   0.018   0.001   TYR A 740 
 PHE   0.031   0.001   PHE A1130 
 TRP   0.006   0.001   TRP A 283 
 HIS   0.002   0.000   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9524)
  covalent geometry    : angle       0.53561 (12898)
  hydrogen bonds       : bond        0.02781 (  229)
  hydrogen bonds       : angle       4.56863 (  642)

*********************** 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
  111 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.7945 (mttp) cc_final: 0.7671 (pttm)
REVERT: A  218 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: A  576 GLN cc_start: 0.8040 (pm20) cc_final: 0.7616 (tm-30)
REVERT: A  697 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8326 (t)
REVERT: A 1014 HIS cc_start: 0.7874 (m90) cc_final: 0.7409 (m-70)
REVERT: A 1026 MET cc_start: 0.5878 (mmt) cc_final: 0.5640 (mmm)
REVERT: A 1070 MET cc_start: 0.8413 (tpp) cc_final: 0.8015 (tpp)
  outliers start: 23
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1128
  time to fit residues: 16.3011
Evaluate side-chains
  108 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain A residue  734 TYR
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1063 ASP
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1157 ILE
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1198 ARG
Chi-restraints excluded: chain A residue 1203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 117 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 89 optimal weight:    0.6980
   chunk 111 optimal weight:    4.9990
   overall best weight:    2.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.187522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.139231 restraints weight = 12485.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.135125 restraints weight = 9037.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.136370 restraints weight = 8461.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.136979 restraints weight = 5548.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.137295 restraints weight = 4716.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   9524  Z= 0.262
  Angle     :  0.662   9.381  12898  Z= 0.347
  Chirality :  0.046   0.142   1492
  Planarity :  0.004   0.073   1640
  Dihedral  :  6.281  52.141   1407
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.86 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.27 (0.23), residues: 1213
  helix: -1.94 (0.19), residues: 642
  sheet: -2.12 (0.57), residues: 87
  loop : -2.31 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 295 
 TYR   0.018   0.002   TYR A 740 
 PHE   0.035   0.002   PHE A1130 
 TRP   0.009   0.002   TRP A 283 
 HIS   0.003   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 ( 9524)
  covalent geometry    : angle       0.66216 (12898)
  hydrogen bonds       : bond        0.03979 (  229)
  hydrogen bonds       : angle       5.16657 (  642)

********************** 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
  111 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: A  576 GLN cc_start: 0.8114 (pm20) cc_final: 0.7651 (tm-30)
REVERT: A  604 MET cc_start: 0.3729 (ttt) cc_final: 0.3243 (ptm)
REVERT: A 1014 HIS cc_start: 0.8008 (m90) cc_final: 0.7502 (m-70)
REVERT: A 1070 MET cc_start: 0.8441 (tpp) cc_final: 0.8033 (tpp)
REVERT: A 1193 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7572 (mtm180)
  outliers start: 20
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1088
  time to fit residues: 16.0223
Evaluate side-chains
  106 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  697 SER
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1172 LEU
Chi-restraints excluded: chain A residue 1198 ARG
Chi-restraints excluded: chain A residue 1203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 104 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 100 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 118 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.190736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.142623 restraints weight = 12285.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.138023 restraints weight = 9422.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.139696 restraints weight = 7389.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.140634 restraints weight = 4996.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.140696 restraints weight = 4498.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9524  Z= 0.145
  Angle     :  0.567   9.129  12898  Z= 0.301
  Chirality :  0.042   0.134   1492
  Planarity :  0.004   0.074   1640
  Dihedral  :  5.931  47.494   1407
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.58 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.07 (0.23), residues: 1213
  helix: -1.72 (0.20), residues: 642
  sheet: -2.13 (0.57), residues: 87
  loop : -2.29 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1007 
 TYR   0.019   0.001   TYR A 740 
 PHE   0.032   0.001   PHE A1130 
 TRP   0.009   0.001   TRP A 185 
 HIS   0.002   0.000   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9524)
  covalent geometry    : angle       0.56697 (12898)
  hydrogen bonds       : bond        0.03113 (  229)
  hydrogen bonds       : angle       4.80557 (  642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1548.94 seconds
wall clock time: 27 minutes 31.38 seconds (1651.38 seconds total)