Starting phenix.real_space_refine
on Sun Dec 29 03:25:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jw4_36679/12_2024/8jw4_36679_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jw4_36679/12_2024/8jw4_36679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jw4_36679/12_2024/8jw4_36679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jw4_36679/12_2024/8jw4_36679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jw4_36679/12_2024/8jw4_36679_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jw4_36679/12_2024/8jw4_36679_neut.cif"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.074
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      40      5.16       5
     C    6215      2.51       5
     N    1580      2.21       5
     O    1747      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 9582
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1191, 9582
          Classifications: {'peptide': 1191}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 26, 'TRANS': 1164}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 5.71, per 1000 atoms: 0.60
  Number of scatterers: 9582
  At special positions: 0
  Unit cell: (72.6, 119.9, 143, 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      40     16.00
     O    1747      8.00
     N    1580      7.00
     C    6215      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: 2.40
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2260

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      62.1% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 37
      removed outlier: 3.780A  pdb=" N   LEU A  31 " --> pdb=" O   SER A  27 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG A  33 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASN A  37 " --> pdb=" O   ARG A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 48
      removed outlier: 3.563A  pdb=" N   LYS A  47 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   CYS A  48 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 44 through 48'
    Processing helix  chain 'A' and resid 50 through 54
    Processing helix  chain 'A' and resid 55 through 63
    Processing helix  chain 'A' and resid 70 through 86
      removed outlier: 3.818A  pdb=" N   SER A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   GLY A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A  82 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 137
      removed outlier: 3.564A  pdb=" N   SER A  97 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   SER A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   ILE A 101 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   SER A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TYR A 114 " --> pdb=" O   MET A 110 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL A 118 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ILE A 119 " --> pdb=" O   CYS A 115 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LYS A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ARG A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 159
      removed outlier: 3.920A  pdb=" N   ARG A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASP A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 171
      removed outlier: 3.796A  pdb=" N   PHE A 170 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 191
      removed outlier: 3.553A  pdb=" N   LYS A 190 " --> pdb=" O   TRP A 186 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ASN A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 200
      removed outlier: 3.527A  pdb=" N   CYS A 197 " --> pdb=" O   ARG A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 240
      removed outlier: 3.583A  pdb=" N   CYS A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LYS A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS A 215 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ASN A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   THR A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASN A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ASN A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   THR A 230 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLY A 240 " --> pdb=" O   GLU A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
    Processing helix  chain 'A' and resid 250 through 260
      removed outlier: 4.001A  pdb=" N   LEU A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN A 255 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LYS A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 305
      removed outlier: 3.531A  pdb=" N   SER A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   HIS A 278 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ILE A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   LEU A 287 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL A 288 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ALA A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ARG A 299 " --> pdb=" O   TRP A 295 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ILE A 302 " --> pdb=" O   THR A 298 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN A 303 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 332
      removed outlier: 3.542A  pdb=" N   LEU A 323 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   MET A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   MET A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 335
      No H-bonds generated for 'chain 'A' and resid 333 through 335'
    Processing helix  chain 'A' and resid 336 through 352
      removed outlier: 3.501A  pdb=" N   ILE A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
    Processing helix  chain 'A' and resid 449 through 454
      removed outlier: 3.658A  pdb=" N   ARG A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 476
      removed outlier: 3.700A  pdb=" N   ILE A 475 " --> pdb=" O   ILE A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
      removed outlier: 3.703A  pdb=" N   ALA A 487 " --> pdb=" O   LYS A 483 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   MET A 488 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 483 through 488'
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 530 through 539
      removed outlier: 3.754A  pdb=" N   ASP A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL A 539 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 548
      removed outlier: 3.725A  pdb=" N   LEU A 548 " --> pdb=" O   PHE A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 579
      removed outlier: 4.634A  pdb=" N   ARG A 579 " --> pdb=" O   ARG A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 607
      removed outlier: 4.455A  pdb=" N   GLU A 598 " --> pdb=" O   ASP A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 614
      removed outlier: 3.573A  pdb=" N   ASN A 613 " --> pdb=" O   GLY A 610 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ARG A 614 " --> pdb=" O   ASN A 611 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 610 through 614'
    Processing helix  chain 'A' and resid 685 through 694
    Processing helix  chain 'A' and resid 772 through 783
      removed outlier: 3.994A  pdb=" N   ILE A 778 " --> pdb=" O   ASN A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 803
      removed outlier: 4.161A  pdb=" N   THR A 790 " --> pdb=" O   LYS A 786 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ILE A 791 " --> pdb=" O   LYS A 787 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ILE A 792 " --> pdb=" O   ASP A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 816
      removed outlier: 3.920A  pdb=" N   ARG A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 849
      removed outlier: 3.909A  pdb=" N   ASN A 826 " --> pdb=" O   ASN A 822 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ILE A 832 " --> pdb=" O   ASN A 828 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   TYR A 833 " --> pdb=" O   LYS A 829 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ILE A 834 " --> pdb=" O   TYR A 830 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 843 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 873
      removed outlier: 3.976A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 859 " --> pdb=" O   ILE A 855 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU A 860 " --> pdb=" O   GLY A 856 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ARG A 865 " --> pdb=" O   LYS A 861 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ARG A 866 " --> pdb=" O   THR A 862 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   TYR A 873 " --> pdb=" O   GLU A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 927
      removed outlier: 3.513A  pdb=" N   ALA A 891 " --> pdb=" O   GLY A 887 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ILE A 893 " --> pdb=" O   LEU A 889 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   ASN A 894 " --> pdb=" O   SER A 890 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL A 897 " --> pdb=" O   ILE A 893 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LEU A 904 " --> pdb=" O   LEU A 900 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   VAL A 905 " --> pdb=" O   LYS A 901 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   VAL A 909 " --> pdb=" O   VAL A 905 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 920 " --> pdb=" O   MET A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 945
      removed outlier: 3.927A  pdb=" N   ALA A 933 " --> pdb=" O   CYS A 929 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA A 934 " --> pdb=" O   PRO A 930 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL A 935 " --> pdb=" O   ILE A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 963
      removed outlier: 3.568A  pdb=" N   ARG A 952 " --> pdb=" O   ALA A 948 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 959 " --> pdb=" O   LYS A 955 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   GLU A 960 " --> pdb=" O   SER A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 986
      removed outlier: 3.938A  pdb=" N   ILE A 986 " --> pdb=" O   PRO A 982 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 982 through 986'
    Processing helix  chain 'A' and resid 986 through 991
      removed outlier: 3.694A  pdb=" N   TYR A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 999
      removed outlier: 3.871A  pdb=" N   VAL A 996 " --> pdb=" O   ASN A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1001 through 1006
      removed outlier: 3.530A  pdb=" N   PHE A1005 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1028
      removed outlier: 4.177A  pdb=" N   TYR A1015 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ASN A1017 " --> pdb=" O   ILE A1013 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   LYS A1018 " --> pdb=" O   ASP A1014 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   GLY A1019 " --> pdb=" O   TYR A1015 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   ARG A1022 " --> pdb=" O   LYS A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1036
      removed outlier: 3.604A  pdb=" N   PHE A1033 " --> pdb=" O   ALA A1029 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   SER A1034 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLN A1035 " --> pdb=" O   TRP A1031 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1054
      removed outlier: 3.714A  pdb=" N   LYS A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1059 through 1081
      removed outlier: 4.282A  pdb=" N   PHE A1063 " --> pdb=" O   LEU A1059 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE A1068 " --> pdb=" O   MET A1064 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   THR A1069 " --> pdb=" O   LYS A1065 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   PHE A1070 " --> pdb=" O   SER A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1087 through 1098
      removed outlier: 3.559A  pdb=" N   LYS A1091 " --> pdb=" O   SER A1087 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE A1094 " --> pdb=" O   ALA A1090 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLU A1095 " --> pdb=" O   LYS A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1099 through 1102
      removed outlier: 3.584A  pdb=" N   ILE A1102 " --> pdb=" O   PRO A1099 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1099 through 1102'
    Processing helix  chain 'A' and resid 1169 through 1175
    Processing helix  chain 'A' and resid 1246 through 1250
      removed outlier: 3.902A  pdb=" N   LEU A1250 " --> pdb=" O   LEU A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1270
      removed outlier: 3.847A  pdb=" N   ILE A1269 " --> pdb=" O   ILE A1265 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LYS A1270 " --> pdb=" O   TYR A1266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1278 through 1289
      removed outlier: 3.504A  pdb=" N   PHE A1287 " --> pdb=" O   ARG A1283 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA A1288 " --> pdb=" O   VAL A1284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1293 through 1297
      removed outlier: 3.942A  pdb=" N   LEU A1297 " --> pdb=" O   ILE A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1299 through 1303
      removed outlier: 4.005A  pdb=" N   THR A1303 " --> pdb=" O   LYS A1300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1310
    Processing helix  chain 'A' and resid 1313 through 1327
      removed outlier: 3.605A  pdb=" N   GLN A1318 " --> pdb=" O   GLY A1314 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ARG A1319 " --> pdb=" O   GLY A1315 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A1327 " --> pdb=" O   ALA A1323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1344 through 1358
    Processing helix  chain 'A' and resid 1371 through 1376
    Processing helix  chain 'A' and resid 1410 through 1417
    Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379
    Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460
      removed outlier: 6.351A  pdb=" N   GLY A 458 " --> pdb=" O   ILE A 585 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ASP A 587 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL A 460 " --> pdb=" O   ASP A 587 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 634 through 636
      removed outlier: 5.993A  pdb=" N   SER A 636 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ILE A 670 " --> pdb=" O   SER A 636 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1144 through 1145
      removed outlier: 3.984A  pdb=" N   TYR A1144 " --> pdb=" O   PHE A1133 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE A1133 " --> pdb=" O   TYR A1144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1144 through 1145
      removed outlier: 3.984A  pdb=" N   TYR A1144 " --> pdb=" O   PHE A1133 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE A1133 " --> pdb=" O   TYR A1144 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LYS A1129 " --> pdb=" O   GLU A1231 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   GLU A1231 " --> pdb=" O   LYS A1129 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1332 through 1334
      removed outlier: 7.059A  pdb=" N   ILE A1381 " --> pdb=" O   HIS A1397 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   HIS A1397 " --> pdb=" O   ILE A1381 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   VAL A1383 " --> pdb=" O   GLN A1395 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN A1395 " --> pdb=" O   VAL A1383 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASN A1385 " --> pdb=" O   PHE A1393 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A1393 " --> pdb=" O   ASN A1385 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1188 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: 3.32

  Time building geometry restraints manager: 2.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2977
        1.34 -     1.46: 2039
        1.46 -     1.58: 4676
        1.58 -     1.70: 0
        1.70 -     1.82: 67
  Bond restraints: 9759
  Sorted by residual:
  bond pdb=" C   TYR A 803 "
       pdb=" N   PRO A 804 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.027 1.28e-02 6.10e+03 4.41e+00
  bond pdb=" C   SER A 455 "
       pdb=" N   LYS A 456 "
    ideal  model  delta    sigma   weight residual
    1.330  1.356 -0.026 1.36e-02 5.41e+03 3.66e+00
  bond pdb=" C   SER A 547 "
       pdb=" N   LEU A 548 "
    ideal  model  delta    sigma   weight residual
    1.327  1.358 -0.031 1.71e-02 3.42e+03 3.38e+00
  bond pdb=" C   LYS A 360 "
       pdb=" N   PRO A 361 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 9.80e-03 1.04e+04 3.29e+00
  bond pdb=" CA  ASP A1275 "
       pdb=" CB  ASP A1275 "
    ideal  model  delta    sigma   weight residual
    1.525  1.548 -0.024 1.47e-02 4.63e+03 2.61e+00
  ... (remaining 9754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 12799
        1.91 -     3.82: 302
        3.82 -     5.73: 41
        5.73 -     7.64: 6
        7.64 -     9.56: 3
  Bond angle restraints: 13151
  Sorted by residual:
  angle pdb=" C   SER A1105 "
        pdb=" N   ASN A1106 "
        pdb=" CA  ASN A1106 "
      ideal   model   delta    sigma   weight residual
     121.54  130.14   -8.60 1.91e+00 2.74e-01 2.03e+01
  angle pdb=" C   HIS A 892 "
        pdb=" N   ILE A 893 "
        pdb=" CA  ILE A 893 "
      ideal   model   delta    sigma   weight residual
     120.53  125.77   -5.24 1.41e+00 5.03e-01 1.38e+01
  angle pdb=" CA  ASN A1106 "
        pdb=" CB  ASN A1106 "
        pdb=" CG  ASN A1106 "
      ideal   model   delta    sigma   weight residual
     112.60  115.85   -3.25 1.00e+00 1.00e+00 1.06e+01
  angle pdb=" C   ALA A 821 "
        pdb=" N   ASN A 822 "
        pdb=" CA  ASN A 822 "
      ideal   model   delta    sigma   weight residual
     121.54  127.42   -5.88 1.91e+00 2.74e-01 9.47e+00
  angle pdb=" N   ASN A1007 "
        pdb=" CA  ASN A1007 "
        pdb=" C   ASN A1007 "
      ideal   model   delta    sigma   weight residual
     114.56  111.03    3.53 1.27e+00 6.20e-01 7.74e+00
  ... (remaining 13146 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.35: 5580
       15.35 -    30.70: 268
       30.70 -    46.05: 40
       46.05 -    61.40: 3
       61.40 -    76.75: 3
  Dihedral angle restraints: 5894
    sinusoidal: 2393
      harmonic: 3501
  Sorted by residual:
  dihedral pdb=" CA  LYS A1016 "
           pdb=" C   LYS A1016 "
           pdb=" N   ASN A1017 "
           pdb=" CA  ASN A1017 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.41  -25.59     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  ASN A1243 "
           pdb=" C   ASN A1243 "
           pdb=" N   LEU A1244 "
           pdb=" CA  LEU A1244 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.50  -23.50     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  VAL A 905 "
           pdb=" C   VAL A 905 "
           pdb=" N   ASN A 906 "
           pdb=" CA  ASN A 906 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.00   23.00     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 5891 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1232
       0.055 -    0.110: 242
       0.110 -    0.165: 34
       0.165 -    0.220: 2
       0.220 -    0.275: 1
  Chirality restraints: 1511
  Sorted by residual:
  chirality pdb=" CA  ASP A 441 "
            pdb=" N   ASP A 441 "
            pdb=" C   ASP A 441 "
            pdb=" CB  ASP A 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CB  ILE A 437 "
            pdb=" CA  ILE A 437 "
            pdb=" CG1 ILE A 437 "
            pdb=" CG2 ILE A 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.35e-01
  chirality pdb=" CA  ASN A 440 "
            pdb=" N   ASN A 440 "
            pdb=" C   ASN A 440 "
            pdb=" CB  ASN A 440 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.26e-01
  ... (remaining 1508 not shown)

  Planarity restraints: 1635
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A1016 "    0.011 2.00e-02 2.50e+03   2.13e-02 4.52e+00
        pdb=" C   LYS A1016 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   LYS A1016 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASN A1017 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  71 "    0.033 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO A  72 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A  72 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  72 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1257 "    0.032 5.00e-02 4.00e+02   4.77e-02 3.65e+00
        pdb=" N   PRO A1258 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A1258 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A1258 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1632 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1112
        2.75 -     3.29: 9782
        3.29 -     3.83: 13818
        3.83 -     4.36: 16632
        4.36 -     4.90: 28644
  Nonbonded interactions: 69988
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 396 "
            pdb=" O   GLY A 418 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD2 ASP A 144 "
            pdb=" OH  TYR A 430 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   ASN A 637 "
            pdb=" N   ASN A 665 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   ARG A 384 "
            pdb=" OG1 THR A 433 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   LYS A 220 "
            pdb=" OG  SER A 223 "
     model   vdw
     2.304 3.040
  ... (remaining 69983 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.820
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
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   0.045   9759  Z= 0.322
  Angle     :  0.755   9.556  13151  Z= 0.420
  Chirality :  0.045   0.275   1511
  Planarity :  0.004   0.049   1635
  Dihedral  :  9.531  76.754   3634
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.14 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.20), residues: 1177
  helix: -2.16 (0.17), residues: 689
  sheet: -4.02 (0.45), residues: 58
  loop : -3.30 (0.26), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1047 
 HIS   0.007   0.001   HIS A 278 
 PHE   0.027   0.002   PHE A 294 
 TYR   0.021   0.002   TYR A 290 
 ARG   0.008   0.001   ARG A 575 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 223
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7464 (m-80) cc_final: 0.7195 (m-80)
REVERT: A  381 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8035 (ttpp)
REVERT: A  382 ASN cc_start: 0.8129 (m110) cc_final: 0.7536 (p0)
REVERT: A  404 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8110 (ptpt)
REVERT: A  463 ASP cc_start: 0.8328 (p0) cc_final: 0.7525 (t0)
REVERT: A  475 ILE cc_start: 0.7953 (mt) cc_final: 0.7446 (mm)
REVERT: A  520 MET cc_start: 0.5059 (mtm) cc_final: 0.4813 (ptm)
REVERT: A  524 TYR cc_start: 0.7599 (m-10) cc_final: 0.7247 (m-80)
REVERT: A  588 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7655 (tp30)
REVERT: A  987 GLN cc_start: 0.8089 (tt0) cc_final: 0.7253 (tm-30)
REVERT: A 1101 MET cc_start: 0.7749 (ptp) cc_final: 0.7525 (ptp)
REVERT: A 1267 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7449 (tp30)
REVERT: A 1308 TYR cc_start: 0.7914 (m-80) cc_final: 0.7609 (m-80)
REVERT: A 1336 ASP cc_start: 0.6170 (t0) cc_final: 0.5443 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 226
  average time/residue: 0.2631
  time to fit residues: 80.2935
Evaluate side-chains
  115 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0870
   chunk 93 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   overall best weight:    0.9960

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN
A 443 HIS
A 580 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9759  Z= 0.210
  Angle     :  0.638   8.994  13151  Z= 0.337
  Chirality :  0.046   0.173   1511
  Planarity :  0.004   0.045   1635
  Dihedral  :  5.213  23.165   1287
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  8.29 %
    Favored  : 90.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.22), residues: 1177
  helix: -1.19 (0.19), residues: 708
  sheet: -3.59 (0.49), residues: 64
  loop : -2.93 (0.27), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1047 
 HIS   0.019   0.002   HIS A 676 
 PHE   0.016   0.001   PHE A  43 
 TYR   0.021   0.002   TYR A1097 
 ARG   0.006   0.001   ARG A 384 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7292 (m-80) cc_final: 0.7050 (m-80)
REVERT: A   89 ASP cc_start: 0.6331 (OUTLIER) cc_final: 0.6054 (p0)
REVERT: A  379 GLU cc_start: 0.6359 (tm-30) cc_final: 0.5827 (tm-30)
REVERT: A  382 ASN cc_start: 0.8162 (m110) cc_final: 0.7563 (p0)
REVERT: A  404 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7878 (ptpt)
REVERT: A  456 LYS cc_start: 0.4418 (mmtp) cc_final: 0.3516 (pttm)
REVERT: A  463 ASP cc_start: 0.8298 (p0) cc_final: 0.7535 (t0)
REVERT: A  520 MET cc_start: 0.5032 (mtm) cc_final: 0.4761 (ptm)
REVERT: A  524 TYR cc_start: 0.7374 (m-10) cc_final: 0.7060 (m-10)
REVERT: A  588 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7635 (tp30)
REVERT: A  622 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7991 (tpp-160)
REVERT: A  916 MET cc_start: 0.8040 (tpt) cc_final: 0.7783 (tpt)
REVERT: A  987 GLN cc_start: 0.8235 (tt0) cc_final: 0.7675 (tm-30)
REVERT: A 1267 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7807 (tp30)
  outliers start: 11
  outliers final: 7
  residues processed: 137
  average time/residue: 0.2358
  time to fit residues: 44.8436
Evaluate side-chains
  107 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  488 MET
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1295 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 89 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 116 optimal weight:    9.9990
   chunk 96 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
A 191 ASN
A 826 ASN
** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9759  Z= 0.168
  Angle     :  0.573   9.531  13151  Z= 0.302
  Chirality :  0.043   0.180   1511
  Planarity :  0.004   0.042   1635
  Dihedral  :  4.834  22.600   1287
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.25 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.23), residues: 1177
  helix: -0.62 (0.20), residues: 705
  sheet: -3.02 (0.55), residues: 64
  loop : -2.69 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1047 
 HIS   0.004   0.001   HIS A 892 
 PHE   0.012   0.001   PHE A  43 
 TYR   0.017   0.001   TYR A1097 
 ARG   0.007   0.001   ARG A1371 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7149 (m-80) cc_final: 0.6494 (m-80)
REVERT: A  382 ASN cc_start: 0.8290 (m110) cc_final: 0.7661 (p0)
REVERT: A  404 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7852 (ptpt)
REVERT: A  456 LYS cc_start: 0.4543 (mmtp) cc_final: 0.3458 (pttm)
REVERT: A  463 ASP cc_start: 0.8334 (p0) cc_final: 0.7619 (t0)
REVERT: A  520 MET cc_start: 0.5027 (mtm) cc_final: 0.4789 (ptm)
REVERT: A  524 TYR cc_start: 0.7287 (m-10) cc_final: 0.6845 (m-80)
REVERT: A  588 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7223 (tm-30)
REVERT: A  776 ARG cc_start: 0.8028 (ptt90) cc_final: 0.7426 (ptt-90)
REVERT: A  916 MET cc_start: 0.8021 (tpt) cc_final: 0.7804 (tpt)
REVERT: A  987 GLN cc_start: 0.8457 (tt0) cc_final: 0.7869 (tm-30)
REVERT: A 1011 LYS cc_start: 0.5991 (mmmt) cc_final: 0.5757 (tppt)
REVERT: A 1267 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7943 (tp30)
  outliers start: 13
  outliers final: 6
  residues processed: 125
  average time/residue: 0.2225
  time to fit residues: 39.6332
Evaluate side-chains
  101 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.0020
   chunk 81 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0270
   chunk 51 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 108 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.7648

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9759  Z= 0.164
  Angle     :  0.546   8.949  13151  Z= 0.289
  Chirality :  0.042   0.151   1511
  Planarity :  0.004   0.043   1635
  Dihedral  :  4.647  21.646   1287
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 12.02 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.24), residues: 1177
  helix: -0.36 (0.20), residues: 711
  sheet: -2.53 (0.59), residues: 63
  loop : -2.62 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1047 
 HIS   0.003   0.001   HIS A 892 
 PHE   0.024   0.001   PHE A1293 
 TYR   0.017   0.001   TYR A1097 
 ARG   0.005   0.000   ARG A 384 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7097 (m-80) cc_final: 0.6280 (m-80)
REVERT: A  382 ASN cc_start: 0.8182 (m110) cc_final: 0.7623 (p0)
REVERT: A  404 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7822 (ptpt)
REVERT: A  434 GLU cc_start: 0.5819 (mt-10) cc_final: 0.5426 (mm-30)
REVERT: A  456 LYS cc_start: 0.4600 (mmtp) cc_final: 0.3564 (pttm)
REVERT: A  463 ASP cc_start: 0.8373 (p0) cc_final: 0.7630 (t0)
REVERT: A  520 MET cc_start: 0.4879 (mtm) cc_final: 0.4625 (ptm)
REVERT: A  524 TYR cc_start: 0.7315 (m-10) cc_final: 0.6898 (m-80)
REVERT: A  588 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7560 (tp30)
REVERT: A  776 ARG cc_start: 0.8125 (ptt90) cc_final: 0.7605 (ptt-90)
REVERT: A  987 GLN cc_start: 0.8529 (tt0) cc_final: 0.8079 (tm-30)
REVERT: A 1092 LEU cc_start: 0.8108 (mt) cc_final: 0.7844 (pp)
REVERT: A 1267 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7999 (tp30)
REVERT: A 1362 ASP cc_start: 0.7822 (p0) cc_final: 0.7396 (p0)
  outliers start: 12
  outliers final: 9
  residues processed: 115
  average time/residue: 0.2355
  time to fit residues: 38.5578
Evaluate side-chains
  102 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1138 ARG
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1349 LEU
Chi-restraints excluded: chain A residue 1367 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 103 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A1262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9759  Z= 0.229
  Angle     :  0.592  10.079  13151  Z= 0.313
  Chirality :  0.044   0.159   1511
  Planarity :  0.004   0.041   1635
  Dihedral  :  4.725  22.709   1287
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.67 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.24), residues: 1177
  helix: -0.36 (0.20), residues: 719
  sheet: -2.12 (0.63), residues: 63
  loop : -2.59 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1047 
 HIS   0.003   0.001   HIS A 892 
 PHE   0.016   0.001   PHE A1293 
 TYR   0.019   0.001   TYR A1097 
 ARG   0.004   0.000   ARG A 622 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7070 (m-80) cc_final: 0.6253 (m-80)
REVERT: A  226 TYR cc_start: 0.8076 (m-10) cc_final: 0.7788 (m-80)
REVERT: A  256 LYS cc_start: 0.7032 (mmtt) cc_final: 0.6761 (mtpt)
REVERT: A  382 ASN cc_start: 0.7918 (m110) cc_final: 0.7304 (p0)
REVERT: A  404 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7827 (pttm)
REVERT: A  407 LYS cc_start: 0.7349 (mttt) cc_final: 0.7044 (mtpt)
REVERT: A  434 GLU cc_start: 0.5723 (mt-10) cc_final: 0.5273 (mm-30)
REVERT: A  456 LYS cc_start: 0.4835 (mmtp) cc_final: 0.3726 (pttm)
REVERT: A  463 ASP cc_start: 0.8396 (p0) cc_final: 0.7654 (t0)
REVERT: A  520 MET cc_start: 0.4955 (mtm) cc_final: 0.4660 (ptm)
REVERT: A  524 TYR cc_start: 0.7308 (m-10) cc_final: 0.6887 (m-80)
REVERT: A  588 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7536 (tp30)
REVERT: A  776 ARG cc_start: 0.8187 (ptt90) cc_final: 0.7665 (ptt-90)
REVERT: A  987 GLN cc_start: 0.8610 (tt0) cc_final: 0.8223 (tm-30)
REVERT: A 1267 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8101 (tp30)
  outliers start: 21
  outliers final: 16
  residues processed: 118
  average time/residue: 0.2381
  time to fit residues: 39.3537
Evaluate side-chains
  111 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1138 ARG
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1349 LEU
Chi-restraints excluded: chain A residue 1367 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    0.0970
   chunk 22 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0370
   chunk 60 optimal weight:    7.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    0.7860

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
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      :  0.002   0.031   9759  Z= 0.157
  Angle     :  0.543  10.614  13151  Z= 0.285
  Chirality :  0.042   0.144   1511
  Planarity :  0.003   0.043   1635
  Dihedral  :  4.556  21.483   1287
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.05 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.24), residues: 1177
  helix: -0.09 (0.20), residues: 711
  sheet: -1.83 (0.66), residues: 63
  loop : -2.53 (0.27), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1047 
 HIS   0.003   0.001   HIS A 443 
 PHE   0.021   0.001   PHE A1293 
 TYR   0.015   0.001   TYR A1097 
 ARG   0.003   0.000   ARG A 384 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7000 (m-80) cc_final: 0.6183 (m-80)
REVERT: A  152 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6679 (ptm160)
REVERT: A  226 TYR cc_start: 0.7991 (m-80) cc_final: 0.7691 (m-80)
REVERT: A  256 LYS cc_start: 0.6955 (mmtt) cc_final: 0.6716 (mtpt)
REVERT: A  382 ASN cc_start: 0.7910 (m110) cc_final: 0.7286 (p0)
REVERT: A  404 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7818 (pttm)
REVERT: A  407 LYS cc_start: 0.7374 (mttt) cc_final: 0.7053 (mtpt)
REVERT: A  434 GLU cc_start: 0.5705 (mt-10) cc_final: 0.5462 (mm-30)
REVERT: A  463 ASP cc_start: 0.8399 (p0) cc_final: 0.7655 (t0)
REVERT: A  520 MET cc_start: 0.4925 (mtm) cc_final: 0.4653 (ptm)
REVERT: A  524 TYR cc_start: 0.7278 (m-10) cc_final: 0.6824 (m-80)
REVERT: A  588 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7234 (tm-30)
REVERT: A  776 ARG cc_start: 0.8165 (ptt90) cc_final: 0.7606 (ptt-90)
REVERT: A  987 GLN cc_start: 0.8570 (tt0) cc_final: 0.8366 (tm-30)
REVERT: A 1267 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8146 (tp30)
  outliers start: 24
  outliers final: 13
  residues processed: 119
  average time/residue: 0.2346
  time to fit residues: 39.4375
Evaluate side-chains
  107 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  348 GLU
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1138 ARG
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1344 SER
Chi-restraints excluded: chain A residue 1349 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 64 optimal weight:    0.4980
   chunk 114 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0980
   chunk 69 optimal weight:    0.2980
   chunk 52 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.4180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9759  Z= 0.133
  Angle     :  0.545  11.559  13151  Z= 0.280
  Chirality :  0.042   0.165   1511
  Planarity :  0.003   0.044   1635
  Dihedral  :  4.412  20.772   1287
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.26 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.24), residues: 1177
  helix:  0.11 (0.20), residues: 708
  sheet: -1.60 (0.68), residues: 63
  loop : -2.44 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1047 
 HIS   0.003   0.001   HIS A 443 
 PHE   0.023   0.001   PHE A1293 
 TYR   0.013   0.001   TYR A1097 
 ARG   0.005   0.000   ARG A 622 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.6896 (m-80) cc_final: 0.6124 (m-80)
REVERT: A  133 ARG cc_start: 0.6439 (tmm160) cc_final: 0.6055 (tmm160)
REVERT: A  152 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6618 (ptm160)
REVERT: A  256 LYS cc_start: 0.6944 (mmtt) cc_final: 0.6728 (mtpt)
REVERT: A  382 ASN cc_start: 0.7958 (m110) cc_final: 0.7328 (p0)
REVERT: A  404 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7763 (pttm)
REVERT: A  407 LYS cc_start: 0.7422 (mttt) cc_final: 0.7073 (mtpt)
REVERT: A  463 ASP cc_start: 0.8394 (p0) cc_final: 0.7655 (t0)
REVERT: A  520 MET cc_start: 0.4880 (mtm) cc_final: 0.4618 (ptm)
REVERT: A  524 TYR cc_start: 0.7410 (m-10) cc_final: 0.6994 (m-80)
REVERT: A  588 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7423 (tp30)
REVERT: A  776 ARG cc_start: 0.8102 (ptt90) cc_final: 0.7558 (ptt-90)
REVERT: A 1118 ASN cc_start: 0.7670 (p0) cc_final: 0.7464 (p0)
REVERT: A 1267 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8148 (tp30)
  outliers start: 16
  outliers final: 12
  residues processed: 119
  average time/residue: 0.2242
  time to fit residues: 37.5383
Evaluate side-chains
  109 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1138 ARG
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1336 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9980
   chunk 109 optimal weight:    0.0980
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.4327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9759  Z= 0.150
  Angle     :  0.556  12.159  13151  Z= 0.285
  Chirality :  0.042   0.155   1511
  Planarity :  0.003   0.044   1635
  Dihedral  :  4.362  20.892   1287
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.91 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.24), residues: 1177
  helix:  0.15 (0.20), residues: 702
  sheet: -2.04 (0.63), residues: 73
  loop : -2.37 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1047 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.022   0.001   PHE A1293 
 TYR   0.014   0.001   TYR A1097 
 ARG   0.007   0.000   ARG A1371 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.6892 (m-80) cc_final: 0.6112 (m-80)
REVERT: A  133 ARG cc_start: 0.6443 (tmm160) cc_final: 0.6029 (tmm160)
REVERT: A  256 LYS cc_start: 0.6925 (mmtt) cc_final: 0.6719 (mtpt)
REVERT: A  382 ASN cc_start: 0.8039 (m110) cc_final: 0.7283 (p0)
REVERT: A  404 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7753 (pttm)
REVERT: A  407 LYS cc_start: 0.7385 (mttt) cc_final: 0.7035 (mtpt)
REVERT: A  463 ASP cc_start: 0.8398 (p0) cc_final: 0.7656 (t0)
REVERT: A  520 MET cc_start: 0.4918 (mtm) cc_final: 0.4683 (ptm)
REVERT: A  524 TYR cc_start: 0.7417 (m-10) cc_final: 0.7004 (m-80)
REVERT: A  588 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7233 (tm-30)
REVERT: A 1118 ASN cc_start: 0.7577 (p0) cc_final: 0.7357 (p0)
REVERT: A 1267 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8163 (tp30)
  outliers start: 18
  outliers final: 15
  residues processed: 110
  average time/residue: 0.2106
  time to fit residues: 33.3868
Evaluate side-chains
  111 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  348 GLU
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1138 ARG
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1367 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 64 optimal weight:    0.4980
   chunk 46 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 101 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9759  Z= 0.208
  Angle     :  0.580  12.316  13151  Z= 0.300
  Chirality :  0.043   0.174   1511
  Planarity :  0.003   0.041   1635
  Dihedral  :  4.479  21.609   1287
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.00 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.24), residues: 1177
  helix:  0.06 (0.20), residues: 705
  sheet: -2.02 (0.63), residues: 73
  loop : -2.38 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 186 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.021   0.001   PHE A1293 
 TYR   0.017   0.001   TYR A1097 
 ARG   0.006   0.000   ARG A1371 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.6939 (m-80) cc_final: 0.6149 (m-80)
REVERT: A  133 ARG cc_start: 0.6438 (tmm160) cc_final: 0.6044 (tmm160)
REVERT: A  256 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6856 (mtpt)
REVERT: A  382 ASN cc_start: 0.8080 (m110) cc_final: 0.7377 (p0)
REVERT: A  404 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7783 (pttm)
REVERT: A  407 LYS cc_start: 0.7353 (mttt) cc_final: 0.7015 (mtpt)
REVERT: A  463 ASP cc_start: 0.8353 (p0) cc_final: 0.7555 (t0)
REVERT: A  520 MET cc_start: 0.5055 (mtm) cc_final: 0.4775 (ptm)
REVERT: A  524 TYR cc_start: 0.7338 (m-10) cc_final: 0.6919 (m-80)
REVERT: A  588 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7352 (tm-30)
REVERT: A 1259 MET cc_start: 0.8257 (tpt) cc_final: 0.7747 (tpt)
REVERT: A 1267 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8196 (tp30)
  outliers start: 19
  outliers final: 16
  residues processed: 109
  average time/residue: 0.2184
  time to fit residues: 34.1680
Evaluate side-chains
  107 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  348 GLU
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1138 ARG
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1367 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   chunk 118 optimal weight:    8.9990
   chunk 109 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   chunk 74 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.4523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9759  Z= 0.166
  Angle     :  0.558  12.949  13151  Z= 0.286
  Chirality :  0.042   0.166   1511
  Planarity :  0.003   0.043   1635
  Dihedral  :  4.389  21.747   1287
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.28 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.25), residues: 1177
  helix:  0.19 (0.20), residues: 699
  sheet: -1.70 (0.69), residues: 63
  loop : -2.30 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A 892 
 PHE   0.024   0.001   PHE A1293 
 TYR   0.013   0.001   TYR A1097 
 ARG   0.006   0.000   ARG A1371 

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.6942 (m-80) cc_final: 0.6142 (m-80)
REVERT: A  133 ARG cc_start: 0.6439 (tmm160) cc_final: 0.6060 (tmm160)
REVERT: A  256 LYS cc_start: 0.7064 (mmtt) cc_final: 0.6821 (mtpt)
REVERT: A  382 ASN cc_start: 0.8062 (m110) cc_final: 0.7395 (p0)
REVERT: A  404 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7783 (pttm)
REVERT: A  407 LYS cc_start: 0.7373 (mttt) cc_final: 0.7034 (mtpt)
REVERT: A  434 GLU cc_start: 0.5732 (pt0) cc_final: 0.4771 (mm-30)
REVERT: A  463 ASP cc_start: 0.8308 (p0) cc_final: 0.7455 (t0)
REVERT: A  520 MET cc_start: 0.5082 (mtm) cc_final: 0.4813 (ptm)
REVERT: A  524 TYR cc_start: 0.7394 (m-10) cc_final: 0.6997 (m-80)
REVERT: A  588 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7334 (tm-30)
REVERT: A 1259 MET cc_start: 0.8335 (tpt) cc_final: 0.7879 (tpt)
REVERT: A 1267 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8335 (mm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 107
  average time/residue: 0.2234
  time to fit residues: 34.5329
Evaluate side-chains
  107 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  348 GLU
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue 1080 LEU
Chi-restraints excluded: chain A residue 1138 ARG
Chi-restraints excluded: chain A residue 1148 SER
Chi-restraints excluded: chain A residue 1150 THR
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1367 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4277 r_free = 0.4277 target = 0.174133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.123779 restraints weight = 12938.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 3.14
r_work: 0.3580 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9759  Z= 0.152
  Angle     :  0.550  12.771  13151  Z= 0.281
  Chirality :  0.042   0.164   1511
  Planarity :  0.003   0.043   1635
  Dihedral  :  4.306  21.466   1287
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.03 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.25), residues: 1177
  helix:  0.26 (0.20), residues: 697
  sheet: -1.54 (0.70), residues: 63
  loop : -2.28 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1047 
 HIS   0.003   0.001   HIS A 443 
 PHE   0.023   0.001   PHE A1293 
 TYR   0.013   0.001   TYR A1097 
 ARG   0.006   0.000   ARG A1371 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2068.39 seconds
wall clock time: 38 minutes 55.04 seconds (2335.04 seconds total)