Starting phenix.real_space_refine
on Sat Aug 23 10:59:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j1p_35929/08_2025/8j1p_35929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j1p_35929/08_2025/8j1p_35929.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j1p_35929/08_2025/8j1p_35929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j1p_35929/08_2025/8j1p_35929.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j1p_35929/08_2025/8j1p_35929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j1p_35929/08_2025/8j1p_35929.map"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      50      5.16       5
     C    7349      2.51       5
     N    1914      2.21       5
     O    2210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11523
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1234, 9769
          Classifications: {'peptide': 1234}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'CIS': 9, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 1186}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "C"
      Number of atoms: 592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 592
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 581
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 581
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N   LEU C  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU C  73 " occ=0.45
    residue:
      pdb=" N   ARG C  74 " occ=0.45
      ... (3 atoms not shown)
      pdb=" CB  ARG C  74 " occ=0.45
    residue:
      pdb=" N   GLY C  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY C  75 " occ=0.25
    residue:
      pdb=" N   GLY C  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY C  76 " occ=0.25
    residue:
      pdb=" N   LEU D  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU D  73 " occ=0.45
    residue:
      pdb=" N   ARG D  74 " occ=0.45
      ... (3 atoms not shown)
      pdb=" CB  ARG D  74 " occ=0.45
    residue:
      pdb=" N   LEU E  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU E  73 " occ=0.45
  Time building chain proxies: 2.59, per 1000 atoms: 0.22
  Number of scatterers: 11523
  At special positions: 0
  Unit cell: (109.548, 108.474, 132.102, 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      50     16.00
     O    2210      8.00
     N    1914      7.00
     C    7349      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 439.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2768

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 7 sheets defined
      57.4% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 164 through 181
      removed outlier: 3.995A  pdb=" N   GLU A 170 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ARG A 171 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LYS A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 184
      No H-bonds generated for 'chain 'A' and resid 182 through 184'
    Processing helix  chain 'A' and resid 187 through 202
      removed outlier: 3.912A  pdb=" N   GLU A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 201 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET A 202 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 210
      removed outlier: 3.866A  pdb=" N   ARG A 210 " --> pdb=" O   MET A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 227
    Processing helix  chain 'A' and resid 233 through 251
      removed outlier: 3.505A  pdb=" N   MET A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLN A 239 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL A 250 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 3.925A  pdb=" N   ILE A 257 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 273
      removed outlier: 3.559A  pdb=" N   GLY A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LYS A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 271 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLU A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 292
      removed outlier: 3.971A  pdb=" N   ALA A 280 " --> pdb=" O   TYR A 276 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLN A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLU A 285 " --> pdb=" O   GLU A 281 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TYR A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG A 292 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 302
      removed outlier: 3.572A  pdb=" N   THR A 301 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLY A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 316 through 330
      removed outlier: 4.274A  pdb=" N   ILE A 323 " --> pdb=" O   GLN A 319 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE A 325 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   VAL A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 336
      No H-bonds generated for 'chain 'A' and resid 334 through 336'
    Processing helix  chain 'A' and resid 337 through 354
      removed outlier: 3.605A  pdb=" N   ILE A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      Proline residue:  A 346  - end of helix
      Proline residue:  A 350  - end of helix
    Processing helix  chain 'A' and resid 357 through 362
    Processing helix  chain 'A' and resid 363 through 376
      removed outlier: 3.597A  pdb=" N   MET A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 374 " --> pdb=" O   GLY A 370 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   HIS A 376 " --> pdb=" O   CYS A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
    Processing helix  chain 'A' and resid 403 through 420
    Processing helix  chain 'A' and resid 422 through 431
      removed outlier: 3.958A  pdb=" N   ARG A 429 " --> pdb=" O   SER A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 444
      removed outlier: 3.880A  pdb=" N   SER A 441 " --> pdb=" O   MET A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 460
      removed outlier: 4.282A  pdb=" N   ILE A 458 " --> pdb=" O   HIS A 454 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   TYR A 459 " --> pdb=" O   GLU A 455 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL A 460 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 475
      removed outlier: 3.713A  pdb=" N   ILE A 472 " --> pdb=" O   ILE A 468 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL A 474 " --> pdb=" O   ARG A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 521
      removed outlier: 4.348A  pdb=" N   VAL A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   CYS A 510 " --> pdb=" O   SER A 506 " (cutoff:3.500A)
      Proline residue:  A 513  - end of helix
      removed outlier: 4.488A  pdb=" N   GLU A 517 " --> pdb=" O   PRO A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 539
    Processing helix  chain 'A' and resid 543 through 548
      removed outlier: 3.855A  pdb=" N   LYS A 548 " --> pdb=" O   ASN A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 562
      removed outlier: 3.987A  pdb=" N   LEU A 554 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A 555 " --> pdb=" O   ASN A 551 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS A 556 " --> pdb=" O   ASP A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 569
      removed outlier: 3.928A  pdb=" N   ALA A 568 " --> pdb=" O   GLN A 564 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER A 569 " --> pdb=" O   LYS A 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 564 through 569'
    Processing helix  chain 'A' and resid 576 through 597
      removed outlier: 3.735A  pdb=" N   GLY A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU A 582 " --> pdb=" O   GLU A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 609
      Proline residue:  A 603  - end of helix
    Processing helix  chain 'A' and resid 610 through 624
    Processing helix  chain 'A' and resid 684 through 702
      removed outlier: 3.910A  pdb=" N   LYS A 689 " --> pdb=" O   LEU A 685 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN A 694 " --> pdb=" O   ASN A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 726
    Processing helix  chain 'A' and resid 733 through 749
      removed outlier: 3.860A  pdb=" N   GLY A 739 " --> pdb=" O   GLU A 735 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 743 " --> pdb=" O   GLY A 739 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A 744 " --> pdb=" O   ILE A 740 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS A 746 " --> pdb=" O   SER A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 763
      removed outlier: 3.951A  pdb=" N   THR A 761 " --> pdb=" O   GLY A 757 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR A 763 " --> pdb=" O   GLU A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 776
      removed outlier: 3.503A  pdb=" N   ARG A 772 " --> pdb=" O   SER A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 791
      removed outlier: 3.573A  pdb=" N   VAL A 790 " --> pdb=" O   SER A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 810
      removed outlier: 3.830A  pdb=" N   ILE A 801 " --> pdb=" O   ARG A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 828
    Processing helix  chain 'A' and resid 863 through 876
      removed outlier: 3.732A  pdb=" N   VAL A 876 " --> pdb=" O   ARG A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 906 through 910
    Processing helix  chain 'A' and resid 928 through 938
    Processing helix  chain 'A' and resid 941 through 948
      removed outlier: 3.700A  pdb=" N   LEU A 945 " --> pdb=" O   ASP A 941 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   TRP A 946 " --> pdb=" O   LEU A 942 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASP A 947 " --> pdb=" O   LYS A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 982
      removed outlier: 4.181A  pdb=" N   TYR A 981 " --> pdb=" O   ARG A 978 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS A 982 " --> pdb=" O   ASP A 979 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 978 through 982'
    Processing helix  chain 'A' and resid 991 through 993
      No H-bonds generated for 'chain 'A' and resid 991 through 993'
    Processing helix  chain 'A' and resid 994 through 1006
    Processing helix  chain 'A' and resid 1016 through 1028
    Processing helix  chain 'A' and resid 1029 through 1034
    Processing helix  chain 'A' and resid 1039 through 1049
    Processing helix  chain 'A' and resid 1054 through 1067
    Processing helix  chain 'A' and resid 1068 through 1072
    Processing helix  chain 'A' and resid 1106 through 1108
      No H-bonds generated for 'chain 'A' and resid 1106 through 1108'
    Processing helix  chain 'A' and resid 1109 through 1122
      removed outlier: 3.526A  pdb=" N   GLY A1114 " --> pdb=" O   ILE A1110 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A1116 " --> pdb=" O   ALA A1112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1139 through 1154
      removed outlier: 3.873A  pdb=" N   THR A1143 " --> pdb=" O   GLY A1139 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   TYR A1147 " --> pdb=" O   THR A1143 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A1149 " --> pdb=" O   GLU A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1160
      removed outlier: 6.663A  pdb=" N   SER A1158 " --> pdb=" O   ALA A1155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1199 through 1217
      removed outlier: 3.634A  pdb=" N   THR A1209 " --> pdb=" O   GLY A1205 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A1217 " --> pdb=" O   ARG A1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1226 through 1238
      removed outlier: 3.658A  pdb=" N   PHE A1230 " --> pdb=" O   SER A1226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1256
    Processing helix  chain 'A' and resid 1259 through 1272
    Processing helix  chain 'A' and resid 1275 through 1283
      removed outlier: 3.604A  pdb=" N   LEU A1282 " --> pdb=" O   THR A1278 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER A1283 " --> pdb=" O   LEU A1279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1309 through 1322
    Processing helix  chain 'A' and resid 1326 through 1341
      removed outlier: 3.596A  pdb=" N   LEU A1330 " --> pdb=" O   ILE A1326 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA A1332 " --> pdb=" O   LYS A1328 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU A1335 " --> pdb=" O   LYS A1331 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A1339 " --> pdb=" O   GLU A1335 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL A1340 " --> pdb=" O   GLY A1336 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE A1341 " --> pdb=" O   PHE A1337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1342 through 1349
      removed outlier: 3.534A  pdb=" N   LEU A1347 " --> pdb=" O   GLU A1344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1350 through 1353
    Processing helix  chain 'A' and resid 1354 through 1359
    Processing helix  chain 'A' and resid 1366 through 1372
      removed outlier: 3.773A  pdb=" N   LEU A1370 " --> pdb=" O   SER A1366 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   TYR A1371 " --> pdb=" O   MET A1367 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR A1372 " --> pdb=" O   ALA A1368 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1366 through 1372'
    Processing helix  chain 'A' and resid 1387 through 1395
      removed outlier: 3.676A  pdb=" N   ILE A1394 " --> pdb=" O   PHE A1390 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER A1395 " --> pdb=" O   ILE A1391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1398 through 1410
      removed outlier: 3.710A  pdb=" N   ARG A1403 " --> pdb=" O   LYS A1399 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A1408 " --> pdb=" O   LEU A1404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1419 through 1423
      removed outlier: 3.559A  pdb=" N   SER A1422 " --> pdb=" O   GLY A1419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1461 through 1477
    Processing helix  chain 'C' and resid 22 through 35
    Processing helix  chain 'C' and resid 37 through 41
    Processing helix  chain 'D' and resid 23 through 34
    Processing helix  chain 'D' and resid 37 through 41
    Processing helix  chain 'E' and resid 24 through 34
    Processing helix  chain 'E' and resid 37 through 41
    Processing sheet with id=AA1, first strand: chain 'A' and resid 831 through 835
      removed outlier: 3.739A  pdb=" N   VAL A 856 " --> pdb=" O   ILE A 834 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 837 through 838
      removed outlier: 6.523A  pdb=" N   VAL A 837 " --> pdb=" O   PHE A 954 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1100 through 1105
      removed outlier: 5.988A  pdb=" N   ARG A1101 " --> pdb=" O   GLU A1129 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   GLU A1131 " --> pdb=" O   ARG A1101 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   LEU A1103 " --> pdb=" O   GLU A1131 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1429 through 1432
      removed outlier: 6.035A  pdb=" N   VAL A1430 " --> pdb=" O   LEU A1456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 12 through 14
      removed outlier: 3.683A  pdb=" N   ILE C  13 " --> pdb=" O   VAL C   5 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE C   4 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   LEU C  69 " --> pdb=" O   PHE C   4 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   LYS C   6 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 14
    Processing sheet with id=AA7, first strand: chain 'E' and resid 12 through 16
      removed outlier: 9.851A  pdb=" N   LEU E  67 " --> pdb=" O   GLN E   2 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   PHE E   4 " --> pdb=" O   LEU E  67 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   LEU E  69 " --> pdb=" O   PHE E   4 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LYS E   6 " --> pdb=" O   LEU E  69 " (cutoff:3.500A)

    475 hydrogen bonds defined for protein.
    1353 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: 2.23

  Time building geometry restraints manager: 1.10 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: 3761
        1.34 -     1.46: 2475
        1.46 -     1.58: 5396
        1.58 -     1.70: 0
        1.70 -     1.82: 77
  Bond restraints: 11709
  Sorted by residual:
  bond pdb=" CA  THR E   9 "
       pdb=" CB  THR E   9 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.024 1.46e-02 4.69e+03 2.61e+00
  bond pdb=" CG  LEU A 643 "
       pdb=" CD1 LEU A 643 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.19e+00
  bond pdb=" N   ASN A1452 "
       pdb=" CA  ASN A1452 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.90e-02 2.77e+03 2.15e+00
  bond pdb=" C   LEU A1444 "
       pdb=" N   PRO A1445 "
    ideal  model  delta    sigma   weight residual
    1.332  1.348 -0.016 1.12e-02 7.97e+03 2.09e+00
  bond pdb=" CG1 ILE A 176 "
       pdb=" CD1 ILE A 176 "
    ideal  model  delta    sigma   weight residual
    1.513  1.457  0.056 3.90e-02 6.57e+02 2.04e+00
  ... (remaining 11704 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 15608
        2.80 -     5.60: 173
        5.60 -     8.40: 21
        8.40 -    11.19: 12
       11.19 -    13.99: 3
  Bond angle restraints: 15817
  Sorted by residual:
  angle pdb=" N   ILE A1386 "
        pdb=" CA  ILE A1386 "
        pdb=" C   ILE A1386 "
      ideal   model   delta    sigma   weight residual
     113.47  106.67    6.80 1.01e+00 9.80e-01 4.54e+01
  angle pdb=" C   THR D  22 "
        pdb=" CA  THR D  22 "
        pdb=" CB  THR D  22 "
      ideal   model   delta    sigma   weight residual
     115.79  108.46    7.33 1.19e+00 7.06e-01 3.79e+01
  angle pdb=" N   ILE D  23 "
        pdb=" CA  ILE D  23 "
        pdb=" C   ILE D  23 "
      ideal   model   delta    sigma   weight residual
     112.12  107.29    4.83 8.40e-01 1.42e+00 3.31e+01
  angle pdb=" C   ALA A1451 "
        pdb=" N   ASN A1452 "
        pdb=" CA  ASN A1452 "
      ideal   model   delta    sigma   weight residual
     121.70  130.95   -9.25 1.80e+00 3.09e-01 2.64e+01
  angle pdb=" N   ASN A1452 "
        pdb=" CA  ASN A1452 "
        pdb=" C   ASN A1452 "
      ideal   model   delta    sigma   weight residual
     111.00  124.99  -13.99 2.80e+00 1.28e-01 2.50e+01
  ... (remaining 15812 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 6508
       16.49 -    32.99: 530
       32.99 -    49.48: 93
       49.48 -    65.98: 10
       65.98 -    82.47: 8
  Dihedral angle restraints: 7149
    sinusoidal: 2901
      harmonic: 4248
  Sorted by residual:
  dihedral pdb=" CA  LEU A 643 "
           pdb=" C   LEU A 643 "
           pdb=" N   HIS A 644 "
           pdb=" CA  HIS A 644 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.82   45.18     0      5.00e+00 4.00e-02 8.16e+01
  dihedral pdb=" CA  GLN A1074 "
           pdb=" C   GLN A1074 "
           pdb=" N   LEU A1075 "
           pdb=" CA  LEU A1075 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.89  -31.11     0      5.00e+00 4.00e-02 3.87e+01
  dihedral pdb=" CA  HIS A 644 "
           pdb=" C   HIS A 644 "
           pdb=" N   SER A 645 "
           pdb=" CA  SER A 645 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.85   29.15     0      5.00e+00 4.00e-02 3.40e+01
  ... (remaining 7146 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1493
       0.055 -    0.110: 334
       0.110 -    0.165: 28
       0.165 -    0.220: 7
       0.220 -    0.274: 2
  Chirality restraints: 1864
  Sorted by residual:
  chirality pdb=" CA  ASN A1452 "
            pdb=" N   ASN A1452 "
            pdb=" C   ASN A1452 "
            pdb=" CB  ASN A1452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  LEU A 643 "
            pdb=" N   LEU A 643 "
            pdb=" C   LEU A 643 "
            pdb=" CB  LEU A 643 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  ILE A 855 "
            pdb=" CA  ILE A 855 "
            pdb=" CG1 ILE A 855 "
            pdb=" CG2 ILE A 855 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1861 not shown)

  Planarity restraints: 2011
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  36 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO D  37 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO D  37 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D  37 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1424 "   -0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO A1425 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A1425 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A1425 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D  18 "    0.029 5.00e-02 4.00e+02   4.38e-02 3.08e+00
        pdb=" N   PRO D  19 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO D  19 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D  19 "    0.024 5.00e-02 4.00e+02
  ... (remaining 2008 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 383
        2.71 -     3.25: 12507
        3.25 -     3.80: 18599
        3.80 -     4.35: 24277
        4.35 -     4.90: 38504
  Nonbonded interactions: 94270
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 625 "
            pdb=" NZ  LYS A 689 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" O   GLY A 824 "
            pdb=" OG  SER A 827 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   GLU A 391 "
            pdb=" NE2 GLN A 395 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" O   ILE A 176 "
            pdb=" OG1 THR A 179 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   ARG A 698 "
            pdb=" OG  SER A 701 "
     model   vdw
     2.212 3.040
  ... (remaining 94265 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' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 2 through 28 or resid 30 through 71 or (resid 72 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 73 through 74))
  selection = (chain 'D' and (resid 1 through 28 or resid 30 through 50 or (resid 51 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 52 through 71 or (resid \ 
 72 and (name N or name CA or name C or name O or name CB )) or resid 73 through \ 
 74))
  selection = (chain 'E' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 2 through 28 or resid 30 through 50 or (resid 51 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 52 through 74))
}

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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.470
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
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      :  0.003   0.056  11709  Z= 0.159
  Angle     :  0.813  13.992  15817  Z= 0.444
  Chirality :  0.045   0.274   1864
  Planarity :  0.004   0.045   2011
  Dihedral  : 12.574  82.474   4381
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.22 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.52 (0.22), residues: 1436
  helix: -0.73 (0.20), residues: 701
  sheet: -0.99 (0.57), residues: 88
  loop : -1.21 (0.25), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 210 
 TYR   0.017   0.002   TYR A 369 
 PHE   0.024   0.002   PHE A 870 
 TRP   0.022   0.002   TRP A 741 
 HIS   0.003   0.001   HIS A1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11709)
  covalent geometry    : angle       0.81311 (15817)
  hydrogen bonds       : bond        0.20184 (  475)
  hydrogen bonds       : angle       6.94206 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.7925 (t80) cc_final: 0.7234 (t80)
REVERT: A  202 MET cc_start: 0.7780 (ppp) cc_final: 0.7530 (ppp)
REVERT: A 1391 ILE cc_start: 0.7772 (mm) cc_final: 0.7431 (mt)
REVERT: D    4 PHE cc_start: 0.7276 (m-80) cc_final: 0.7048 (m-80)
REVERT: D   32 ASP cc_start: 0.8460 (m-30) cc_final: 0.8250 (m-30)
REVERT: D   64 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7535 (tp30)
REVERT: E   50 LEU cc_start: 0.6271 (mt) cc_final: 0.5745 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.1058
  time to fit residues: 30.2051
Evaluate side-chains
  150 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0040
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.3980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 GLN
A 521 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1192 ASN
** C  31 GLN ** 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 = 0.4652 r_free = 0.4652 target = 0.145985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.115771 restraints weight = 27534.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 4.41
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4167 r_free = 0.4167    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11709  Z= 0.138
  Angle     :  0.719  13.541  15817  Z= 0.358
  Chirality :  0.045   0.271   1864
  Planarity :  0.004   0.052   2011
  Dihedral  :  5.402  34.221   1545
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.50 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.79 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.52 (0.22), residues: 1436
  helix: -0.56 (0.19), residues: 734
  sheet: -1.06 (0.54), residues: 94
  loop : -1.43 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1213 
 TYR   0.021   0.002   TYR A 489 
 PHE   0.019   0.002   PHE A 870 
 TRP   0.012   0.002   TRP A1076 
 HIS   0.005   0.001   HIS A1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (11709)
  covalent geometry    : angle       0.71943 (15817)
  hydrogen bonds       : bond        0.04304 (  475)
  hydrogen bonds       : angle       5.24949 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8054 (t80) cc_final: 0.7198 (t80)
REVERT: A  198 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: A  202 MET cc_start: 0.7868 (ppp) cc_final: 0.7338 (ppp)
REVERT: A  244 MET cc_start: 0.7952 (ppp) cc_final: 0.7663 (ppp)
REVERT: A  369 TYR cc_start: 0.6515 (t80) cc_final: 0.5862 (t80)
REVERT: A  954 PHE cc_start: 0.7546 (p90) cc_final: 0.6676 (p90)
REVERT: D    4 PHE cc_start: 0.7427 (m-80) cc_final: 0.7068 (m-80)
REVERT: D   32 ASP cc_start: 0.8427 (m-30) cc_final: 0.8197 (m-30)
REVERT: D   44 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7293 (mm)
REVERT: E   50 LEU cc_start: 0.6244 (mt) cc_final: 0.5811 (mt)
  outliers start: 16
  outliers final: 10
  residues processed: 175
  average time/residue: 0.0966
  time to fit residues: 25.2717
Evaluate side-chains
  156 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  581 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 82 optimal weight:    0.1980
   chunk 29 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 135 optimal weight:    8.9990
   chunk 28 optimal weight:    0.5980
   chunk 139 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.5582

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 317 HIS
A 443 GLN
A 521 ASN
A 820 HIS
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1197 ASN
A1373 ASN
D  49 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.146236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.115469 restraints weight = 27798.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.4166 rms_B_bonded: 4.60
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4166 r_free = 0.4166    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4166 r_free = 0.4166    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11709  Z= 0.126
  Angle     :  0.677  12.455  15817  Z= 0.337
  Chirality :  0.043   0.244   1864
  Planarity :  0.004   0.046   2011
  Dihedral  :  5.126  30.663   1545
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.15 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.16 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.22), residues: 1436
  helix: -0.39 (0.19), residues: 741
  sheet: -1.15 (0.56), residues: 91
  loop : -1.33 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 210 
 TYR   0.012   0.001   TYR A1443 
 PHE   0.015   0.001   PHE A 248 
 TRP   0.012   0.002   TRP A1076 
 HIS   0.005   0.001   HIS A1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11709)
  covalent geometry    : angle       0.67704 (15817)
  hydrogen bonds       : bond        0.03870 (  475)
  hydrogen bonds       : angle       4.95239 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8119 (t80) cc_final: 0.7169 (t80)
REVERT: A  198 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: A  202 MET cc_start: 0.7865 (ppp) cc_final: 0.7349 (ppp)
REVERT: A  244 MET cc_start: 0.8163 (ppp) cc_final: 0.7911 (ppp)
REVERT: A  369 TYR cc_start: 0.6469 (t80) cc_final: 0.5850 (t80)
REVERT: A  954 PHE cc_start: 0.7537 (p90) cc_final: 0.6684 (p90)
REVERT: A 1366 SER cc_start: 0.7757 (t) cc_final: 0.7436 (t)
REVERT: A 1370 LEU cc_start: 0.7388 (pp) cc_final: 0.6685 (tt)
REVERT: D    4 PHE cc_start: 0.7379 (m-80) cc_final: 0.7115 (m-80)
REVERT: D   32 ASP cc_start: 0.8403 (m-30) cc_final: 0.8162 (m-30)
REVERT: D   44 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7411 (mm)
REVERT: E   50 LEU cc_start: 0.5987 (mt) cc_final: 0.5567 (mt)
  outliers start: 24
  outliers final: 13
  residues processed: 181
  average time/residue: 0.1113
  time to fit residues: 29.4080
Evaluate side-chains
  159 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 97 optimal weight:    0.1980
   chunk 137 optimal weight:    3.9990
   chunk 99 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 112 optimal weight:    0.6980
   chunk 125 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 521 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1234 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.146230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.116739 restraints weight = 27679.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 4.08
r_work: 0.4001 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4003 r_free = 0.4003    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4003 r_free = 0.4003    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11709  Z= 0.121
  Angle     :  0.666  13.386  15817  Z= 0.327
  Chirality :  0.043   0.218   1864
  Planarity :  0.004   0.050   2011
  Dihedral  :  5.011  33.173   1545
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.01 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.37 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.22), residues: 1436
  helix: -0.22 (0.20), residues: 737
  sheet: -1.09 (0.57), residues: 91
  loop : -1.29 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 210 
 TYR   0.032   0.002   TYR A 489 
 PHE   0.014   0.001   PHE A 248 
 TRP   0.012   0.001   TRP A1076 
 HIS   0.006   0.001   HIS A1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (11709)
  covalent geometry    : angle       0.66638 (15817)
  hydrogen bonds       : bond        0.03526 (  475)
  hydrogen bonds       : angle       4.80579 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8288 (t80) cc_final: 0.7377 (t80)
REVERT: A  190 MET cc_start: 0.7089 (mmm) cc_final: 0.6742 (mmm)
REVERT: A  198 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: A  202 MET cc_start: 0.8002 (ppp) cc_final: 0.7466 (ppp)
REVERT: A  244 MET cc_start: 0.8254 (ppp) cc_final: 0.7830 (ppp)
REVERT: A  369 TYR cc_start: 0.6405 (t80) cc_final: 0.5943 (t80)
REVERT: A  644 HIS cc_start: 0.5807 (OUTLIER) cc_final: 0.5063 (m90)
REVERT: A  664 MET cc_start: 0.4728 (ppp) cc_final: 0.4512 (ppp)
REVERT: A  954 PHE cc_start: 0.7765 (p90) cc_final: 0.7048 (p90)
REVERT: C    1 MET cc_start: 0.6779 (tmm) cc_final: 0.6259 (tmm)
REVERT: D    4 PHE cc_start: 0.7470 (m-80) cc_final: 0.7214 (m-80)
REVERT: D   32 ASP cc_start: 0.8389 (m-30) cc_final: 0.8154 (m-30)
REVERT: D   44 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7396 (mm)
REVERT: E   41 GLN cc_start: 0.6425 (mm110) cc_final: 0.5095 (tt0)
REVERT: E   50 LEU cc_start: 0.6058 (mt) cc_final: 0.5611 (mt)
  outliers start: 24
  outliers final: 16
  residues processed: 179
  average time/residue: 0.1121
  time to fit residues: 28.9743
Evaluate side-chains
  165 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  644 HIS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  833 LYS
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 GLN
** A 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 939 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1078 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.139930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.107928 restraints weight = 27791.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 4.11
r_work: 0.3880 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3882 r_free = 0.3882    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3882 r_free = 0.3882    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  11709  Z= 0.224
  Angle     :  0.770  16.568  15817  Z= 0.380
  Chirality :  0.047   0.209   1864
  Planarity :  0.005   0.050   2011
  Dihedral  :  5.465  37.730   1545
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.92 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.06 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.22), residues: 1436
  helix: -0.46 (0.19), residues: 733
  sheet: -1.20 (0.57), residues: 92
  loop : -1.35 (0.25), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 168 
 TYR   0.024   0.002   TYR A 489 
 PHE   0.032   0.002   PHE A 248 
 TRP   0.011   0.002   TRP A 737 
 HIS   0.014   0.002   HIS A1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (11709)
  covalent geometry    : angle       0.77001 (15817)
  hydrogen bonds       : bond        0.04272 (  475)
  hydrogen bonds       : angle       5.18520 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 156
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8427 (t80) cc_final: 0.7608 (t80)
REVERT: A  198 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: A  202 MET cc_start: 0.8125 (ppp) cc_final: 0.7616 (ppp)
REVERT: A  244 MET cc_start: 0.8117 (ppp) cc_final: 0.7847 (ppp)
REVERT: A  245 TYR cc_start: 0.8078 (t80) cc_final: 0.7767 (t80)
REVERT: A  304 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6898 (pp)
REVERT: A  369 TYR cc_start: 0.6522 (t80) cc_final: 0.5955 (t80)
REVERT: A  954 PHE cc_start: 0.7762 (p90) cc_final: 0.6927 (p90)
REVERT: A 1001 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7415 (mp)
REVERT: A 1045 LEU cc_start: 0.7834 (mt) cc_final: 0.7625 (mt)
REVERT: A 1100 ARG cc_start: 0.6242 (mmp80) cc_final: 0.5967 (mmt-90)
REVERT: C    1 MET cc_start: 0.6953 (tmm) cc_final: 0.6287 (tmm)
REVERT: D   32 ASP cc_start: 0.8287 (m-30) cc_final: 0.8043 (m-30)
REVERT: D   44 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7437 (mm)
REVERT: E   50 LEU cc_start: 0.5985 (mt) cc_final: 0.5533 (mt)
  outliers start: 39
  outliers final: 22
  residues processed: 185
  average time/residue: 0.1033
  time to fit residues: 28.2314
Evaluate side-chains
  168 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  581 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  833 LYS
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1257 LEU
Chi-restraints excluded: chain A residue 1366 SER
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain C residue   58 ASP
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 85 optimal weight:    0.0970
   chunk 86 optimal weight:    6.9990
   chunk 131 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 136 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 GLN
A 521 ASN
A 572 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 GLN ** 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 = 0.4622 r_free = 0.4622 target = 0.143686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.111570 restraints weight = 27804.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.4104 rms_B_bonded: 4.14
r_work: 0.3944 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11709  Z= 0.130
  Angle     :  0.698  16.955  15817  Z= 0.342
  Chirality :  0.044   0.198   1864
  Planarity :  0.004   0.051   2011
  Dihedral  :  5.162  34.515   1545
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.29 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.97 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.23), residues: 1436
  helix: -0.21 (0.20), residues: 739
  sheet: -1.07 (0.58), residues: 91
  loop : -1.17 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 210 
 TYR   0.022   0.002   TYR A1069 
 PHE   0.030   0.001   PHE A 248 
 TRP   0.016   0.002   TRP A1076 
 HIS   0.002   0.001   HIS A1005 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (11709)
  covalent geometry    : angle       0.69816 (15817)
  hydrogen bonds       : bond        0.03454 (  475)
  hydrogen bonds       : angle       4.89545 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 160
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8404 (t80) cc_final: 0.7511 (t80)
REVERT: A  202 MET cc_start: 0.8089 (ppp) cc_final: 0.7606 (ppp)
REVERT: A  244 MET cc_start: 0.8121 (ppp) cc_final: 0.7817 (ppp)
REVERT: A  304 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6605 (pp)
REVERT: A  369 TYR cc_start: 0.6564 (t80) cc_final: 0.6060 (t80)
REVERT: A  548 LYS cc_start: 0.7692 (mttt) cc_final: 0.7227 (mtmt)
REVERT: A  954 PHE cc_start: 0.7666 (p90) cc_final: 0.6818 (p90)
REVERT: A 1045 LEU cc_start: 0.7835 (mt) cc_final: 0.7614 (mt)
REVERT: A 1059 MET cc_start: 0.8521 (mmm) cc_final: 0.8294 (mmm)
REVERT: A 1267 LYS cc_start: 0.7869 (ptpp) cc_final: 0.7520 (ptpp)
REVERT: A 1367 MET cc_start: 0.5141 (mmm) cc_final: 0.4900 (tpt)
REVERT: C    1 MET cc_start: 0.6880 (tmm) cc_final: 0.6218 (tmm)
REVERT: C    6 LYS cc_start: 0.9237 (mmpt) cc_final: 0.8995 (mmmt)
REVERT: D   32 ASP cc_start: 0.8106 (m-30) cc_final: 0.7887 (m-30)
REVERT: D   44 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7504 (mm)
REVERT: E   41 GLN cc_start: 0.6375 (mm110) cc_final: 0.5113 (tt0)
REVERT: E   50 LEU cc_start: 0.6066 (mt) cc_final: 0.5744 (mt)
  outliers start: 27
  outliers final: 16
  residues processed: 180
  average time/residue: 0.0936
  time to fit residues: 24.9264
Evaluate side-chains
  161 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  644 HIS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1255 ILE
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0570
   chunk 114 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 125 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 126 optimal weight:    0.3980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 246 ASN
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 406 ASN
A 521 ASN
A 697 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.143912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.112400 restraints weight = 27193.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.4123 rms_B_bonded: 4.11
r_work: 0.3963 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3965 r_free = 0.3965    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3965 r_free = 0.3965    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  11709  Z= 0.123
  Angle     :  0.677  16.780  15817  Z= 0.331
  Chirality :  0.043   0.179   1864
  Planarity :  0.004   0.050   2011
  Dihedral  :  4.977  33.010   1545
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.29 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.88 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.23), residues: 1436
  helix: -0.10 (0.20), residues: 738
  sheet: -0.85 (0.61), residues: 82
  loop : -1.12 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 537 
 TYR   0.022   0.002   TYR A 489 
 PHE   0.032   0.001   PHE A 248 
 TRP   0.018   0.002   TRP A1076 
 HIS   0.003   0.001   HIS A1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (11709)
  covalent geometry    : angle       0.67716 (15817)
  hydrogen bonds       : bond        0.03293 (  475)
  hydrogen bonds       : angle       4.76152 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8485 (t80) cc_final: 0.7604 (t80)
REVERT: A  202 MET cc_start: 0.8062 (ppp) cc_final: 0.7572 (ppp)
REVERT: A  256 SER cc_start: 0.8633 (m) cc_final: 0.8317 (p)
REVERT: A  304 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6518 (pp)
REVERT: A  369 TYR cc_start: 0.6491 (t80) cc_final: 0.6061 (t80)
REVERT: A  800 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7831 (mm-30)
REVERT: A  954 PHE cc_start: 0.7462 (p90) cc_final: 0.6581 (p90)
REVERT: A 1001 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7103 (mp)
REVERT: A 1045 LEU cc_start: 0.7814 (mt) cc_final: 0.7553 (mt)
REVERT: A 1059 MET cc_start: 0.8527 (mmm) cc_final: 0.8288 (mmm)
REVERT: A 1256 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7766 (pm20)
REVERT: A 1267 LYS cc_start: 0.7910 (ptpp) cc_final: 0.7586 (ptpp)
REVERT: A 1367 MET cc_start: 0.4985 (mmm) cc_final: 0.4707 (tpt)
REVERT: A 1424 ASN cc_start: 0.8063 (m-40) cc_final: 0.7575 (p0)
REVERT: C    6 LYS cc_start: 0.9242 (mmpt) cc_final: 0.8936 (mmmt)
REVERT: D   32 ASP cc_start: 0.8070 (m-30) cc_final: 0.7848 (m-30)
REVERT: D   44 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7527 (mm)
REVERT: E   41 GLN cc_start: 0.6355 (mm110) cc_final: 0.5142 (tt0)
REVERT: E   50 LEU cc_start: 0.6142 (mt) cc_final: 0.5823 (mt)
  outliers start: 25
  outliers final: 18
  residues processed: 176
  average time/residue: 0.1033
  time to fit residues: 26.7911
Evaluate side-chains
  170 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  644 HIS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  833 LYS
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1255 ILE
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1366 SER
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain C residue   58 ASP
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 34 optimal weight:    0.3980
   chunk 94 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0070
   chunk 119 optimal weight:    0.6980
   chunk 135 optimal weight:   10.0000
   chunk 101 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 72 optimal weight:    0.4980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 521 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.145228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.114748 restraints weight = 27716.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.4150 rms_B_bonded: 4.33
r_work: 0.3970 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3971 r_free = 0.3971    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3971 r_free = 0.3971    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11709  Z= 0.120
  Angle     :  0.687  16.618  15817  Z= 0.334
  Chirality :  0.043   0.179   1864
  Planarity :  0.004   0.050   2011
  Dihedral  :  4.862  33.847   1545
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.08 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.50 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.23), residues: 1436
  helix: -0.00 (0.20), residues: 741
  sheet: -0.42 (0.61), residues: 88
  loop : -1.08 (0.26), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 168 
 TYR   0.020   0.002   TYR A 489 
 PHE   0.031   0.001   PHE A 248 
 TRP   0.019   0.002   TRP A1076 
 HIS   0.002   0.001   HIS A1005 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (11709)
  covalent geometry    : angle       0.68693 (15817)
  hydrogen bonds       : bond        0.03221 (  475)
  hydrogen bonds       : angle       4.67130 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 159
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8515 (t80) cc_final: 0.7615 (t80)
REVERT: A  202 MET cc_start: 0.8070 (ppp) cc_final: 0.7571 (ppp)
REVERT: A  238 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5277 (ttp)
REVERT: A  256 SER cc_start: 0.8608 (m) cc_final: 0.8280 (p)
REVERT: A  304 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6473 (pp)
REVERT: A  369 TYR cc_start: 0.6538 (t80) cc_final: 0.6192 (t80)
REVERT: A  548 LYS cc_start: 0.7433 (mttt) cc_final: 0.7073 (mtmt)
REVERT: A  644 HIS cc_start: 0.5897 (OUTLIER) cc_final: 0.5653 (m90)
REVERT: A  800 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7827 (mm-30)
REVERT: A  954 PHE cc_start: 0.7447 (p90) cc_final: 0.6833 (p90)
REVERT: A 1045 LEU cc_start: 0.7693 (mt) cc_final: 0.7427 (mt)
REVERT: A 1059 MET cc_start: 0.8547 (mmm) cc_final: 0.8294 (mmm)
REVERT: A 1152 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7793 (ttpt)
REVERT: A 1267 LYS cc_start: 0.7906 (ptpp) cc_final: 0.7598 (ptpp)
REVERT: A 1424 ASN cc_start: 0.8087 (m-40) cc_final: 0.7616 (p0)
REVERT: C    6 LYS cc_start: 0.9273 (mmpt) cc_final: 0.8918 (mmmt)
REVERT: D   32 ASP cc_start: 0.8124 (m-30) cc_final: 0.7900 (m-30)
REVERT: D   44 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7467 (mm)
REVERT: E   41 GLN cc_start: 0.6397 (mm110) cc_final: 0.5253 (tt0)
REVERT: E   50 LEU cc_start: 0.6342 (mt) cc_final: 0.6053 (mt)
  outliers start: 25
  outliers final: 17
  residues processed: 178
  average time/residue: 0.1020
  time to fit residues: 26.6804
Evaluate side-chains
  171 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  644 HIS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1255 ILE
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1366 SER
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain C residue   58 ASP
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 118 optimal weight:    0.4980
   chunk 32 optimal weight:    0.1980
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 76 optimal weight:    0.2980
   chunk 127 optimal weight:    0.7980
   chunk 134 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.145593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.115418 restraints weight = 27584.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 4.23
r_work: 0.3978 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3981 r_free = 0.3981    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3981 r_free = 0.3981    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  11709  Z= 0.122
  Angle     :  0.694  16.351  15817  Z= 0.338
  Chirality :  0.043   0.201   1864
  Planarity :  0.004   0.050   2011
  Dihedral  :  4.792  33.663   1545
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.94 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 19.42 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.23), residues: 1436
  helix:  0.04 (0.20), residues: 741
  sheet: -0.67 (0.62), residues: 82
  loop : -1.03 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 171 
 TYR   0.020   0.002   TYR A 489 
 PHE   0.032   0.001   PHE A 248 
 TRP   0.026   0.003   TRP A 741 
 HIS   0.003   0.001   HIS A1005 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (11709)
  covalent geometry    : angle       0.69356 (15817)
  hydrogen bonds       : bond        0.03208 (  475)
  hydrogen bonds       : angle       4.64434 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 157
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8471 (t80) cc_final: 0.7589 (t80)
REVERT: A  202 MET cc_start: 0.8066 (ppp) cc_final: 0.7576 (ppp)
REVERT: A  238 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5345 (ttp)
REVERT: A  256 SER cc_start: 0.8564 (m) cc_final: 0.8243 (p)
REVERT: A  304 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6417 (pp)
REVERT: A  369 TYR cc_start: 0.6602 (t80) cc_final: 0.6195 (t80)
REVERT: A  482 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7477 (mtm-85)
REVERT: A  548 LYS cc_start: 0.7400 (mttt) cc_final: 0.6969 (mtmt)
REVERT: A  800 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7797 (mm-30)
REVERT: A  954 PHE cc_start: 0.7580 (p90) cc_final: 0.7047 (p90)
REVERT: A 1001 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7161 (mp)
REVERT: A 1045 LEU cc_start: 0.7618 (mt) cc_final: 0.7332 (mt)
REVERT: A 1059 MET cc_start: 0.8483 (mmm) cc_final: 0.8216 (mmm)
REVERT: A 1152 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7757 (ttpt)
REVERT: A 1267 LYS cc_start: 0.7893 (ptpp) cc_final: 0.7577 (ptpp)
REVERT: A 1391 ILE cc_start: 0.7978 (mm) cc_final: 0.7613 (mt)
REVERT: A 1424 ASN cc_start: 0.8072 (m-40) cc_final: 0.7611 (p0)
REVERT: C    6 LYS cc_start: 0.9262 (mmpt) cc_final: 0.8955 (mmmt)
REVERT: D   32 ASP cc_start: 0.8146 (m-30) cc_final: 0.7930 (m-30)
REVERT: D   44 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7527 (mm)
REVERT: E   41 GLN cc_start: 0.6321 (mm110) cc_final: 0.5170 (tt0)
REVERT: E   50 LEU cc_start: 0.6294 (mt) cc_final: 0.6012 (mt)
  outliers start: 26
  outliers final: 20
  residues processed: 175
  average time/residue: 0.0933
  time to fit residues: 24.0934
Evaluate side-chains
  171 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  644 HIS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  833 LYS
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1255 ILE
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1366 SER
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain C residue   58 ASP
Chi-restraints excluded: chain C residue   66 THR
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0970
   chunk 75 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 130 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.144599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.114522 restraints weight = 27747.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 4.28
r_work: 0.3962 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  11709  Z= 0.132
  Angle     :  0.709  16.580  15817  Z= 0.345
  Chirality :  0.044   0.245   1864
  Planarity :  0.004   0.049   2011
  Dihedral  :  4.815  33.811   1545
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.22 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 19.88 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.23), residues: 1436
  helix:  0.05 (0.20), residues: 741
  sheet: -0.36 (0.61), residues: 88
  loop : -0.99 (0.26), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 210 
 TYR   0.021   0.002   TYR A 489 
 PHE   0.035   0.001   PHE A 248 
 TRP   0.019   0.002   TRP A1076 
 HIS   0.004   0.001   HIS A1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (11709)
  covalent geometry    : angle       0.70885 (15817)
  hydrogen bonds       : bond        0.03282 (  475)
  hydrogen bonds       : angle       4.70358 ( 1353)

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

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

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2872 Ramachandran restraints generated.
    1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8510 (t80) cc_final: 0.7274 (t80)
REVERT: A  191 GLU cc_start: 0.8384 (mp0) cc_final: 0.8076 (mp0)
REVERT: A  202 MET cc_start: 0.8092 (ppp) cc_final: 0.7599 (ppp)
REVERT: A  256 SER cc_start: 0.8593 (m) cc_final: 0.8278 (p)
REVERT: A  304 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6503 (pp)
REVERT: A  369 TYR cc_start: 0.6551 (t80) cc_final: 0.6100 (t80)
REVERT: A  437 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7304 (tpt)
REVERT: A  482 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7459 (mtm-85)
REVERT: A  548 LYS cc_start: 0.7421 (mttt) cc_final: 0.7109 (mtmt)
REVERT: A  800 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7893 (mm-30)
REVERT: A  954 PHE cc_start: 0.7570 (p90) cc_final: 0.7049 (p90)
REVERT: A 1001 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7155 (mp)
REVERT: A 1045 LEU cc_start: 0.7683 (mt) cc_final: 0.7388 (mt)
REVERT: A 1059 MET cc_start: 0.8544 (mmm) cc_final: 0.8336 (mmm)
REVERT: A 1152 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7801 (ttpt)
REVERT: A 1267 LYS cc_start: 0.7899 (ptpp) cc_final: 0.7589 (ptpp)
REVERT: A 1391 ILE cc_start: 0.7904 (mm) cc_final: 0.7578 (mt)
REVERT: A 1424 ASN cc_start: 0.8263 (m-40) cc_final: 0.7689 (p0)
REVERT: C    1 MET cc_start: 0.6750 (tmm) cc_final: 0.6180 (tmm)
REVERT: C    6 LYS cc_start: 0.9263 (mmpt) cc_final: 0.8933 (mmmt)
REVERT: D   32 ASP cc_start: 0.8141 (m-30) cc_final: 0.7932 (m-30)
REVERT: D   44 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7427 (mm)
REVERT: E   41 GLN cc_start: 0.6332 (mm110) cc_final: 0.5196 (tt0)
REVERT: E   50 LEU cc_start: 0.6277 (mt) cc_final: 0.5991 (mt)
  outliers start: 28
  outliers final: 21
  residues processed: 178
  average time/residue: 0.1060
  time to fit residues: 27.4844
Evaluate side-chains
  178 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  437 MET
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  644 HIS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  815 VAL
Chi-restraints excluded: chain A residue  833 LYS
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1255 ILE
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1366 SER
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain C residue   58 ASP
Chi-restraints excluded: chain C residue   66 THR
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 65 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 127 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 141 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 118 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9990
   chunk 119 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 521 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.144899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.115181 restraints weight = 27133.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.4155 rms_B_bonded: 4.11
r_work: 0.3968 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11709  Z= 0.128
  Angle     :  0.704  16.640  15817  Z= 0.343
  Chirality :  0.043   0.233   1864
  Planarity :  0.004   0.070   2011
  Dihedral  :  4.788  33.872   1545
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.29 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 19.95 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.23), residues: 1436
  helix:  0.07 (0.20), residues: 741
  sheet: -0.30 (0.61), residues: 88
  loop : -0.94 (0.27), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 210 
 TYR   0.025   0.002   TYR A 245 
 PHE   0.035   0.001   PHE A 248 
 TRP   0.026   0.002   TRP A1076 
 HIS   0.003   0.001   HIS A1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11709)
  covalent geometry    : angle       0.70440 (15817)
  hydrogen bonds       : bond        0.03234 (  475)
  hydrogen bonds       : angle       4.66491 ( 1353)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3796.71 seconds
wall clock time: 65 minutes 40.35 seconds (3940.35 seconds total)