Starting phenix.real_space_refine
on Tue Jun 10 11:30:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j1p_35929/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j1p_35929/06_2025/8j1p_35929.cif"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1}
          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: 7.06, per 1000 atoms: 0.61
  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: 2.77
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.46
  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: 3.39

  Time building geometry restraints manager: 3.28 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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     28.400
  Find NCS groups from input model:        0.180
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.820
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (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
 TRP   0.022   0.002   TRP A 741 
 HIS   0.003   0.001   HIS A1234 
 PHE   0.024   0.002   PHE A 870 
 TYR   0.017   0.002   TYR A 369 
 ARG   0.005   0.000   ARG A 210 

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

*********************** 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  : 1.311 
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: 0.2343
  time to fit residues: 66.1395
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  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 112 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 130 optimal weight:    0.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 521 ASN
A 572 ASN
A 939 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.142240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.112162 restraints weight = 27618.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.4101 rms_B_bonded: 4.16
r_work: 0.3916 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3913 r_free = 0.3913    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  11709  Z= 0.191
  Angle     :  0.762  14.727  15817  Z= 0.381
  Chirality :  0.046   0.292   1864
  Planarity :  0.005   0.053   2011
  Dihedral  :  5.661  36.364   1545
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.06 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.55 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.22), residues: 1436
  helix: -0.70 (0.19), residues: 741
  sheet: -1.14 (0.54), residues: 94
  loop : -1.55 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 741 
 HIS   0.014   0.002   HIS A1234 
 PHE   0.023   0.002   PHE A 248 
 TYR   0.021   0.002   TYR A 489 
 ARG   0.005   0.001   ARG A1213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 (  475)
  hydrogen bonds       : angle       5.43648 ( 1353)
  covalent geometry    : bond        0.00445 (11709)
  covalent geometry    : angle       0.76225 (15817)

*********************** 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: 21
    poor density    : 162
  time to evaluate  : 1.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 MET cc_start: 0.8033 (ppp) cc_final: 0.7524 (ppp)
REVERT: A  600 LEU cc_start: 0.8474 (tt) cc_final: 0.8240 (mt)
REVERT: A  954 PHE cc_start: 0.7567 (p90) cc_final: 0.6676 (p90)
REVERT: C   43 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7195 (mm)
REVERT: D    4 PHE cc_start: 0.7510 (m-80) cc_final: 0.7202 (m-80)
REVERT: D   32 ASP cc_start: 0.8421 (m-30) cc_final: 0.8171 (m-30)
REVERT: D   44 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7342 (mm)
  outliers start: 21
  outliers final: 14
  residues processed: 174
  average time/residue: 0.2597
  time to fit residues: 66.5207
Evaluate side-chains
  160 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
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  833 LYS
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue 1127 VAL
Chi-restraints excluded: chain A residue 1160 ASN
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain D residue   17 VAL
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 17 optimal weight:    0.2980
   chunk 82 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    0.4980
   chunk 118 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 820 HIS
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1197 ASN
A1373 ASN
D  49 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.144142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.114258 restraints weight = 27678.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.4144 rms_B_bonded: 4.20
r_work: 0.3960 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3962 r_free = 0.3962    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3962 r_free = 0.3962    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.1792

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= 0.130
  Angle     :  0.691  14.139  15817  Z= 0.342
  Chirality :  0.043   0.254   1864
  Planarity :  0.004   0.048   2011
  Dihedral  :  5.318  32.485   1545
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.74 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.30 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.22), residues: 1436
  helix: -0.46 (0.19), residues: 741
  sheet: -1.10 (0.57), residues: 82
  loop : -1.36 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1076 
 HIS   0.006   0.001   HIS A1234 
 PHE   0.018   0.001   PHE A 248 
 TYR   0.012   0.001   TYR A1443 
 ARG   0.004   0.000   ARG A 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03926 (  475)
  hydrogen bonds       : angle       5.01428 ( 1353)
  covalent geometry    : bond        0.00296 (11709)
  covalent geometry    : angle       0.69081 (15817)

*********************** 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
  193 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 168
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 MET cc_start: 0.8033 (ppp) cc_final: 0.7547 (ppp)
REVERT: A  244 MET cc_start: 0.8073 (ppp) cc_final: 0.7801 (ppp)
REVERT: A  369 TYR cc_start: 0.6593 (t80) cc_final: 0.6147 (t80)
REVERT: A  600 LEU cc_start: 0.8465 (tt) cc_final: 0.8258 (mt)
REVERT: A  954 PHE cc_start: 0.7579 (p90) cc_final: 0.6762 (p90)
REVERT: A 1001 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7206 (mp)
REVERT: A 1256 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7727 (pm20)
REVERT: A 1267 LYS cc_start: 0.7804 (ptpp) cc_final: 0.7551 (ptpp)
REVERT: A 1366 SER cc_start: 0.7761 (t) cc_final: 0.7431 (t)
REVERT: A 1370 LEU cc_start: 0.7525 (pp) cc_final: 0.6659 (tt)
REVERT: D    4 PHE cc_start: 0.7443 (m-80) cc_final: 0.7233 (m-80)
REVERT: D   32 ASP cc_start: 0.8389 (m-30) cc_final: 0.8132 (m-30)
REVERT: D   44 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7385 (mm)
REVERT: E   50 LEU cc_start: 0.5646 (mm) cc_final: 0.5426 (mm)
  outliers start: 25
  outliers final: 12
  residues processed: 184
  average time/residue: 0.2346
  time to fit residues: 62.5772
Evaluate side-chains
  164 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
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 1001 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1256 GLU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 143 optimal weight:   10.0000
   chunk 48 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0000
   chunk 11 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 95 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.5984

-------------------------------------------------------------------------------
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 521 ASN
** A 950 HIS ** 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 = 0.4639 r_free = 0.4639 target = 0.144972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.113253 restraints weight = 27714.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 4.18
r_work: 0.3969 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3974 r_free = 0.3974    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 = 0.3974 r_free = 0.3974    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  11709  Z= 0.124
  Angle     :  0.677  14.479  15817  Z= 0.332
  Chirality :  0.043   0.243   1864
  Planarity :  0.004   0.048   2011
  Dihedral  :  5.170  33.964   1545
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.22 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.29 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.22), residues: 1436
  helix: -0.37 (0.19), residues: 740
  sheet: -1.18 (0.56), residues: 91
  loop : -1.34 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1076 
 HIS   0.006   0.001   HIS A1234 
 PHE   0.018   0.001   PHE A1061 
 TYR   0.029   0.002   TYR A 489 
 ARG   0.004   0.000   ARG A 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03634 (  475)
  hydrogen bonds       : angle       4.88365 ( 1353)
  covalent geometry    : bond        0.00288 (11709)
  covalent geometry    : angle       0.67719 (15817)

*********************** 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
  188 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8517 (t80) cc_final: 0.7540 (t80)
REVERT: A  190 MET cc_start: 0.7087 (mmm) cc_final: 0.6683 (mmm)
REVERT: A  202 MET cc_start: 0.7999 (ppp) cc_final: 0.7478 (ppp)
REVERT: A  238 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5337 (ttp)
REVERT: A  244 MET cc_start: 0.8151 (ppp) cc_final: 0.7840 (ppp)
REVERT: A  304 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6503 (pp)
REVERT: A  369 TYR cc_start: 0.6387 (t80) cc_final: 0.6094 (t80)
REVERT: A  644 HIS cc_start: 0.5900 (OUTLIER) cc_final: 0.5354 (m90)
REVERT: A  954 PHE cc_start: 0.7720 (p90) cc_final: 0.6926 (p90)
REVERT: C    1 MET cc_start: 0.6897 (tmm) cc_final: 0.6071 (tmm)
REVERT: D    4 PHE cc_start: 0.7481 (m-80) cc_final: 0.7195 (m-80)
REVERT: D   32 ASP cc_start: 0.8369 (m-30) cc_final: 0.8111 (m-30)
REVERT: D   44 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7413 (mm)
REVERT: E   41 GLN cc_start: 0.6430 (mm110) cc_final: 0.5206 (tt0)
  outliers start: 29
  outliers final: 16
  residues processed: 178
  average time/residue: 0.2444
  time to fit residues: 63.2634
Evaluate side-chains
  161 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
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  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 1220 ILE
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 C residue   58 ASP
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 12 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 90 optimal weight:    0.1980
   chunk 4 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 115 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 123 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 521 ASN
A 697 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.145031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.115286 restraints weight = 27578.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 4.18
r_work: 0.3976 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3979 r_free = 0.3979    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3979 r_free = 0.3979    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.2221

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= 0.128
  Angle     :  0.677  15.708  15817  Z= 0.330
  Chirality :  0.043   0.213   1864
  Planarity :  0.005   0.131   2011
  Dihedral  :  5.060  33.602   1545
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.15 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.36 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.22), residues: 1436
  helix: -0.22 (0.20), residues: 733
  sheet: -1.11 (0.57), residues: 91
  loop : -1.24 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1076 
 HIS   0.004   0.001   HIS A1234 
 PHE   0.017   0.001   PHE A1061 
 TYR   0.021   0.001   TYR A 489 
 ARG   0.014   0.000   ARG A1224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03507 (  475)
  hydrogen bonds       : angle       4.79923 ( 1353)
  covalent geometry    : bond        0.00300 (11709)
  covalent geometry    : angle       0.67678 (15817)

*********************** 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
  194 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 154
  time to evaluate  : 1.281 
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: 0.8538 (t80) cc_final: 0.7668 (t80)
REVERT: A  202 MET cc_start: 0.7974 (ppp) cc_final: 0.7498 (ppp)
REVERT: A  238 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5511 (ttp)
REVERT: A  244 MET cc_start: 0.8011 (ppp) cc_final: 0.7797 (ppp)
REVERT: A  304 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6620 (pp)
REVERT: A  954 PHE cc_start: 0.7757 (p90) cc_final: 0.6982 (p90)
REVERT: A 1001 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7238 (mp)
REVERT: A 1100 ARG cc_start: 0.6334 (mmp80) cc_final: 0.6044 (mmt180)
REVERT: A 1224 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.6150 (tpm170)
REVERT: A 1256 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7766 (pm20)
REVERT: D    4 PHE cc_start: 0.7463 (m-80) cc_final: 0.7202 (m-80)
REVERT: D   32 ASP cc_start: 0.8353 (m-30) cc_final: 0.8092 (m-30)
REVERT: D   44 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7421 (mm)
REVERT: E   41 GLN cc_start: 0.6414 (mm110) cc_final: 0.5230 (tt0)
  outliers start: 40
  outliers final: 21
  residues processed: 183
  average time/residue: 0.2401
  time to fit residues: 62.9138
Evaluate side-chains
  173 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 1.670 
-------------------------------------------------------------------------------
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  535 LEU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  689 LYS
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 1220 ILE
Chi-restraints excluded: chain A residue 1224 ARG
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1254 MET
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1361 VAL
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   13 ILE
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   43 LEU
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 63 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 129 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 104 optimal weight:    0.0980
   chunk 61 optimal weight:    0.0770
   chunk 131 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.6142

-------------------------------------------------------------------------------
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 521 ASN
A 939 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.145929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.116582 restraints weight = 27686.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 4.21
r_work: 0.3969 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3969
-------------------------------------------------------------------------------
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 = 0.61   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 = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  11709  Z= 0.127
  Angle     :  0.683  15.909  15817  Z= 0.334
  Chirality :  0.043   0.196   1864
  Planarity :  0.004   0.102   2011
  Dihedral  :  4.988  38.134   1545
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.15 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.35 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.22), residues: 1436
  helix: -0.20 (0.20), residues: 734
  sheet: -1.10 (0.57), residues: 91
  loop : -1.22 (0.26), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1076 
 HIS   0.020   0.001   HIS A 644 
 PHE   0.031   0.001   PHE A 248 
 TYR   0.017   0.001   TYR A 245 
 ARG   0.011   0.000   ARG A1224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03422 (  475)
  hydrogen bonds       : angle       4.76303 ( 1353)
  covalent geometry    : bond        0.00296 (11709)
  covalent geometry    : angle       0.68257 (15817)

*********************** 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: 31
    poor density    : 156
  time to evaluate  : 1.452 
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: 0.8609 (t80) cc_final: 0.7726 (t80)
REVERT: A  202 MET cc_start: 0.8016 (ppp) cc_final: 0.7520 (ppp)
REVERT: A  244 MET cc_start: 0.8106 (ppp) cc_final: 0.7852 (ppp)
REVERT: A  304 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6724 (pp)
REVERT: A  482 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7568 (mtm-85)
REVERT: A  954 PHE cc_start: 0.7768 (p90) cc_final: 0.7038 (p90)
REVERT: A 1001 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7133 (mp)
REVERT: A 1256 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7789 (pm20)
REVERT: A 1367 MET cc_start: 0.5160 (mmm) cc_final: 0.4896 (tpt)
REVERT: C    6 LYS cc_start: 0.9226 (mmpt) cc_final: 0.8966 (mmmt)
REVERT: D    4 PHE cc_start: 0.7478 (m-80) cc_final: 0.7196 (m-80)
REVERT: D   32 ASP cc_start: 0.8191 (m-30) cc_final: 0.7973 (m-30)
REVERT: D   44 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7426 (mm)
REVERT: E   41 GLN cc_start: 0.6458 (mm110) cc_final: 0.5345 (tt0)
  outliers start: 31
  outliers final: 21
  residues processed: 176
  average time/residue: 0.2804
  time to fit residues: 71.1399
Evaluate side-chains
  166 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
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  643 LEU
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  689 LYS
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  939 ASN
Chi-restraints excluded: chain A residue 1001 LEU
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 1361 VAL
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain C residue   58 ASP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 143 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 139 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0170
   chunk 7 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.4618

-------------------------------------------------------------------------------
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 406 ASN
A 939 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.146160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.116179 restraints weight = 28126.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 4.39
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4168 r_free = 0.4168    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4168 r_free = 0.4168    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  11709  Z= 0.120
  Angle     :  0.679  16.126  15817  Z= 0.332
  Chirality :  0.043   0.179   1864
  Planarity :  0.004   0.053   2011
  Dihedral  :  4.841  34.357   1545
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.87 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.27 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.23), residues: 1436
  helix: -0.13 (0.20), residues: 736
  sheet: -1.06 (0.57), residues: 91
  loop : -1.16 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A1076 
 HIS   0.006   0.001   HIS A 644 
 PHE   0.032   0.001   PHE A 248 
 TYR   0.017   0.001   TYR A 245 
 ARG   0.008   0.000   ARG A1224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03339 (  475)
  hydrogen bonds       : angle       4.69255 ( 1353)
  covalent geometry    : bond        0.00277 (11709)
  covalent geometry    : angle       0.67852 (15817)

*********************** 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
  186 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 1.401 
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: 0.8466 (t80) cc_final: 0.7582 (t80)
REVERT: A  202 MET cc_start: 0.7820 (ppp) cc_final: 0.7372 (ppp)
REVERT: A  238 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4745 (ttp)
REVERT: A  244 MET cc_start: 0.8019 (ppp) cc_final: 0.7770 (ppp)
REVERT: A  256 SER cc_start: 0.8480 (m) cc_final: 0.8142 (p)
REVERT: A  304 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6465 (pp)
REVERT: A  482 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7123 (mtm-85)
REVERT: A  954 PHE cc_start: 0.7449 (p90) cc_final: 0.6663 (p90)
REVERT: A 1001 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7178 (mp)
REVERT: A 1367 MET cc_start: 0.5201 (mmm) cc_final: 0.4902 (tpt)
REVERT: C    6 LYS cc_start: 0.9148 (mmpt) cc_final: 0.8871 (mmmt)
REVERT: D    4 PHE cc_start: 0.7412 (m-80) cc_final: 0.7163 (m-80)
REVERT: D   32 ASP cc_start: 0.8104 (m-30) cc_final: 0.7873 (m-30)
REVERT: D   44 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7377 (mm)
REVERT: E   41 GLN cc_start: 0.6372 (mm110) cc_final: 0.5304 (tt0)
  outliers start: 31
  outliers final: 22
  residues processed: 175
  average time/residue: 0.2420
  time to fit residues: 61.0105
Evaluate side-chains
  170 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
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  351 ILE
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  689 LYS
Chi-restraints excluded: chain A residue  811 ASN
Chi-restraints excluded: chain A residue  864 PHE
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue 1001 LEU
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 1361 VAL
Chi-restraints excluded: chain A residue 1474 GLU
Chi-restraints excluded: chain C residue   58 ASP
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   43 LEU
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 41 optimal weight:    1.9990
   chunk 40 optimal weight:    0.1980
   chunk 117 optimal weight:    0.7980
   chunk 103 optimal weight:    0.1980
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0060
   chunk 52 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0170
   overall best weight:    0.2434

-------------------------------------------------------------------------------
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 521 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1026 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.147517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.117573 restraints weight = 27907.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.4189 rms_B_bonded: 4.43
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4189 r_free = 0.4189    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4189 r_free = 0.4189    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11709  Z= 0.116
  Angle     :  0.669  16.258  15817  Z= 0.326
  Chirality :  0.042   0.178   1864
  Planarity :  0.004   0.048   2011
  Dihedral  :  4.699  32.592   1545
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.15 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 19.57 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.23), residues: 1436
  helix: -0.05 (0.20), residues: 736
  sheet: -0.81 (0.60), residues: 82
  loop : -1.11 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1076 
 HIS   0.006   0.001   HIS A 644 
 PHE   0.032   0.001   PHE A 248 
 TYR   0.016   0.001   TYR A 245 
 ARG   0.008   0.000   ARG A 938 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03200 (  475)
  hydrogen bonds       : angle       4.60815 ( 1353)
  covalent geometry    : bond        0.00259 (11709)
  covalent geometry    : angle       0.66947 (15817)

*********************** 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
  185 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8398 (t80) cc_final: 0.7570 (t80)
REVERT: A  202 MET cc_start: 0.7802 (ppp) cc_final: 0.7385 (ppp)
REVERT: A  238 MET cc_start: 0.5409 (OUTLIER) cc_final: 0.4709 (ttp)
REVERT: A  244 MET cc_start: 0.8017 (ppp) cc_final: 0.7804 (ppp)
REVERT: A  256 SER cc_start: 0.8449 (m) cc_final: 0.8112 (p)
REVERT: A  304 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6379 (pp)
REVERT: A  482 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7166 (mtm-85)
REVERT: A  548 LYS cc_start: 0.7302 (mttt) cc_final: 0.6897 (mtmt)
REVERT: A  954 PHE cc_start: 0.7256 (p90) cc_final: 0.6444 (p90)
REVERT: A 1001 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7177 (mp)
REVERT: A 1391 ILE cc_start: 0.7720 (mm) cc_final: 0.7308 (mt)
REVERT: A 1424 ASN cc_start: 0.7858 (m-40) cc_final: 0.7497 (p0)
REVERT: C    6 LYS cc_start: 0.9164 (mmpt) cc_final: 0.8843 (mmmt)
REVERT: D    4 PHE cc_start: 0.7441 (m-80) cc_final: 0.7212 (m-80)
REVERT: D   32 ASP cc_start: 0.8083 (m-30) cc_final: 0.7851 (m-30)
REVERT: D   44 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7475 (mm)
  outliers start: 28
  outliers final: 16
  residues processed: 176
  average time/residue: 0.2429
  time to fit residues: 62.3199
Evaluate side-chains
  165 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
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  488 LYS
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  864 PHE
Chi-restraints excluded: chain A residue 1001 LEU
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 1361 VAL
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   15 LEU
Chi-restraints excluded: chain D residue   17 VAL
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 88 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0670
   chunk 141 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 86 optimal weight:    7.9990
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 521 ASN
A 694 ASN
A 939 ASN
** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  41 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 = 0.4678 r_free = 0.4678 target = 0.147407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.117288 restraints weight = 28028.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 4.44
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4183 r_free = 0.4183    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4183 r_free = 0.4183    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11709  Z= 0.119
  Angle     :  0.683  16.148  15817  Z= 0.333
  Chirality :  0.043   0.176   1864
  Planarity :  0.004   0.047   2011
  Dihedral  :  4.681  29.279   1545
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.08 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 20.34 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.71 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.23), residues: 1436
  helix:  0.01 (0.20), residues: 736
  sheet: -0.81 (0.60), residues: 82
  loop : -1.03 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 741 
 HIS   0.005   0.001   HIS A 644 
 PHE   0.033   0.001   PHE A 248 
 TYR   0.022   0.001   TYR A 245 
 ARG   0.005   0.000   ARG A 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03243 (  475)
  hydrogen bonds       : angle       4.64017 ( 1353)
  covalent geometry    : bond        0.00273 (11709)
  covalent geometry    : angle       0.68264 (15817)

*********************** 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
  178 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 1.334 
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: 0.8393 (t80) cc_final: 0.7512 (t80)
REVERT: A  202 MET cc_start: 0.7847 (ppp) cc_final: 0.7399 (ppp)
REVERT: A  256 SER cc_start: 0.8495 (m) cc_final: 0.8157 (p)
REVERT: A  304 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6358 (pp)
REVERT: A  482 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.7192 (mtm-85)
REVERT: A  548 LYS cc_start: 0.7365 (mttt) cc_final: 0.6944 (mtmt)
REVERT: A  954 PHE cc_start: 0.7216 (p90) cc_final: 0.6640 (p90)
REVERT: A 1001 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7200 (mp)
REVERT: A 1391 ILE cc_start: 0.7639 (mm) cc_final: 0.7323 (mt)
REVERT: A 1424 ASN cc_start: 0.7919 (m-40) cc_final: 0.7523 (p0)
REVERT: C    6 LYS cc_start: 0.9165 (mmpt) cc_final: 0.8831 (mmmt)
REVERT: D    4 PHE cc_start: 0.7428 (m-80) cc_final: 0.7203 (m-80)
REVERT: D   32 ASP cc_start: 0.8102 (m-30) cc_final: 0.7881 (m-30)
REVERT: D   44 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7465 (mm)
  outliers start: 25
  outliers final: 18
  residues processed: 170
  average time/residue: 0.2336
  time to fit residues: 58.5999
Evaluate side-chains
  168 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
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  488 LYS
Chi-restraints excluded: chain A residue  521 ASN
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  864 PHE
Chi-restraints excluded: chain A residue  939 ASN
Chi-restraints excluded: chain A residue 1001 LEU
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 1361 VAL
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   15 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5344 > 50:
  distance: 13 - 36:   7.893
  distance: 19 - 44:   9.709
  distance: 23 - 51:   6.532
  distance: 28 - 36:   4.138
  distance: 29 - 60:  11.830
  distance: 36 - 37:   5.112
  distance: 37 - 38:  12.686
  distance: 37 - 40:  10.542
  distance: 38 - 39:  18.834
  distance: 40 - 41:  13.488
  distance: 40 - 42:  11.189
  distance: 41 - 43:   7.375
  distance: 44 - 45:  15.925
  distance: 45 - 46:  11.131
  distance: 45 - 48:   9.363
  distance: 48 - 49:   5.095
  distance: 48 - 50:   6.592
  distance: 51 - 52:  27.482
  distance: 52 - 53:  32.805
  distance: 52 - 55:  52.340
  distance: 53 - 54:  14.869
  distance: 53 - 60:  22.885
  distance: 55 - 56:  53.678
  distance: 56 - 57:  53.439
  distance: 57 - 58:  48.610
  distance: 57 - 59:  35.714
  distance: 60 - 61:  23.241
  distance: 61 - 62:  26.154
  distance: 61 - 64:  32.532
  distance: 62 - 63:  32.302
  distance: 62 - 68:   9.496
  distance: 64 - 65:  21.765
  distance: 65 - 66:   6.703
  distance: 65 - 67:   7.152
  distance: 68 - 69:  28.134
  distance: 69 - 70:  17.799
  distance: 69 - 72:  30.637
  distance: 70 - 71:  22.282
  distance: 70 - 75:  21.016
  distance: 72 - 73:  26.742
  distance: 72 - 74:  17.789
  distance: 75 - 76:  33.864
  distance: 76 - 77:  49.637
  distance: 76 - 79:  32.921
  distance: 77 - 78:  23.406
  distance: 77 - 81:  44.496
  distance: 79 - 80:  17.499
  distance: 81 - 82:  34.102
  distance: 82 - 83:  18.704
  distance: 82 - 85:  16.024
  distance: 83 - 84:  12.621
  distance: 83 - 89:  20.885
  distance: 85 - 86:  14.317
  distance: 85 - 87:  13.860
  distance: 86 - 88:   9.112
  distance: 89 - 90:  45.509
  distance: 90 - 91:  50.644
  distance: 90 - 93:  51.655
  distance: 91 - 92:  29.819
  distance: 91 - 98:  22.182
  distance: 93 - 94:  54.247
  distance: 94 - 95:  56.534
  distance: 95 - 96:  50.377
  distance: 95 - 97:  31.750
  distance: 98 - 99:   8.613
  distance: 99 - 100:  13.857
  distance: 99 - 102:  17.888
  distance: 100 - 101:  16.778
  distance: 100 - 106:  18.616
  distance: 102 - 103:   6.625
  distance: 103 - 104:   5.722
  distance: 103 - 105:   4.962
  distance: 106 - 107:  15.949
  distance: 107 - 108:   6.236
  distance: 107 - 110:  14.736
  distance: 108 - 109:  11.135
  distance: 108 - 113:   3.197
  distance: 110 - 111:  14.071
  distance: 110 - 112:  11.603