Starting phenix.real_space_refine
on Fri Jan 17 17:30:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vqc_43438/01_2025/8vqc_43438.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vqc_43438/01_2025/8vqc_43438.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vqc_43438/01_2025/8vqc_43438.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vqc_43438/01_2025/8vqc_43438.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vqc_43438/01_2025/8vqc_43438.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vqc_43438/01_2025/8vqc_43438.cif"
  }
  resolution = 3.9
  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=  -0.000 sd=   0.020
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      69      5.16       5
     C    7242      2.51       5
     N    1733      2.21       5
     O    1910      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10954
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 10225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1288, 10225
          Classifications: {'peptide': 1288}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PTRANS': 45, 'TRANS': 1242}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 328
          Unresolved non-hydrogen angles: 417
          Unresolved non-hydrogen dihedrals: 269
          Unresolved non-hydrogen chiralities: 30
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 187
    Chain: "H"
      Number of atoms: 506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 506
          Classifications: {'peptide': 64}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 60}
    Chain: "B"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 5, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 7.75, per 1000 atoms: 0.71
  Number of scatterers: 10954
  At special positions: 0
  Unit cell: (127.38, 133.98, 125.4, 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      69     16.00
     O    1910      8.00
     N    1733      7.00
     C    7242      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 337 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 328 " - pdb=" SG  CYS A 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 709 " - pdb=" SG  CYS A 717 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1011 " - pdb=" SG  CYS A1030 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1368 " - pdb=" SG  CYS A1381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  12 " - pdb=" SG  CYS H  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  16 " - pdb=" SG  CYS H  36 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  46 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  26 " - pdb=" SG  CYS H  48 " distance=2.03

  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
  Links applied
    BETA1-3
      " BMA B   3 " - " BMA B   4 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG G   1 " - " NAG G   2 "
    BETA1-6
      " BMA B   3 " - " BMA B   6 "
      " BMA B   4 " - " BMA B   5 "
      " BMA B   6 " - " BMA B   7 "
    NAG-ASN
      " NAG A1601 " - " ASN A 308 "
      " NAG A1602 " - " ASN A1028 "
      " NAG B   1 " - " ASN A 330 "
      " NAG C   1 " - " ASN A1034 "
      " NAG D   1 " - " ASN A1015 "
      " NAG E   1 " - " ASN A 312 "
      " NAG G   1 " - " ASN A 300 "
  Time building additional restraints: 3.03
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2568

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 3 sheets defined
      70.3% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 111
    Processing helix  chain 'A' and resid 128 through 139
      removed outlier: 3.622A  pdb=" N   VAL A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 157
      removed outlier: 3.679A  pdb=" N   SER A 143 " --> pdb=" O   GLN A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 188
    Processing helix  chain 'A' and resid 191 through 197
      removed outlier: 3.994A  pdb=" N   ALA A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 216
      removed outlier: 3.564A  pdb=" N   LEU A 204 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP A 205 " --> pdb=" O   TRP A 201 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A 216 " --> pdb=" O   GLY A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 240
      removed outlier: 3.911A  pdb=" N   VAL A 231 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ARG A 233 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 280
      removed outlier: 4.282A  pdb=" N   ILE A 247 " --> pdb=" O   GLY A 243 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   ASP A 260 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   LEU A 261 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 311
      removed outlier: 4.058A  pdb=" N   PHE A 307 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 373
    Processing helix  chain 'A' and resid 376 through 389
      removed outlier: 4.397A  pdb=" N   LEU A 380 " --> pdb=" O   TYR A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 402
      removed outlier: 3.752A  pdb=" N   PHE A 396 " --> pdb=" O   HIS A 392 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 431
      removed outlier: 4.625A  pdb=" N   ASN A 409 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 518
    Processing helix  chain 'A' and resid 518 through 537
      removed outlier: 3.712A  pdb=" N   GLU A 522 " --> pdb=" O   SER A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 573
    Processing helix  chain 'A' and resid 574 through 579
    Processing helix  chain 'A' and resid 581 through 601
      removed outlier: 3.879A  pdb=" N   VAL A 585 " --> pdb=" O   ASP A 581 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU A 601 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 613
      removed outlier: 4.202A  pdb=" N   PHE A 612 " --> pdb=" O   VAL A 608 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ARG A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 608 through 613'
    Processing helix  chain 'A' and resid 614 through 619
      removed outlier: 4.144A  pdb=" N   PHE A 618 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG A 619 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 614 through 619'
    Processing helix  chain 'A' and resid 620 through 623
    Processing helix  chain 'A' and resid 626 through 636
      removed outlier: 4.188A  pdb=" N   LYS A 636 " --> pdb=" O   SER A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 670
      removed outlier: 3.776A  pdb=" N   VAL A 642 " --> pdb=" O   TYR A 638 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   ASN A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   MET A 665 " --> pdb=" O   GLN A 661 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   ASN A 666 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ASN A 670 " --> pdb=" O   ASN A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 700
    Processing helix  chain 'A' and resid 702 through 712
      removed outlier: 3.533A  pdb=" N   VAL A 712 " --> pdb=" O   ASP A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 716
      No H-bonds generated for 'chain 'A' and resid 714 through 716'
    Processing helix  chain 'A' and resid 717 through 727
      removed outlier: 3.797A  pdb=" N   PHE A 721 " --> pdb=" O   CYS A 717 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL A 722 " --> pdb=" O   ILE A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 744
    Processing helix  chain 'A' and resid 834 through 855
    Processing helix  chain 'A' and resid 855 through 875
      removed outlier: 3.812A  pdb=" N   GLN A 859 " --> pdb=" O   ASN A 855 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LEU A 875 " --> pdb=" O   VAL A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 883 through 912
      removed outlier: 4.081A  pdb=" N   VAL A 887 " --> pdb=" O   ARG A 883 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ASN A 888 " --> pdb=" O   PRO A 884 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ILE A 889 " --> pdb=" O   VAL A 885 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 896 " --> pdb=" O   TYR A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 920
    Processing helix  chain 'A' and resid 920 through 942
      removed outlier: 3.743A  pdb=" N   TRP A 924 " --> pdb=" O   SER A 920 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU A 925 " --> pdb=" O   LYS A 921 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASP A 926 " --> pdb=" O   TRP A 922 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A 942 " --> pdb=" O   VAL A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 958
      removed outlier: 3.793A  pdb=" N   ARG A 957 " --> pdb=" O   LEU A 953 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU A 958 " --> pdb=" O   ARG A 954 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 953 through 958'
    Processing helix  chain 'A' and resid 958 through 963
    Processing helix  chain 'A' and resid 964 through 966
      No H-bonds generated for 'chain 'A' and resid 964 through 966'
    Processing helix  chain 'A' and resid 967 through 1005
      removed outlier: 4.009A  pdb=" N   VAL A 971 " --> pdb=" O   GLY A 967 " (cutoff:3.500A)
      Proline residue:  A 980  - end of helix
      removed outlier: 4.410A  pdb=" N   MET A 999 " --> pdb=" O   VAL A 995 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLN A1002 " --> pdb=" O   ILE A 998 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1033
      removed outlier: 3.715A  pdb=" N   CYS A1030 " --> pdb=" O   ASP A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1046 through 1059
    Processing helix  chain 'A' and resid 1062 through 1071
      removed outlier: 4.190A  pdb=" N   ILE A1066 " --> pdb=" O   GLY A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1088 through 1097
      removed outlier: 3.719A  pdb=" N   PHE A1092 " --> pdb=" O   MET A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1124
      removed outlier: 4.092A  pdb=" N   CYS A1109 " --> pdb=" O   LYS A1105 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP A1113 " --> pdb=" O   CYS A1109 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE A1114 " --> pdb=" O   ILE A1110 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLY A1124 " --> pdb=" O   ARG A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1146
    Processing helix  chain 'A' and resid 1157 through 1168
    Processing helix  chain 'A' and resid 1169 through 1189
      removed outlier: 3.699A  pdb=" N   GLU A1173 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ILE A1189 " --> pdb=" O   ALA A1185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1195 through 1224
      removed outlier: 3.724A  pdb=" N   GLU A1200 " --> pdb=" O   MET A1196 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A1201 " --> pdb=" O   GLU A1197 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A1222 " --> pdb=" O   VAL A1218 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLY A1223 " --> pdb=" O   ILE A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1257
      removed outlier: 3.811A  pdb=" N   PHE A1238 " --> pdb=" O   ASN A1234 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU A1243 " --> pdb=" O   LEU A1239 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   ASP A1252 " --> pdb=" O   LEU A1248 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   VAL A1253 " --> pdb=" O   MET A1249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1268
      removed outlier: 4.658A  pdb=" N   LEU A1263 " --> pdb=" O   ILE A1259 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LEU A1264 " --> pdb=" O   SER A1260 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   ARG A1265 " --> pdb=" O   PRO A1261 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A1268 " --> pdb=" O   LEU A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1269 through 1273
      removed outlier: 3.632A  pdb=" N   GLY A1273 " --> pdb=" O   LEU A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1282 through 1295
      removed outlier: 4.047A  pdb=" N   ARG A1286 " --> pdb=" O   ALA A1282 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A1295 " --> pdb=" O   ALA A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1295 through 1321
    Processing helix  chain 'A' and resid 1338 through 1351
      removed outlier: 4.260A  pdb=" N   THR A1351 " --> pdb=" O   PHE A1347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1354 through 1363
      removed outlier: 3.709A  pdb=" N   VAL A1358 " --> pdb=" O   GLY A1354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1384 through 1398
      removed outlier: 3.973A  pdb=" N   SER A1393 " --> pdb=" O   ALA A1389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1401 through 1424
      removed outlier: 3.688A  pdb=" N   ILE A1410 " --> pdb=" O   TYR A1406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1426 through 1439
      removed outlier: 3.728A  pdb=" N   GLN A1439 " --> pdb=" O   GLU A1435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1451 through 1459
      removed outlier: 3.889A  pdb=" N   GLU A1455 " --> pdb=" O   ASP A1451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1470 through 1477
    Processing helix  chain 'A' and resid 1488 through 1505
      removed outlier: 3.523A  pdb=" N   VAL A1492 " --> pdb=" O   PHE A1488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1508 through 1521
      Proline residue:  A1516  - end of helix
      removed outlier: 3.507A  pdb=" N   ALA A1521 " --> pdb=" O   ASN A1517 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 18 through 29
      removed outlier: 3.610A  pdb=" N   CYS H  26 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ASN H  29 " --> pdb=" O   LEU H  25 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1009 through 1012
    Processing sheet with id=AA3, first strand: chain 'H' and resid 34 through 35

    631 hydrogen bonds defined for protein.
    1857 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: 3.65

  Time building geometry restraints manager: 3.42 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: 3306
        1.34 -     1.46: 3016
        1.46 -     1.58: 4817
        1.58 -     1.70: 0
        1.70 -     1.82: 111
  Bond restraints: 11250
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.472 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" C   LEU A1276 "
       pdb=" N   ARG A1277 "
    ideal  model  delta    sigma   weight residual
    1.335  1.308  0.027 1.30e-02 5.92e+03 4.25e+00
  bond pdb=" C5  BMA B   3 "
       pdb=" O5  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.452 -0.035 2.00e-02 2.50e+03 3.01e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.80e+00
  bond pdb=" CA  LEU A1276 "
       pdb=" C   LEU A1276 "
    ideal  model  delta    sigma   weight residual
    1.522  1.500  0.022 1.39e-02 5.18e+03 2.59e+00
  ... (remaining 11245 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 15025
        2.36 -     4.72: 228
        4.72 -     7.08: 47
        7.08 -     9.44: 10
        9.44 -    11.79: 5
  Bond angle restraints: 15315
  Sorted by residual:
  angle pdb=" CA  GLU A1443 "
        pdb=" CB  GLU A1443 "
        pdb=" CG  GLU A1443 "
      ideal   model   delta    sigma   weight residual
     114.10  123.56   -9.46 2.00e+00 2.50e-01 2.24e+01
  angle pdb=" CB  ARG H   2 "
        pdb=" CG  ARG H   2 "
        pdb=" CD  ARG H   2 "
      ideal   model   delta    sigma   weight residual
     111.30  120.75   -9.45 2.30e+00 1.89e-01 1.69e+01
  angle pdb=" CB  MET A1196 "
        pdb=" CG  MET A1196 "
        pdb=" SD  MET A1196 "
      ideal   model   delta    sigma   weight residual
     112.70  124.49  -11.79 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" CB  GLU A1443 "
        pdb=" CG  GLU A1443 "
        pdb=" CD  GLU A1443 "
      ideal   model   delta    sigma   weight residual
     112.60  119.20   -6.60 1.70e+00 3.46e-01 1.51e+01
  angle pdb=" C   ILE A 146 "
        pdb=" N   MET A 147 "
        pdb=" CA  MET A 147 "
      ideal   model   delta    sigma   weight residual
     121.14  115.02    6.12 1.75e+00 3.27e-01 1.22e+01
  ... (remaining 15310 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.84: 5957
       21.84 -    43.68: 642
       43.68 -    65.52: 78
       65.52 -    87.37: 43
       87.37 -   109.21: 29
  Dihedral angle restraints: 6749
    sinusoidal: 2766
      harmonic: 3983
  Sorted by residual:
  dihedral pdb=" CB  CYS A1368 "
           pdb=" SG  CYS A1368 "
           pdb=" SG  CYS A1381 "
           pdb=" CB  CYS A1381 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.84  -82.16     1      1.00e+01 1.00e-02 8.29e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  46 "
           pdb=" CB  CYS H  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.21   77.21     1      1.00e+01 1.00e-02 7.47e+01
  dihedral pdb=" CB  CYS A1011 "
           pdb=" SG  CYS A1011 "
           pdb=" SG  CYS A1030 "
           pdb=" CB  CYS A1030 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -148.92   62.92     1      1.00e+01 1.00e-02 5.23e+01
  ... (remaining 6746 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1639
       0.078 -    0.156: 134
       0.156 -    0.234: 6
       0.234 -    0.312: 5
       0.312 -    0.389: 2
  Chirality restraints: 1786
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 330 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.79    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" C4  NAG B   1 "
            pdb=" C3  NAG B   1 "
            pdb=" C5  NAG B   1 "
            pdb=" O4  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.20   -0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" C5  BMA B   6 "
            pdb=" C4  BMA B   6 "
            pdb=" C6  BMA B   6 "
            pdb=" O5  BMA B   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 1783 not shown)

  Planarity restraints: 1883
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 244 "    0.016 2.00e-02 2.50e+03   1.69e-02 7.13e+00
        pdb=" CG  TRP A 244 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 244 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 244 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 244 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 244 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 244 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 244 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 244 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 244 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1443 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.12e+00
        pdb=" C   GLU A1443 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLU A1443 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A1444 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 192 "   -0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO A 193 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 193 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 193 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1880 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 40
        2.41 -     3.03: 7161
        3.03 -     3.66: 16889
        3.66 -     4.28: 22951
        4.28 -     4.90: 36867
  Nonbonded interactions: 83908
  Sorted by model distance:
  nonbonded pdb=" O   THR A1059 "
            pdb=" NZ  LYS A1061 "
     model   vdw
     1.791 3.120
  nonbonded pdb=" O   SER A 632 "
            pdb=" OG1 THR A 635 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OD1 ASP A1129 "
            pdb=" N   SER A1130 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" ND2 ASN H  23 "
            pdb=" O   GLY H  34 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   LYS A 915 "
            pdb=" OG1 THR A 919 "
     model   vdw
     2.243 3.040
  ... (remaining 83903 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'G'
}

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:             6.930
  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:          0.500
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     28.070
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.060
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
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      :  0.004   0.066  11250  Z= 0.246
  Angle     :  0.756  11.795  15315  Z= 0.369
  Chirality :  0.047   0.389   1786
  Planarity :  0.004   0.058   1876
  Dihedral  : 19.496 109.206   4154
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.45 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 28.18 %
    Favored  : 71.09 %
  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: -0.22 (0.24), residues: 1342
  helix:  0.88 (0.18), residues: 854
  sheet: -2.32 (1.42), residues: 12
  loop : -2.01 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A1486 
 PHE   0.027   0.001   PHE A 861 
 TYR   0.022   0.001   TYR H  21 
 ARG   0.014   0.000   ARG H   2 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 230
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  947 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7529 (tt)
REVERT: A 1275 LEU cc_start: 0.8036 (mp) cc_final: 0.7704 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 234
  average time/residue: 0.2211
  time to fit residues: 74.7957
Evaluate side-chains
  228 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 223
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue 1226 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    0.0270
   chunk 101 optimal weight:   10.0000
   chunk 56 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 105 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 121 optimal weight:    6.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A1079 GLN
A1169 ASN
A1227 HIS
H  23 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.160666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.120179 restraints weight = 21729.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121032 restraints weight = 13255.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121188 restraints weight = 9396.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.0836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11250  Z= 0.174
  Angle     :  0.636   9.765  15315  Z= 0.315
  Chirality :  0.044   0.307   1786
  Planarity :  0.004   0.053   1876
  Dihedral  : 12.730  88.702   1829
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.00 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 24.57 %
    Favored  : 71.54 %
  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: -0.11 (0.24), residues: 1342
  helix:  0.96 (0.18), residues: 891
  sheet: -2.73 (1.23), residues: 12
  loop : -2.18 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A 291 
 PHE   0.016   0.001   PHE A 861 
 TYR   0.022   0.001   TYR A1240 
 ARG   0.010   0.001   ARG H   2 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 242
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8181 (p)
REVERT: A  715 TRP cc_start: 0.6695 (p90) cc_final: 0.6218 (p90)
REVERT: A 1102 PHE cc_start: 0.8765 (t80) cc_final: 0.8532 (t80)
REVERT: A 1227 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.7088 (t70)
REVERT: H    2 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7505 (mmm160)
  outliers start: 43
  outliers final: 21
  residues processed: 268
  average time/residue: 0.2238
  time to fit residues: 87.6556
Evaluate side-chains
  250 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 227
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1227 HIS
Chi-restraints excluded: chain A residue 1248 LEU
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1362 ILE
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 127 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 742 ASN
A1056 GLN
** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1234 ASN
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.159113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.118804 restraints weight = 21957.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.119665 restraints weight = 13373.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.119992 restraints weight = 9939.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11250  Z= 0.214
  Angle     :  0.642   8.831  15315  Z= 0.318
  Chirality :  0.044   0.293   1786
  Planarity :  0.004   0.054   1876
  Dihedral  : 10.160  78.626   1822
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.08 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 25.47 %
    Favored  : 69.74 %
  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: -0.12 (0.24), residues: 1342
  helix:  0.92 (0.18), residues: 893
  sheet: -2.89 (1.18), residues: 12
  loop : -2.11 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 244 
 HIS   0.008   0.001   HIS A1227 
 PHE   0.016   0.001   PHE A1321 
 TYR   0.017   0.001   TYR A 895 
 ARG   0.007   0.000   ARG A 613 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 233
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  547 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8331 (t80)
REVERT: A  715 TRP cc_start: 0.6798 (p90) cc_final: 0.6328 (p90)
REVERT: A  984 ASN cc_start: 0.8267 (t0) cc_final: 0.8029 (t0)
REVERT: A 1102 PHE cc_start: 0.8808 (t80) cc_final: 0.8604 (t80)
REVERT: A 1224 LEU cc_start: 0.7072 (tp) cc_final: 0.6777 (tt)
REVERT: A 1276 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8355 (tt)
REVERT: A 1432 MET cc_start: 0.7689 (ptt) cc_final: 0.7230 (ptt)
  outliers start: 53
  outliers final: 29
  residues processed: 264
  average time/residue: 0.2313
  time to fit residues: 90.2014
Evaluate side-chains
  251 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 220
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1248 LEU
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1324 ILE
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1418 TYR
Chi-restraints excluded: chain A residue 1492 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0670
   chunk 120 optimal weight:    0.0010
   chunk 77 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.5324

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

Flipped N/Q/H residues before XYZ refinement:
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1226 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 = 0.4127 r_free = 0.4127 target = 0.160028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.119641 restraints weight = 21845.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.121911 restraints weight = 13545.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.121944 restraints weight = 8795.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11250  Z= 0.176
  Angle     :  0.641  14.122  15315  Z= 0.313
  Chirality :  0.044   0.279   1786
  Planarity :  0.004   0.054   1876
  Dihedral  :  8.380  66.027   1822
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.08 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 26.11 %
    Favored  : 69.38 %
  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: -0.07 (0.24), residues: 1342
  helix:  0.95 (0.18), residues: 892
  sheet: -2.58 (1.25), residues: 12
  loop : -2.10 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A1227 
 PHE   0.022   0.001   PHE A 900 
 TYR   0.016   0.001   TYR A 895 
 ARG   0.008   0.000   ARG A 613 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 229
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8140 (p)
REVERT: A  378 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7641 (mt-10)
REVERT: A  420 THR cc_start: 0.9225 (t) cc_final: 0.8979 (t)
REVERT: A  715 TRP cc_start: 0.6713 (p90) cc_final: 0.6263 (p90)
REVERT: A  984 ASN cc_start: 0.8269 (t0) cc_final: 0.8034 (t0)
REVERT: A 1102 PHE cc_start: 0.8781 (t80) cc_final: 0.8573 (t80)
REVERT: A 1197 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6636 (tt0)
REVERT: A 1276 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8397 (tt)
REVERT: A 1341 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7747 (mp10)
  outliers start: 50
  outliers final: 29
  residues processed: 259
  average time/residue: 0.2197
  time to fit residues: 83.1964
Evaluate side-chains
  257 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 223
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1341 GLN
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1362 ILE
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0980
   chunk 119 optimal weight:    0.9990
   chunk 110 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 111 optimal weight:    0.8980
   chunk 129 optimal weight:    8.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A1194 GLN
A1226 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.159703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.119055 restraints weight = 21945.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.120751 restraints weight = 13355.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.120942 restraints weight = 9101.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11250  Z= 0.188
  Angle     :  0.645  13.897  15315  Z= 0.314
  Chirality :  0.044   0.275   1786
  Planarity :  0.004   0.053   1876
  Dihedral  :  7.434  57.300   1820
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.30 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 25.65 %
    Favored  : 68.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.04 (0.24), residues: 1342
  helix:  0.98 (0.18), residues: 892
  sheet: -2.78 (1.24), residues: 12
  loop : -2.07 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 244 
 HIS   0.005   0.001   HIS A1226 
 PHE   0.026   0.001   PHE A 900 
 TYR   0.018   0.001   TYR A 895 
 ARG   0.009   0.000   ARG A 613 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 228
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8224 (p)
REVERT: A  378 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7612 (mt-10)
REVERT: A  379 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7191 (t0)
REVERT: A  420 THR cc_start: 0.9227 (t) cc_final: 0.8976 (t)
REVERT: A  636 LYS cc_start: 0.8068 (pttm) cc_final: 0.7730 (tppt)
REVERT: A  715 TRP cc_start: 0.6718 (p90) cc_final: 0.6291 (p90)
REVERT: A  876 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6726 (tm-30)
REVERT: A  947 LEU cc_start: 0.8163 (tp) cc_final: 0.7892 (tt)
REVERT: A  984 ASN cc_start: 0.8280 (t0) cc_final: 0.8049 (t0)
REVERT: A 1019 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8518 (mm)
REVERT: A 1102 PHE cc_start: 0.8795 (t80) cc_final: 0.8517 (t80)
REVERT: A 1197 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6621 (tt0)
REVERT: A 1258 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7090 (t80)
REVERT: A 1276 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8662 (tt)
REVERT: A 1341 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7756 (mp10)
  outliers start: 61
  outliers final: 33
  residues processed: 270
  average time/residue: 0.2098
  time to fit residues: 83.9210
Evaluate side-chains
  264 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 222
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1104 LEU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1145 SER
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1341 GLN
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Chi-restraints excluded: chain H residue    1 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 132 optimal weight:   20.0000
   chunk 79 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 126 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 111 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 120 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.159937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.119059 restraints weight = 22227.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.120436 restraints weight = 14215.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.120667 restraints weight = 9814.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11250  Z= 0.190
  Angle     :  0.664  12.536  15315  Z= 0.321
  Chirality :  0.043   0.269   1786
  Planarity :  0.004   0.053   1876
  Dihedral  :  6.835  57.972   1820
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.30 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 26.02 %
    Favored  : 68.38 %
  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:  0.01 (0.24), residues: 1342
  helix:  1.01 (0.18), residues: 887
  sheet: -2.53 (1.33), residues: 12
  loop : -2.00 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A 291 
 PHE   0.019   0.001   PHE A 858 
 TYR   0.015   0.001   TYR A 895 
 ARG   0.012   0.000   ARG A 613 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 234
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.7750 (p)
REVERT: A  344 LEU cc_start: 0.8887 (mp) cc_final: 0.8569 (mp)
REVERT: A  378 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7638 (mt-10)
REVERT: A  379 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7213 (t0)
REVERT: A  715 TRP cc_start: 0.6690 (p90) cc_final: 0.6275 (p90)
REVERT: A  876 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6728 (tm-30)
REVERT: A  984 ASN cc_start: 0.8273 (t0) cc_final: 0.8027 (t0)
REVERT: A 1019 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8567 (mm)
REVERT: A 1102 PHE cc_start: 0.8804 (t80) cc_final: 0.8544 (t80)
REVERT: A 1196 MET cc_start: 0.8653 (mmm) cc_final: 0.8426 (mmm)
REVERT: A 1197 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6704 (tt0)
REVERT: A 1258 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7145 (t80)
REVERT: A 1499 ASP cc_start: 0.8249 (m-30) cc_final: 0.8045 (t0)
REVERT: H    2 ARG cc_start: 0.8486 (mmm160) cc_final: 0.7805 (mmm160)
  outliers start: 62
  outliers final: 39
  residues processed: 275
  average time/residue: 0.2056
  time to fit residues: 84.1438
Evaluate side-chains
  265 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 219
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1324 ILE
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1346 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1418 TYR
Chi-restraints excluded: chain H residue    1 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 42 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0270
   chunk 32 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.160026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.119918 restraints weight = 22096.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.120892 restraints weight = 13465.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.121201 restraints weight = 9981.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11250  Z= 0.185
  Angle     :  0.667  11.684  15315  Z= 0.323
  Chirality :  0.043   0.260   1786
  Planarity :  0.004   0.052   1876
  Dihedral  :  6.401  58.822   1820
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.45 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 27.19 %
    Favored  : 67.84 %
  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:  0.01 (0.24), residues: 1342
  helix:  1.02 (0.18), residues: 888
  sheet: -2.77 (1.33), residues: 12
  loop : -2.04 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A 421 
 PHE   0.026   0.001   PHE A 900 
 TYR   0.016   0.001   TYR A 895 
 ARG   0.011   0.000   ARG A 613 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 231
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.7698 (p)
REVERT: A  344 LEU cc_start: 0.8901 (mp) cc_final: 0.8569 (mp)
REVERT: A  378 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7621 (mt-10)
REVERT: A  379 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7210 (t0)
REVERT: A  715 TRP cc_start: 0.6651 (p90) cc_final: 0.6237 (p90)
REVERT: A  876 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6729 (tm-30)
REVERT: A  947 LEU cc_start: 0.8067 (tp) cc_final: 0.7797 (tt)
REVERT: A  984 ASN cc_start: 0.8242 (t0) cc_final: 0.8006 (t0)
REVERT: A 1019 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8555 (mm)
REVERT: A 1102 PHE cc_start: 0.8811 (t80) cc_final: 0.8525 (t80)
REVERT: A 1197 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6669 (tt0)
REVERT: A 1258 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7125 (t80)
REVERT: A 1499 ASP cc_start: 0.8239 (m-30) cc_final: 0.8029 (t0)
  outliers start: 55
  outliers final: 42
  residues processed: 269
  average time/residue: 0.2083
  time to fit residues: 83.3661
Evaluate side-chains
  271 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 222
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1178 ILE
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1346 LEU
Chi-restraints excluded: chain A residue 1362 ILE
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 61 optimal weight:    9.9990
   chunk 92 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0970
   chunk 4 optimal weight:    0.0970
   chunk 118 optimal weight:    0.6980
   chunk 120 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 742 ASN
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.161248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.121113 restraints weight = 21941.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.122683 restraints weight = 13477.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.122911 restraints weight = 9425.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11250  Z= 0.173
  Angle     :  0.687  10.910  15315  Z= 0.329
  Chirality :  0.043   0.251   1786
  Planarity :  0.004   0.055   1876
  Dihedral  :  6.137  59.688   1820
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.00 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 28.27 %
    Favored  : 67.21 %
  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: -0.05 (0.24), residues: 1342
  helix:  1.00 (0.18), residues: 887
  sheet: -2.83 (1.35), residues: 12
  loop : -2.10 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 244 
 HIS   0.003   0.000   HIS A1021 
 PHE   0.035   0.001   PHE A 900 
 TYR   0.017   0.001   TYR H  21 
 ARG   0.014   0.001   ARG A 613 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 230
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.7669 (p)
REVERT: A  344 LEU cc_start: 0.8857 (mp) cc_final: 0.8548 (mp)
REVERT: A  378 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7601 (mt-10)
REVERT: A  379 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7197 (t0)
REVERT: A  715 TRP cc_start: 0.6614 (p90) cc_final: 0.6175 (p90)
REVERT: A  984 ASN cc_start: 0.8223 (t0) cc_final: 0.7989 (t0)
REVERT: A 1019 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8550 (mm)
REVERT: A 1102 PHE cc_start: 0.8802 (t80) cc_final: 0.8501 (t80)
REVERT: A 1197 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6663 (tt0)
REVERT: A 1258 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7127 (t80)
REVERT: A 1275 LEU cc_start: 0.8220 (mp) cc_final: 0.7859 (tt)
REVERT: A 1499 ASP cc_start: 0.8199 (m-30) cc_final: 0.7995 (t0)
REVERT: H    2 ARG cc_start: 0.8428 (mmm160) cc_final: 0.7724 (mmm160)
  outliers start: 50
  outliers final: 33
  residues processed: 267
  average time/residue: 0.2054
  time to fit residues: 81.8792
Evaluate side-chains
  262 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 223
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1145 SER
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 36 optimal weight:   40.0000
   chunk 47 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0770
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:   30.0000
   chunk 35 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 742 ASN
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1194 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.160379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.120093 restraints weight = 22134.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.120807 restraints weight = 13476.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.121261 restraints weight = 10084.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11250  Z= 0.189
  Angle     :  0.692  11.700  15315  Z= 0.331
  Chirality :  0.043   0.252   1786
  Planarity :  0.004   0.064   1876
  Dihedral  :  5.988  59.559   1820
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.53 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 28.00 %
    Favored  : 67.30 %
  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: -0.04 (0.24), residues: 1342
  helix:  1.00 (0.18), residues: 888
  sheet: -3.12 (1.37), residues: 10
  loop : -2.09 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A1021 
 PHE   0.029   0.001   PHE A 900 
 TYR   0.014   0.001   TYR A1240 
 ARG   0.014   0.000   ARG A 613 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 225
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.7654 (p)
REVERT: A  344 LEU cc_start: 0.8897 (mp) cc_final: 0.8573 (mp)
REVERT: A  378 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7596 (mt-10)
REVERT: A  379 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7174 (t0)
REVERT: A  589 ILE cc_start: 0.8950 (mm) cc_final: 0.8721 (mm)
REVERT: A  715 TRP cc_start: 0.6658 (p90) cc_final: 0.6219 (p90)
REVERT: A  984 ASN cc_start: 0.8220 (t0) cc_final: 0.7993 (t0)
REVERT: A 1019 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8566 (mm)
REVERT: A 1102 PHE cc_start: 0.8807 (t80) cc_final: 0.8541 (t80)
REVERT: A 1197 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6603 (tt0)
REVERT: A 1258 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7189 (t80)
REVERT: A 1275 LEU cc_start: 0.8252 (mp) cc_final: 0.7732 (tt)
REVERT: H    2 ARG cc_start: 0.8439 (mmm160) cc_final: 0.7776 (mmm160)
  outliers start: 52
  outliers final: 35
  residues processed: 264
  average time/residue: 0.1999
  time to fit residues: 79.0949
Evaluate side-chains
  266 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 225
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 110 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 124 optimal weight:    0.5980
   chunk 86 optimal weight:    0.8980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 742 ASN
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1191 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.158896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.113955 restraints weight = 22002.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.115267 restraints weight = 13508.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.116353 restraints weight = 8554.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11250  Z= 0.229
  Angle     :  0.718  11.680  15315  Z= 0.344
  Chirality :  0.044   0.255   1786
  Planarity :  0.004   0.057   1876
  Dihedral  :  5.963  58.839   1820
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.68 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 28.36 %
    Favored  : 67.30 %
  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: -0.04 (0.24), residues: 1342
  helix:  0.98 (0.18), residues: 890
  sheet: -3.23 (1.35), residues: 10
  loop : -2.07 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A1077 
 PHE   0.039   0.001   PHE A 900 
 TYR   0.013   0.001   TYR A1240 
 ARG   0.013   0.001   ARG A 613 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 224
  time to evaluate  : 1.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.7744 (p)
REVERT: A  344 LEU cc_start: 0.8872 (mp) cc_final: 0.8525 (mp)
REVERT: A  378 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7720 (mt-10)
REVERT: A  379 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7315 (t0)
REVERT: A  589 ILE cc_start: 0.9021 (mm) cc_final: 0.8816 (mm)
REVERT: A  715 TRP cc_start: 0.6744 (p90) cc_final: 0.6280 (p90)
REVERT: A  948 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7422 (tp-100)
REVERT: A  984 ASN cc_start: 0.8281 (t0) cc_final: 0.8057 (t0)
REVERT: A 1019 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8341 (mm)
REVERT: A 1102 PHE cc_start: 0.8860 (t80) cc_final: 0.8448 (t80)
REVERT: A 1197 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6637 (tt0)
REVERT: A 1229 PHE cc_start: 0.6998 (p90) cc_final: 0.6311 (t80)
REVERT: A 1258 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7533 (t80)
REVERT: H    2 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8404 (mmt180)
  outliers start: 48
  outliers final: 33
  residues processed: 257
  average time/residue: 0.2100
  time to fit residues: 80.5660
Evaluate side-chains
  256 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 216
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  948 GLN
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 129 optimal weight:    3.9990
   chunk 132 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 106 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 742 ASN
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1191 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.156615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.112324 restraints weight = 21962.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.112747 restraints weight = 12332.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.113603 restraints weight = 8762.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11250  Z= 0.280
  Angle     :  0.739  11.693  15315  Z= 0.359
  Chirality :  0.045   0.265   1786
  Planarity :  0.004   0.054   1876
  Dihedral  :  6.026  57.852   1820
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.75 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 28.36 %
    Favored  : 67.48 %
  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: -0.09 (0.24), residues: 1342
  helix:  0.94 (0.18), residues: 890
  sheet: -3.25 (1.31), residues: 10
  loop : -2.06 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A 244 
 HIS   0.004   0.001   HIS A 421 
 PHE   0.024   0.001   PHE A 858 
 TYR   0.013   0.001   TYR A1334 
 ARG   0.013   0.001   ARG A 613 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3997.48 seconds
wall clock time: 73 minutes 43.42 seconds (4423.42 seconds total)