Starting phenix.real_space_refine
on Sat Jun 14 14:23:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qru_14124/06_2025/7qru_14124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qru_14124/06_2025/7qru_14124.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qru_14124/06_2025/7qru_14124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qru_14124/06_2025/7qru_14124.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qru_14124/06_2025/7qru_14124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qru_14124/06_2025/7qru_14124.cif"
  }
  resolution = 2.24
  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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      92      5.16       5
     C   10600      2.51       5
     N    2388      2.21       5
     O    3017      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16100
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "D"
      Number of atoms: 3906
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 491, 3844
          Classifications: {'peptide': 491}
          Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 474}
      Conformer: "B"
        Number of residues, atoms: 491, 3844
          Classifications: {'peptide': 491}
          Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 474}
          bond proxies already assigned to first conformer: 3877
    Chain: "A"
      Number of atoms: 6440
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 805, 6306
          Classifications: {'peptide': 805}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 776}
      Conformer: "B"
        Number of residues, atoms: 805, 6306
          Classifications: {'peptide': 805}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 776}
          bond proxies already assigned to first conformer: 6327
    Chain: "B"
      Number of atoms: 1089
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 140, 1078
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 134}
      Conformer: "B"
        Number of residues, atoms: 140, 1078
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 134}
          bond proxies already assigned to first conformer: 1090
    Chain: "C"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 859
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
    Chain: "E"
      Number of atoms: 1305
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 158, 1297
          Classifications: {'peptide': 158}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 152}
      Conformer: "B"
        Number of residues, atoms: 158, 1297
          Classifications: {'peptide': 158}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 152}
          bond proxies already assigned to first conformer: 1317
    Chain: "F"
      Number of atoms: 723
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 91, 701
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'TRANS': 89}
      Conformer: "B"
        Number of residues, atoms: 91, 701
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'TRANS': 89}
          bond proxies already assigned to first conformer: 685
    Chain: "G"
      Number of atoms: 888
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 113, 877
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 3, 'TRANS': 109}
      Conformer: "B"
        Number of residues, atoms: 113, 877
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 3, 'TRANS': 109}
          bond proxies already assigned to first conformer: 883
    Chain: "e"
      Number of atoms: 395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 395
          Classifications: {'peptide': 47}
          Link IDs: {'TRANS': 46}
    Chain: "A"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'3PE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "E"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 86
          Unusual residues: {'3PE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 16
    Chain: "D"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 113
          Classifications: {'water': 113}
          Link IDs: {None: 112}
    Chain: "A"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 140
          Classifications: {'water': 140}
          Link IDs: {None: 139}
    Chain: "B"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 24
          Classifications: {'water': 24}
          Link IDs: {None: 23}
    Chain: "C"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 36
          Classifications: {'water': 36}
          Link IDs: {None: 35}
    Chain: "E"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
    Chain: "F"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "G"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
    Chain: "e"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 29
    residue:
      pdb=" N  AMET D 139 " occ=0.47
      ... (14 atoms not shown)
      pdb=" CE BMET D 139 " occ=0.53
    residue:
      pdb=" N  ALEU D 172 " occ=0.43
      ... (14 atoms not shown)
      pdb=" CD2BLEU D 172 " occ=0.57
    residue:
      pdb=" N  AMET D 218 " occ=0.45
      ... (14 atoms not shown)
      pdb=" CE BMET D 218 " occ=0.55
    residue:
      pdb=" N  ALYS D 219 " occ=0.45
      ... (16 atoms not shown)
      pdb=" NZ BLYS D 219 " occ=0.55
    residue:
      pdb=" N  AGLN D 307 " occ=0.69
      ... (16 atoms not shown)
      pdb=" NE2BGLN D 307 " occ=0.31
    residue:
      pdb=" N  ATYR D 328 " occ=0.54
      ... (22 atoms not shown)
      pdb=" OH BTYR D 328 " occ=0.46
    residue:
      pdb=" N  AMET D 423 " occ=0.54
      ... (14 atoms not shown)
      pdb=" CE BMET D 423 " occ=0.46
    residue:
      pdb=" N  AMET A 118 " occ=0.45
      ... (14 atoms not shown)
      pdb=" CE BMET A 118 " occ=0.55
    residue:
      pdb=" N  APHE A 119 " occ=0.45
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 119 " occ=0.55
    residue:
      pdb=" N  AMET A 167 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A 167 " occ=0.50
    residue:
      pdb=" N  ATYR A 246 " occ=0.43
      ... (22 atoms not shown)
      pdb=" OH BTYR A 246 " occ=0.57
    residue:
      pdb=" N  ALEU A 247 " occ=0.43
      ... (14 atoms not shown)
      pdb=" CD2BLEU A 247 " occ=0.57
    ... (remaining 17 not shown)
  Time building chain proxies: 15.68, per 1000 atoms: 0.97
  Number of scatterers: 16100
  At special positions: 0
  Unit cell: (175.703, 92.137, 96.4224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      92     16.00
     P       3     15.00
     O    3017      8.00
     N    2388      7.00
     C   10600      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: 3.92
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3678

  Finding SS restraints...
    Secondary structure from input PDB file:
      91 helices and 4 sheets defined
      81.7% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'D' and resid 2 through 5
    Processing helix  chain 'D' and resid 6 through 19
      Proline residue:  D  12  - end of helix
    Processing helix  chain 'D' and resid 25 through 55
    Processing helix  chain 'D' and resid 62 through 64
      No H-bonds generated for 'chain 'D' and resid 62 through 64'
    Processing helix  chain 'D' and resid 75 through 98
      removed outlier: 3.699A  pdb=" N   GLN D  98 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 106
      removed outlier: 3.900A  pdb=" N   GLU D 105 " --> pdb=" O   SER D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 126
    Processing helix  chain 'D' and resid 128 through 149
      removed outlier: 3.687A  pdb=" N   VAL D 148 " --> pdb=" O   TYR D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 152 through 185
    Processing helix  chain 'D' and resid 188 through 199
    Processing helix  chain 'D' and resid 203 through 221
      removed outlier: 4.001A  pdb=" N   VAL D 207 " --> pdb=" O   GLY D 203 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 235
    Processing helix  chain 'D' and resid 237 through 263
      removed outlier: 5.540A  pdb=" N   THR D 249 " --> pdb=" O   GLY D 245 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   LYS D 250 " --> pdb=" O   GLY D 246 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL D 251 " --> pdb=" O   LEU D 247 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLY D 252 " --> pdb=" O   LEU D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 267 through 292
      removed outlier: 4.250A  pdb=" N   MET D 273 " --> pdb=" O   ASP D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 295 through 318
      removed outlier: 3.954A  pdb=" N   ILE D 305 " --> pdb=" O   SER D 301 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR D 310 " --> pdb=" O   SER D 306 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   MET D 311 " --> pdb=" O  AGLN D 307 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU D 315 " --> pdb=" O   MET D 311 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 319 through 352
    Processing helix  chain 'D' and resid 355 through 359
    Processing helix  chain 'D' and resid 361 through 366
      removed outlier: 3.524A  pdb=" N   THR D 365 " --> pdb=" O   GLY D 361 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 366 through 381
    Processing helix  chain 'D' and resid 386 through 402
      removed outlier: 3.649A  pdb=" N   PHE D 390 " --> pdb=" O   LEU D 386 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 430
    Processing helix  chain 'D' and resid 437 through 442
    Processing helix  chain 'D' and resid 445 through 465
      Proline residue:  D 451  - end of helix
      Proline residue:  D 454  - end of helix
    Processing helix  chain 'D' and resid 465 through 481
      removed outlier: 3.706A  pdb=" N   ILE D 469 " --> pdb=" O   ALA D 465 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 482 through 491
      removed outlier: 4.134A  pdb=" N   TYR D 486 " --> pdb=" O   ASP D 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2 through 24
      Proline residue:  A  11  - end of helix
      Proline residue:  A  19  - end of helix
    Processing helix  chain 'A' and resid 29 through 47
      removed outlier: 4.342A  pdb=" N   PHE A  33 " --> pdb=" O   HIS A  29 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ALA A  36 " --> pdb=" O   TRP A  32 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LEU A  37 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
      Proline residue:  A  38  - end of helix
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 66 through 69
    Processing helix  chain 'A' and resid 77 through 102
      removed outlier: 3.814A  pdb=" N   PHE A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 129
    Processing helix  chain 'A' and resid 131 through 151
    Processing helix  chain 'A' and resid 156 through 189
    Processing helix  chain 'A' and resid 192 through 199
    Processing helix  chain 'A' and resid 200 through 205
    Processing helix  chain 'A' and resid 208 through 224
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.034A  pdb=" N   ASP A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 239
      No H-bonds generated for 'chain 'A' and resid 237 through 239'
    Processing helix  chain 'A' and resid 240 through 250
      removed outlier: 3.577A  pdb=" N  BHIS A 248 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N  BSER A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N  AALA A 250 " --> pdb=" O  ATYR A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
      removed outlier: 3.501A  pdb=" N   ALA A 255 " --> pdb=" O  BTHR A 251 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLY A 256 " --> pdb=" O  AMET A 252 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   ILE A 257 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      Proline residue:  A 265  - end of helix
    Processing helix  chain 'A' and resid 270 through 294
      removed outlier: 3.876A  pdb=" N   ARG A 294 " --> pdb=" O   THR A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 321
    Processing helix  chain 'A' and resid 321 through 327
      removed outlier: 3.777A  pdb=" N   TYR A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 332 through 368
      removed outlier: 5.003A  pdb=" N   ALA A 338 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ILE A 339 " --> pdb=" O   TYR A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 398
    Processing helix  chain 'A' and resid 402 through 420
      removed outlier: 3.824A  pdb=" N   LEU A 406 " --> pdb=" O   PHE A 402 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLU A 420 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 457
      removed outlier: 5.985A  pdb=" N   ILE A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   ILE A 432 " --> pdb=" O   THR A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 493
      removed outlier: 4.526A  pdb=" N   SER A 479 " --> pdb=" O   GLY A 475 " (cutoff:3.500A)
      Proline residue:  A 480  - end of helix
      removed outlier: 3.547A  pdb=" N   ILE A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 501 through 510
    Processing helix  chain 'A' and resid 531 through 550
    Processing helix  chain 'A' and resid 550 through 555
    Processing helix  chain 'A' and resid 557 through 562
      removed outlier: 3.684A  pdb=" N   LYS A 562 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 590
      removed outlier: 4.510A  pdb=" N   PHE A 570 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 579 " --> pdb=" O   LEU A 575 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLN A 589 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 616
    Processing helix  chain 'A' and resid 630 through 647
      removed outlier: 3.800A  pdb=" N   TRP A 634 " --> pdb=" O   ALA A 630 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A 635 " --> pdb=" O   PRO A 631 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE A 647 " --> pdb=" O   ALA A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 650
      No H-bonds generated for 'chain 'A' and resid 648 through 650'
    Processing helix  chain 'A' and resid 652 through 674
    Processing helix  chain 'A' and resid 676 through 699
      removed outlier: 3.527A  pdb=" N   TYR A 699 " --> pdb=" O   MET A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 743
    Processing helix  chain 'A' and resid 748 through 755
    Processing helix  chain 'A' and resid 763 through 771
    Processing helix  chain 'A' and resid 773 through 797
      removed outlier: 3.835A  pdb=" N   THR A 777 " --> pdb=" O   ARG A 773 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 33
      removed outlier: 3.908A  pdb=" N   PHE B  20 " --> pdb=" O   ARG B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 58
    Processing helix  chain 'B' and resid 59 through 67
    Processing helix  chain 'B' and resid 70 through 86
      removed outlier: 3.551A  pdb=" N   GLY B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 92
      removed outlier: 3.767A  pdb=" N   LEU B  91 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL B  92 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 87 through 92'
    Processing helix  chain 'B' and resid 116 through 141
    Processing helix  chain 'C' and resid 2 through 21
    Processing helix  chain 'C' and resid 24 through 47
    Processing helix  chain 'C' and resid 56 through 60
    Processing helix  chain 'C' and resid 66 through 99
      removed outlier: 4.195A  pdb=" N   GLN C  70 " --> pdb=" O   ASP C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 3.517A  pdb=" N   ARG C 107 " --> pdb=" O   ASP C 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 19
      removed outlier: 3.654A  pdb=" N   ASN E  17 " --> pdb=" O   VAL E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 23 through 42
      removed outlier: 4.037A  pdb=" N   PHE E  27 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU E  28 " --> pdb=" O   ALA E  24 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 49 through 80
      removed outlier: 4.414A  pdb=" N   ARG E  53 " --> pdb=" O   PHE E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 99 through 113
    Processing helix  chain 'E' and resid 137 through 148
      removed outlier: 3.597A  pdb=" N   MET E 141 " --> pdb=" O   ASN E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 158
      removed outlier: 3.724A  pdb=" N   VAL E 156 " --> pdb=" O   ALA E 152 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 27
      removed outlier: 3.925A  pdb=" N   ARG F  23 " --> pdb=" O   VAL F  19 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR F  24 " --> pdb=" O   CYS F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 55
      removed outlier: 3.538A  pdb=" N   ILE F  45 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLY F  46 " --> pdb=" O   ILE F  42 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 60 through 85
      removed outlier: 3.533A  pdb=" N   VAL F  64 " --> pdb=" O   TYR F  60 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU F  65 " --> pdb=" O   SER F  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 29
    Processing helix  chain 'G' and resid 31 through 63
      removed outlier: 3.570A  pdb=" N   ALA G  38 " --> pdb=" O   GLY G  34 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA G  43 " --> pdb=" O   ALA G  39 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   THR G  44 " --> pdb=" O   THR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 66 through 95
      removed outlier: 3.981A  pdb=" N   LEU G  70 " --> pdb=" O   VAL G  66 " (cutoff:3.500A)
      Proline residue:  G  81  - end of helix
    Processing helix  chain 'G' and resid 105 through 111
      removed outlier: 4.234A  pdb=" N   LYS G 109 " --> pdb=" O   ASP G 105 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   MET G 110 " --> pdb=" O   ASP G 106 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 2 through 20
      removed outlier: 4.001A  pdb=" N   ASN e  17 " --> pdb=" O   VAL e  13 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   PHE e  18 " --> pdb=" O   ILE e  14 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN e  19 " --> pdb=" O   TRP e  15 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 23 through 41
    Processing sheet with id=AA1, first strand: chain 'D' and resid 57 through 60
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 65
      removed outlier: 7.188A  pdb=" N   ILE A  70 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 105
    Processing sheet with id=AA4, first strand: chain 'E' and resid 89 through 94
      removed outlier: 6.826A  pdb=" N   TYR E 127 " --> pdb=" O   PHE E 121 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   PHE E 121 " --> pdb=" O   TYR E 127 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   TYR E 129 " --> pdb=" O  AMET E 119 " (cutoff:3.500A)

    1213 hydrogen bonds defined for protein.
    3611 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: 5.29

  Time building geometry restraints manager: 4.59 seconds

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

  Histogram of bond lengths:
        1.16 -     1.31: 2498
        1.31 -     1.46: 5800
        1.46 -     1.61: 7651
        1.61 -     1.76: 20
        1.76 -     1.91: 168
  Bond restraints: 16137
  Sorted by residual:
  bond pdb=" CE1 HIS D 266 "
       pdb=" NE2 HIS D 266 "
    ideal  model  delta    sigma   weight residual
    1.321  1.451 -0.130 1.00e-02 1.00e+04 1.70e+02
  bond pdb=" C29 3PE A 901 "
       pdb=" C2A 3PE A 901 "
    ideal  model  delta    sigma   weight residual
    1.524  1.292  0.232 2.00e-02 2.50e+03 1.34e+02
  bond pdb=" CE1 HIS D 303 "
       pdb=" NE2 HIS D 303 "
    ideal  model  delta    sigma   weight residual
    1.321  1.428 -0.107 1.00e-02 1.00e+04 1.15e+02
  bond pdb=" C29 3PE E 201 "
       pdb=" C2A 3PE E 201 "
    ideal  model  delta    sigma   weight residual
    1.524  1.331  0.193 2.00e-02 2.50e+03 9.30e+01
  bond pdb=" C29 3PE E 202 "
       pdb=" C2A 3PE E 202 "
    ideal  model  delta    sigma   weight residual
    1.524  1.337  0.187 2.00e-02 2.50e+03 8.76e+01
  ... (remaining 16132 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 17697
        2.69 -     5.38: 3747
        5.38 -     8.07: 425
        8.07 -    10.76: 56
       10.76 -    13.45: 14
  Bond angle restraints: 21939
  Sorted by residual:
  angle pdb=" O   VAL D 453 "
        pdb=" C   VAL D 453 "
        pdb=" N   PRO D 454 "
      ideal   model   delta    sigma   weight residual
     120.42  114.51    5.91 6.40e-01 2.44e+00 8.54e+01
  angle pdb=" O   PRO C  54 "
        pdb=" C   PRO C  54 "
        pdb=" N   PRO C  55 "
      ideal   model   delta    sigma   weight residual
     121.31  117.11    4.20 4.60e-01 4.73e+00 8.32e+01
  angle pdb=" N   PRO B  68 "
        pdb=" CA  PRO B  68 "
        pdb=" CB  PRO B  68 "
      ideal   model   delta    sigma   weight residual
     102.81   96.80    6.01 6.70e-01 2.23e+00 8.04e+01
  angle pdb=" CA  ASP A 297 "
        pdb=" CB  ASP A 297 "
        pdb=" CG  ASP A 297 "
      ideal   model   delta    sigma   weight residual
     112.60  121.15   -8.55 1.00e+00 1.00e+00 7.30e+01
  angle pdb=" C   PRO A 473 "
        pdb=" CA  PRO A 473 "
        pdb=" CB  PRO A 473 "
      ideal   model   delta    sigma   weight residual
     111.56  100.82   10.74 1.27e+00 6.20e-01 7.16e+01
  ... (remaining 21934 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 8468
       17.96 -    35.91: 713
       35.91 -    53.86: 166
       53.86 -    71.81: 28
       71.81 -    89.77: 10
  Dihedral angle restraints: 9385
    sinusoidal: 3631
      harmonic: 5754
  Sorted by residual:
  dihedral pdb=" CA  ARG F  90 "
           pdb=" C   ARG F  90 "
           pdb=" N   GLY F  91 "
           pdb=" CA  GLY F  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.61  -29.39     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" CA  ALA A 333 "
           pdb=" C   ALA A 333 "
           pdb=" N   PHE A 334 "
           pdb=" CA  PHE A 334 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.69  -28.31     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  ASP C 111 "
           pdb=" C   ASP C 111 "
           pdb=" N   GLU C 112 "
           pdb=" CA  GLU C 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.60  -25.40     0      5.00e+00 4.00e-02 2.58e+01
  ... (remaining 9382 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1723
       0.093 -    0.186: 725
       0.186 -    0.278: 159
       0.278 -    0.371: 25
       0.371 -    0.464: 1
  Chirality restraints: 2633
  Sorted by residual:
  chirality pdb=" CA  PRO A 265 "
            pdb=" N   PRO A 265 "
            pdb=" C   PRO A 265 "
            pdb=" CB  PRO A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.25    0.46 2.00e-01 2.50e+01 5.38e+00
  chirality pdb=" CA  ARG F  90 "
            pdb=" N   ARG F  90 "
            pdb=" C   ARG F  90 "
            pdb=" CB  ARG F  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.43e+00
  chirality pdb=" CA  TYR A 113 "
            pdb=" N   TYR A 113 "
            pdb=" C   TYR A 113 "
            pdb=" CB  TYR A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.19e+00
  ... (remaining 2630 not shown)

  Planarity restraints: 2637
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE e  18 "    0.099 2.00e-02 2.50e+03   6.98e-02 8.54e+01
        pdb=" CG  PHE e  18 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE e  18 "   -0.102 2.00e-02 2.50e+03
        pdb=" CD2 PHE e  18 "   -0.090 2.00e-02 2.50e+03
        pdb=" CE1 PHE e  18 "    0.041 2.00e-02 2.50e+03
        pdb=" CE2 PHE e  18 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  PHE e  18 "    0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  28 "   -0.122 2.00e-02 2.50e+03   6.32e-02 7.98e+01
        pdb=" CG  TYR B  28 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  28 "    0.052 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  28 "    0.063 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  28 "    0.032 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  28 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  28 "   -0.018 2.00e-02 2.50e+03
        pdb=" OH  TYR B  28 "   -0.077 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 431 "   -0.078 2.00e-02 2.50e+03   5.32e-02 7.07e+01
        pdb=" CG  TRP D 431 "    0.091 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 431 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 431 "    0.078 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 431 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 431 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 431 "   -0.041 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 431 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 431 "    0.038 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 431 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2634 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 407
        2.63 -     3.20: 15861
        3.20 -     3.76: 28235
        3.76 -     4.33: 40867
        4.33 -     4.90: 64070
  Nonbonded interactions: 149440
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 678 "
            pdb=" O   HOH A1001 "
     model   vdw
     2.058 3.040
  nonbonded pdb=" CE2APHE B  41 "
            pdb=" CD1 LEU B  45 "
     model   vdw
     2.083 3.760
  nonbonded pdb=" NH1 ARG D 231 "
            pdb=" O   HOH D 501 "
     model   vdw
     2.106 3.120
  nonbonded pdb=" O   HOH A1002 "
            pdb=" O   HOH A1008 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" OG1 THR E 113 "
            pdb=" O   HOH E 301 "
     model   vdw
     2.181 3.040
  ... (remaining 149435 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.24 max=1.00 mean=0.98
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:             4.850
  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:          0.640
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     44.790
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:14.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   65.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8937
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      :  0.020   0.232  16137  Z= 1.253
  Angle     :  2.179  13.447  21939  Z= 1.477
  Chirality :  0.102   0.464   2633
  Planarity :  0.022   0.249   2637
  Dihedral  : 14.727  89.768   5707
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.58 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  :  6.60 %
    Favored  : 90.90 %
  Cbeta Deviations :  0.49 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.16), residues: 2010
  helix: -0.87 (0.11), residues: 1509
  sheet: -0.81 (0.71), residues: 48
  loop : -1.15 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.113   0.024   TRP A 273 
 HIS   0.074   0.013   HIS A 349 
 PHE   0.102   0.022   PHE e  18 
 TYR   0.122   0.023   TYR B  28 
 ARG   0.059   0.007   ARG F  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18404 ( 1213)
  hydrogen bonds       : angle       7.34892 ( 3611)
  covalent geometry    : bond        0.02018 (16137)
  covalent geometry    : angle       2.17920 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 256
  time to evaluate  : 1.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   40 MET cc_start: 0.9295 (mtp) cc_final: 0.9010 (mtp)
REVERT: D  103 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (mm-30)
REVERT: D  189 MET cc_start: 0.9283 (mtt) cc_final: 0.9028 (mtp)
REVERT: D  283 MET cc_start: 0.9419 (mtm) cc_final: 0.9203 (mtm)
REVERT: D  311 MET cc_start: 0.9389 (mtt) cc_final: 0.8988 (mtt)
REVERT: D  396 ILE cc_start: 0.8857 (pt) cc_final: 0.8506 (mt)
REVERT: D  439 GLN cc_start: 0.8928 (tt0) cc_final: 0.8159 (pm20)
REVERT: D  467 GLU cc_start: 0.9242 (tp30) cc_final: 0.9005 (tp30)
REVERT: D  488 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8749 (mm-30)
REVERT: A  207 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8329 (mp0)
REVERT: A  314 MET cc_start: 0.9301 (tpp) cc_final: 0.8782 (tpp)
REVERT: A  382 MET cc_start: 0.9371 (mtt) cc_final: 0.9160 (mtp)
REVERT: A  421 MET cc_start: 0.9216 (mtp) cc_final: 0.8879 (mtm)
REVERT: A  459 LYS cc_start: 0.8326 (tttt) cc_final: 0.8107 (mtmm)
REVERT: A  461 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7797 (mtpt)
REVERT: A  496 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8886 (mt)
REVERT: A  518 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7951 (mt-10)
REVERT: A  551 MET cc_start: 0.9057 (ttp) cc_final: 0.8802 (ttt)
REVERT: A  561 MET cc_start: 0.8463 (mmt) cc_final: 0.8116 (mmm)
REVERT: A  563 GLU cc_start: 0.8587 (pt0) cc_final: 0.8177 (pm20)
REVERT: A  706 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7640 (tttm)
REVERT: A  715 ILE cc_start: 0.8589 (mt) cc_final: 0.8319 (tp)
REVERT: B   69 PHE cc_start: 0.8861 (m-80) cc_final: 0.8587 (m-10)
REVERT: B   74 MET cc_start: 0.9392 (ttm) cc_final: 0.9159 (ttp)
REVERT: B  102 GLU cc_start: 0.8403 (tt0) cc_final: 0.8180 (tp30)
REVERT: B  142 ASP cc_start: 0.8977 (t0) cc_final: 0.8756 (t0)
REVERT: C    1 MET cc_start: 0.8863 (tpp) cc_final: 0.8569 (tpt)
REVERT: C   14 MET cc_start: 0.9259 (ttp) cc_final: 0.8953 (ttp)
REVERT: C   46 MET cc_start: 0.9510 (mmp) cc_final: 0.9050 (mmp)
REVERT: C   80 SER cc_start: 0.9224 (t) cc_final: 0.8882 (p)
REVERT: E   51 MET cc_start: 0.8878 (mmm) cc_final: 0.8659 (mmm)
REVERT: E   53 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8151 (ttm-80)
REVERT: E  146 HIS cc_start: 0.8496 (m90) cc_final: 0.8224 (m170)
REVERT: G    1 MET cc_start: 0.8251 (ttt) cc_final: 0.7987 (ttm)
REVERT: G   92 TYR cc_start: 0.9363 (t80) cc_final: 0.8842 (t80)
REVERT: G  109 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7745 (mmmt)
REVERT: e   19 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7142 (mm-40)
  outliers start: 37
  outliers final: 14
  residues processed: 285
  average time/residue: 1.4354
  time to fit residues: 450.2269
Evaluate side-chains
  239 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 222
  time to evaluate  : 1.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 PRO
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  385 PRO
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  401 PRO
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain E residue   13 VAL
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   94 PRO
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain e residue   19 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 162 optimal weight:    3.9990
   chunk 146 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0970
   chunk 78 optimal weight:    0.6980
   chunk 151 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   chunk 112 optimal weight:    0.6980
   chunk 175 optimal weight:    0.9980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
E   8 ASN
E 137 ASN
F  43 ASN
e   8 ASN
e  19 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.102551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.074454 restraints weight = 89787.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.2747 rms_B_bonded: 2.64
r_work: 0.2611 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2501 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2469 r_free = 0.2469    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2469 r_free = 0.2469    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16137  Z= 0.175
  Angle     :  0.653   8.278  21939  Z= 0.357
  Chirality :  0.044   0.202   2633
  Planarity :  0.005   0.045   2637
  Dihedral  :  8.987  80.984   2293
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 10.17 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.18), residues: 2010
  helix:  1.52 (0.13), residues: 1523
  sheet: -0.19 (0.70), residues: 48
  loop : -0.54 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 139 
 HIS   0.011   0.002   HIS D 333 
 PHE   0.048   0.002   PHE A 352 
 TYR   0.029   0.002   TYR A 447 
 ARG   0.010   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06472 ( 1213)
  hydrogen bonds       : angle       4.67172 ( 3611)
  covalent geometry    : bond        0.00372 (16137)
  covalent geometry    : angle       0.65315 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 241
  time to evaluate  : 1.605 
Fit side-chains
   revert: symmetry clash
REVERT: D  103 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7772 (mm-30)
REVERT: D  311 MET cc_start: 0.9384 (mtt) cc_final: 0.9025 (mtt)
REVERT: D  439 GLN cc_start: 0.8686 (tt0) cc_final: 0.8104 (pm20)
REVERT: D  467 GLU cc_start: 0.9116 (tp30) cc_final: 0.8850 (tp30)
REVERT: D  488 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8536 (mm-30)
REVERT: A  207 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8207 (mp0)
REVERT: A  314 MET cc_start: 0.9298 (tpp) cc_final: 0.9062 (tpp)
REVERT: A  461 LYS cc_start: 0.8062 (mmtp) cc_final: 0.7625 (mtpt)
REVERT: A  516 ASP cc_start: 0.8335 (m-30) cc_final: 0.8130 (t70)
REVERT: A  561 MET cc_start: 0.8353 (mmt) cc_final: 0.7972 (mmm)
REVERT: A  563 GLU cc_start: 0.8300 (pt0) cc_final: 0.7886 (pm20)
REVERT: A  706 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7771 (tttm)
REVERT: B   69 PHE cc_start: 0.8904 (m-80) cc_final: 0.8666 (m-10)
REVERT: B  102 GLU cc_start: 0.7950 (tt0) cc_final: 0.7590 (tp30)
REVERT: C   14 MET cc_start: 0.9093 (ttp) cc_final: 0.8817 (ttp)
REVERT: C   46 MET cc_start: 0.9490 (mmp) cc_final: 0.9141 (mmp)
REVERT: C   80 SER cc_start: 0.9212 (t) cc_final: 0.8835 (p)
REVERT: E   51 MET cc_start: 0.8714 (mmm) cc_final: 0.8506 (mmm)
REVERT: E  141 MET cc_start: 0.8755 (ttp) cc_final: 0.8537 (tmm)
REVERT: E  151 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7422 (ttm-80)
REVERT: G   79 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8751 (p)
REVERT: e    7 LEU cc_start: 0.7945 (mt) cc_final: 0.7737 (mt)
REVERT: e    8 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7454 (t0)
  outliers start: 27
  outliers final: 8
  residues processed: 254
  average time/residue: 1.3933
  time to fit residues: 389.6773
Evaluate side-chains
  223 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 212
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain E residue    6 LEU
Chi-restraints excluded: chain E residue   13 VAL
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue   94 VAL
Chi-restraints excluded: chain e residue    8 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 188 optimal weight:    0.2980
   chunk 174 optimal weight:    0.5980
   chunk 159 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 132 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D   2 ASN
A 683 GLN
E   8 ASN
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.104073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.075613 restraints weight = 96483.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 2.81
r_work: 0.2634 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2526 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2487 r_free = 0.2487    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2487 r_free = 0.2487    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  16137  Z= 0.161
  Angle     :  0.591   7.528  21939  Z= 0.320
  Chirality :  0.043   0.240   2633
  Planarity :  0.004   0.043   2637
  Dihedral  :  8.296  77.001   2271
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.18 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.18), residues: 2010
  helix:  1.94 (0.13), residues: 1530
  sheet: -0.10 (0.71), residues: 48
  loop : -0.21 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 139 
 HIS   0.009   0.001   HIS D 333 
 PHE   0.043   0.002   PHE A 352 
 TYR   0.024   0.002   TYR C  92 
 ARG   0.010   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05953 ( 1213)
  hydrogen bonds       : angle       4.41672 ( 3611)
  covalent geometry    : bond        0.00346 (16137)
  covalent geometry    : angle       0.59078 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 216
  time to evaluate  : 1.638 
Fit side-chains
REVERT: D  103 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7875 (mm-30)
REVERT: D  311 MET cc_start: 0.9361 (mtt) cc_final: 0.9010 (mtt)
REVERT: D  439 GLN cc_start: 0.8737 (tt0) cc_final: 0.8170 (pm20)
REVERT: D  467 GLU cc_start: 0.9142 (tp30) cc_final: 0.8915 (tp30)
REVERT: D  488 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8554 (mm-30)
REVERT: A  207 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8127 (mp0)
REVERT: A  461 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7617 (mtpt)
REVERT: A  516 ASP cc_start: 0.8414 (m-30) cc_final: 0.8195 (t70)
REVERT: A  561 MET cc_start: 0.8431 (mmt) cc_final: 0.8073 (mmm)
REVERT: A  563 GLU cc_start: 0.8280 (pt0) cc_final: 0.7989 (pm20)
REVERT: A  570 PHE cc_start: 0.8606 (m-80) cc_final: 0.8329 (m-80)
REVERT: C   14 MET cc_start: 0.9083 (ttp) cc_final: 0.8860 (ttp)
REVERT: C   46 MET cc_start: 0.9480 (mmp) cc_final: 0.9066 (mmp)
REVERT: C   80 SER cc_start: 0.9202 (t) cc_final: 0.8847 (p)
REVERT: C  101 ASP cc_start: 0.8846 (p0) cc_final: 0.8601 (p0)
REVERT: C  105 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7110 (mp10)
REVERT: E   51 MET cc_start: 0.8712 (mmm) cc_final: 0.8492 (mmm)
REVERT: E   72 ASN cc_start: 0.9190 (m-40) cc_final: 0.8985 (m110)
REVERT: E  141 MET cc_start: 0.8781 (ttp) cc_final: 0.8571 (tmm)
REVERT: G   79 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8696 (p)
  outliers start: 24
  outliers final: 5
  residues processed: 227
  average time/residue: 1.5440
  time to fit residues: 383.7413
Evaluate side-chains
  217 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 209
  time to evaluate  : 2.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain C residue  105 GLN
Chi-restraints excluded: chain E residue    6 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain G residue   79 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 167 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 117 optimal weight:    0.6980
   chunk 148 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 136 optimal weight:    0.9990
   chunk 180 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 132 optimal weight:    2.9990
   chunk 191 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D   2 ASN
E   8 ASN
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.103560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.075722 restraints weight = 99935.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.2789 rms_B_bonded: 2.79
r_work: 0.2648 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2540 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2487 r_free = 0.2487    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2487 r_free = 0.2487    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16137  Z= 0.171
  Angle     :  0.586   8.049  21939  Z= 0.317
  Chirality :  0.043   0.236   2633
  Planarity :  0.004   0.042   2637
  Dihedral  :  7.983  75.080   2269
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.53 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.18), residues: 2010
  helix:  2.03 (0.13), residues: 1527
  sheet: -0.10 (0.72), residues: 48
  loop : -0.04 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 139 
 HIS   0.008   0.002   HIS A 349 
 PHE   0.039   0.002   PHE A 352 
 TYR   0.025   0.002   TYR C  92 
 ARG   0.010   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06035 ( 1213)
  hydrogen bonds       : angle       4.39582 ( 3611)
  covalent geometry    : bond        0.00382 (16137)
  covalent geometry    : angle       0.58606 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 212
  time to evaluate  : 1.751 
Fit side-chains
REVERT: D   24 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8421 (mppt)
REVERT: D  103 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7892 (mm-30)
REVERT: D  311 MET cc_start: 0.9382 (mtt) cc_final: 0.9025 (mtt)
REVERT: D  439 GLN cc_start: 0.8733 (tt0) cc_final: 0.8149 (pm20)
REVERT: D  488 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8581 (mm-30)
REVERT: A  207 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8131 (mp0)
REVERT: A  461 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7628 (mtpt)
REVERT: A  561 MET cc_start: 0.8415 (mmt) cc_final: 0.8014 (mmm)
REVERT: A  563 GLU cc_start: 0.8270 (pt0) cc_final: 0.7839 (pm20)
REVERT: B  142 ASP cc_start: 0.8788 (t0) cc_final: 0.8455 (t0)
REVERT: C   14 MET cc_start: 0.9094 (ttp) cc_final: 0.8879 (ttp)
REVERT: C   80 SER cc_start: 0.9183 (t) cc_final: 0.8936 (p)
REVERT: C  105 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7095 (mp10)
REVERT: E   36 PHE cc_start: 0.7663 (m-80) cc_final: 0.7404 (m-10)
REVERT: E  124 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8073 (p0)
REVERT: E  128 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8803 (tp)
REVERT: E  141 MET cc_start: 0.8795 (ttp) cc_final: 0.8591 (tmm)
REVERT: G   79 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8642 (p)
REVERT: e    8 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7812 (t0)
  outliers start: 26
  outliers final: 10
  residues processed: 229
  average time/residue: 1.4444
  time to fit residues: 362.9668
Evaluate side-chains
  225 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 209
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  462 LEU
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain C residue  105 GLN
Chi-restraints excluded: chain E residue    8 ASN
Chi-restraints excluded: chain E residue   13 VAL
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue  124 ASP
Chi-restraints excluded: chain E residue  128 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain e residue    8 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 157 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 158 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 112 optimal weight:    0.5980
   chunk 122 optimal weight:    2.9990
   chunk 170 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 34 optimal weight:    0.7980
   chunk 185 optimal weight:    0.5980
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D   2 ASN
E   8 ASN
** E  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.104140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.075999 restraints weight = 95481.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.75
r_work: 0.2645 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2536 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2498 r_free = 0.2498    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2498 r_free = 0.2498    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  16137  Z= 0.164
  Angle     :  0.570   8.235  21939  Z= 0.308
  Chirality :  0.042   0.231   2633
  Planarity :  0.004   0.043   2637
  Dihedral  :  7.744  73.254   2269
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.01 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.18), residues: 2010
  helix:  2.07 (0.13), residues: 1527
  sheet: -0.09 (0.72), residues: 48
  loop :  0.01 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 139 
 HIS   0.008   0.001   HIS A 349 
 PHE   0.037   0.002   PHE A 352 
 TYR   0.025   0.002   TYR C  92 
 ARG   0.010   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05876 ( 1213)
  hydrogen bonds       : angle       4.36331 ( 3611)
  covalent geometry    : bond        0.00363 (16137)
  covalent geometry    : angle       0.56964 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 216
  time to evaluate  : 1.745 
Fit side-chains
REVERT: D   24 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8422 (mppt)
REVERT: D  103 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7913 (mm-30)
REVERT: D  311 MET cc_start: 0.9375 (mtt) cc_final: 0.9019 (mtt)
REVERT: D  439 GLN cc_start: 0.8737 (tt0) cc_final: 0.8155 (pm20)
REVERT: D  488 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8592 (mm-30)
REVERT: A  207 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8148 (mp0)
REVERT: A  421 MET cc_start: 0.9114 (mtp) cc_final: 0.8901 (mtm)
REVERT: A  461 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7583 (mtpt)
REVERT: A  561 MET cc_start: 0.8412 (mmt) cc_final: 0.8055 (mmm)
REVERT: A  563 GLU cc_start: 0.8270 (pt0) cc_final: 0.7824 (pm20)
REVERT: A  605 MET cc_start: 0.9175 (mtp) cc_final: 0.8946 (mtt)
REVERT: B  142 ASP cc_start: 0.8792 (t0) cc_final: 0.8406 (t0)
REVERT: C   14 MET cc_start: 0.9088 (ttp) cc_final: 0.8876 (ttp)
REVERT: C   99 LYS cc_start: 0.8790 (mttp) cc_final: 0.8392 (mmtt)
REVERT: C  105 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7052 (mp10)
REVERT: E   36 PHE cc_start: 0.7666 (m-80) cc_final: 0.7387 (m-10)
REVERT: E   83 LYS cc_start: 0.7935 (ptmm) cc_final: 0.7732 (ptmm)
REVERT: E  128 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8810 (tp)
REVERT: E  141 MET cc_start: 0.8791 (ttp) cc_final: 0.8587 (tmm)
REVERT: e    8 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7665 (t0)
  outliers start: 25
  outliers final: 12
  residues processed: 231
  average time/residue: 1.5881
  time to fit residues: 401.4005
Evaluate side-chains
  225 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 209
  time to evaluate  : 1.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  462 LEU
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain C residue   96 LYS
Chi-restraints excluded: chain C residue  105 GLN
Chi-restraints excluded: chain E residue    6 LEU
Chi-restraints excluded: chain E residue    8 ASN
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue  128 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain e residue    8 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 189 optimal weight:    1.9990
   chunk 176 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 192 optimal weight:    0.5980
   chunk 180 optimal weight:    1.9990
   chunk 163 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
E   8 ASN
** E  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.103770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.075770 restraints weight = 98256.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 2.80
r_work: 0.2653 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2545 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8895
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16137  Z= 0.178
  Angle     :  0.582   8.488  21939  Z= 0.315
  Chirality :  0.043   0.233   2633
  Planarity :  0.004   0.043   2637
  Dihedral  :  7.664  73.003   2268
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.49 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.18), residues: 2010
  helix:  2.04 (0.13), residues: 1527
  sheet: -0.09 (0.71), residues: 48
  loop :  0.01 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 139 
 HIS   0.008   0.002   HIS A 349 
 PHE   0.035   0.002   PHE A 352 
 TYR   0.025   0.002   TYR C  92 
 ARG   0.010   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06038 ( 1213)
  hydrogen bonds       : angle       4.38225 ( 3611)
  covalent geometry    : bond        0.00403 (16137)
  covalent geometry    : angle       0.58157 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 211
  time to evaluate  : 1.642 
Fit side-chains
REVERT: D   24 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8422 (mppt)
REVERT: D  103 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7966 (mm-30)
REVERT: D  311 MET cc_start: 0.9385 (mtt) cc_final: 0.9026 (mtt)
REVERT: D  439 GLN cc_start: 0.8738 (tt0) cc_final: 0.8168 (pm20)
REVERT: D  488 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8540 (mm-30)
REVERT: A  207 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8133 (mp0)
REVERT: A  421 MET cc_start: 0.9113 (mtp) cc_final: 0.8895 (mtm)
REVERT: A  461 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7594 (mtpt)
REVERT: A  561 MET cc_start: 0.8413 (mmt) cc_final: 0.8060 (mmm)
REVERT: A  563 GLU cc_start: 0.8289 (pt0) cc_final: 0.7967 (pm20)
REVERT: A  605 MET cc_start: 0.9174 (mtp) cc_final: 0.8933 (mtt)
REVERT: B  142 ASP cc_start: 0.8821 (t0) cc_final: 0.8439 (t0)
REVERT: C   14 MET cc_start: 0.9101 (ttp) cc_final: 0.8893 (ttp)
REVERT: C   99 LYS cc_start: 0.8787 (mttp) cc_final: 0.8385 (mmtt)
REVERT: C  105 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7091 (mp10)
REVERT: E   36 PHE cc_start: 0.7584 (m-80) cc_final: 0.7325 (m-10)
REVERT: E  128 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8806 (tp)
REVERT: E  143 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.7657 (ttm-80)
REVERT: F    1 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6871 (tpp)
REVERT: e    8 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7676 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 224
  average time/residue: 1.5699
  time to fit residues: 384.1195
Evaluate side-chains
  227 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 209
  time to evaluate  : 1.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  462 LEU
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain C residue  105 GLN
Chi-restraints excluded: chain E residue    6 LEU
Chi-restraints excluded: chain E residue    8 ASN
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue  128 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain e residue    8 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 182 optimal weight:    0.9990
   chunk 129 optimal weight:    0.9980
   chunk 128 optimal weight:    0.8980
   chunk 185 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 108 optimal weight:    0.3980
   chunk 56 optimal weight:    0.2980
   chunk 131 optimal weight:    0.5980
   chunk 164 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 180 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
D   2 ASN
E   8 ASN
** E  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.103801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.075575 restraints weight = 102882.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 2.88
r_work: 0.2648 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2538 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2505
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2505 r_free = 0.2505    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2504 r_free = 0.2504    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8873
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16137  Z= 0.156
  Angle     :  0.556   8.702  21939  Z= 0.301
  Chirality :  0.042   0.221   2633
  Planarity :  0.004   0.043   2637
  Dihedral  :  7.526  71.344   2268
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.96 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.18), residues: 2010
  helix:  2.10 (0.13), residues: 1527
  sheet: -0.04 (0.72), residues: 48
  loop :  0.04 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 101 
 HIS   0.007   0.001   HIS A 349 
 PHE   0.036   0.002   PHE A 352 
 TYR   0.024   0.002   TYR C  92 
 ARG   0.010   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05772 ( 1213)
  hydrogen bonds       : angle       4.31783 ( 3611)
  covalent geometry    : bond        0.00340 (16137)
  covalent geometry    : angle       0.55626 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 210
  time to evaluate  : 1.711 
Fit side-chains
REVERT: D   24 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8402 (mppt)
REVERT: D  103 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7934 (mm-30)
REVERT: D  311 MET cc_start: 0.9363 (mtt) cc_final: 0.8994 (mtt)
REVERT: D  439 GLN cc_start: 0.8738 (tt0) cc_final: 0.8174 (pm20)
REVERT: D  488 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8562 (mm-30)
REVERT: A  207 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8124 (mp0)
REVERT: A  410 MET cc_start: 0.9457 (mtp) cc_final: 0.9214 (mtm)
REVERT: A  421 MET cc_start: 0.9102 (mtp) cc_final: 0.8882 (mtm)
REVERT: A  461 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7585 (mtpt)
REVERT: A  561 MET cc_start: 0.8377 (mmt) cc_final: 0.8019 (mmm)
REVERT: A  563 GLU cc_start: 0.8255 (pt0) cc_final: 0.7922 (pm20)
REVERT: A  605 MET cc_start: 0.9149 (mtp) cc_final: 0.8904 (mtt)
REVERT: B  142 ASP cc_start: 0.8805 (t0) cc_final: 0.8456 (t0)
REVERT: C   14 MET cc_start: 0.9096 (ttp) cc_final: 0.8891 (ttp)
REVERT: C   99 LYS cc_start: 0.8779 (mttp) cc_final: 0.8383 (mmtt)
REVERT: C  102 ASP cc_start: 0.8828 (t0) cc_final: 0.8416 (t0)
REVERT: C  105 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7033 (mp10)
REVERT: E  128 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8807 (tp)
REVERT: E  143 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7653 (ttm-80)
REVERT: G   92 TYR cc_start: 0.9230 (t80) cc_final: 0.8990 (t80)
REVERT: e    8 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7577 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 223
  average time/residue: 1.5267
  time to fit residues: 372.6473
Evaluate side-chains
  224 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 208
  time to evaluate  : 1.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  462 LEU
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain C residue   96 LYS
Chi-restraints excluded: chain C residue  105 GLN
Chi-restraints excluded: chain E residue    6 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue  128 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain e residue    8 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 183 optimal weight:    0.9990
   chunk 154 optimal weight:    0.6980
   chunk 127 optimal weight:    0.5980
   chunk 105 optimal weight:    0.6980
   chunk 133 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 158 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 151 optimal weight:    0.6980
   chunk 145 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 683 GLN
E   8 ASN
** E  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.103462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.075448 restraints weight = 99509.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.2787 rms_B_bonded: 2.79
r_work: 0.2646 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2535 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2505
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2505 r_free = 0.2505    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2505 r_free = 0.2505    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2505
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8878
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  16137  Z= 0.169
  Angle     :  0.567   8.480  21939  Z= 0.307
  Chirality :  0.042   0.218   2633
  Planarity :  0.004   0.043   2637
  Dihedral  :  7.495  71.029   2268
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.84 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.18), residues: 2010
  helix:  2.08 (0.13), residues: 1527
  sheet: -0.01 (0.72), residues: 48
  loop :  0.04 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 101 
 HIS   0.007   0.001   HIS A 349 
 PHE   0.035   0.002   PHE A 352 
 TYR   0.025   0.002   TYR C  92 
 ARG   0.010   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05903 ( 1213)
  hydrogen bonds       : angle       4.34421 ( 3611)
  covalent geometry    : bond        0.00378 (16137)
  covalent geometry    : angle       0.56678 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 209
  time to evaluate  : 1.766 
Fit side-chains
REVERT: D   24 LYS cc_start: 0.8635 (mmmm) cc_final: 0.8422 (mppt)
REVERT: D  103 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7963 (mm-30)
REVERT: D  311 MET cc_start: 0.9374 (mtt) cc_final: 0.8998 (mtt)
REVERT: D  439 GLN cc_start: 0.8820 (tt0) cc_final: 0.8279 (pm20)
REVERT: D  488 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8556 (mm-30)
REVERT: A  207 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8154 (mp0)
REVERT: A  410 MET cc_start: 0.9452 (mtp) cc_final: 0.9217 (mtm)
REVERT: A  421 MET cc_start: 0.9098 (mtp) cc_final: 0.8877 (mtm)
REVERT: A  461 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7575 (mtpt)
REVERT: A  561 MET cc_start: 0.8338 (mmt) cc_final: 0.7931 (mmm)
REVERT: A  563 GLU cc_start: 0.8255 (pt0) cc_final: 0.7932 (pm20)
REVERT: A  605 MET cc_start: 0.9128 (mtp) cc_final: 0.8881 (mtt)
REVERT: B  142 ASP cc_start: 0.8753 (t0) cc_final: 0.8416 (t0)
REVERT: C   14 MET cc_start: 0.9103 (ttp) cc_final: 0.8898 (ttp)
REVERT: C   99 LYS cc_start: 0.8779 (mttm) cc_final: 0.8383 (mmtt)
REVERT: C  105 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7003 (mp10)
REVERT: E  128 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8809 (tp)
REVERT: E  143 ARG cc_start: 0.7965 (ttp-110) cc_final: 0.7652 (ttm-80)
REVERT: F    1 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6739 (tpp)
REVERT: G   92 TYR cc_start: 0.9225 (t80) cc_final: 0.8973 (t80)
REVERT: e    8 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7595 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 221
  average time/residue: 1.6439
  time to fit residues: 398.1352
Evaluate side-chains
  228 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 209
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  462 LEU
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain C residue  105 GLN
Chi-restraints excluded: chain E residue    8 ASN
Chi-restraints excluded: chain E residue   13 VAL
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue  128 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue  110 MET
Chi-restraints excluded: chain e residue    8 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 142 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 172 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9990
   chunk 188 optimal weight:    0.5980
   chunk 158 optimal weight:    2.9990
   chunk 161 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 683 GLN
E   8 ASN
** E  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.103655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.075575 restraints weight = 97808.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 2.73
r_work: 0.2651 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2540 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2513 r_free = 0.2513    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2513 r_free = 0.2513    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  16137  Z= 0.163
  Angle     :  0.560   8.303  21939  Z= 0.304
  Chirality :  0.042   0.215   2633
  Planarity :  0.004   0.043   2637
  Dihedral  :  7.448  70.491   2268
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.96 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.18), residues: 2010
  helix:  2.09 (0.13), residues: 1527
  sheet:  0.00 (0.72), residues: 48
  loop :  0.05 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 101 
 HIS   0.007   0.001   HIS A 349 
 PHE   0.035   0.002   PHE A 352 
 TYR   0.024   0.002   TYR C  92 
 ARG   0.010   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05830 ( 1213)
  hydrogen bonds       : angle       4.32928 ( 3611)
  covalent geometry    : bond        0.00363 (16137)
  covalent geometry    : angle       0.56023 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 212
  time to evaluate  : 1.876 
Fit side-chains
REVERT: D   24 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8427 (mppt)
REVERT: D  103 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7977 (mm-30)
REVERT: D  311 MET cc_start: 0.9371 (mtt) cc_final: 0.8996 (mtt)
REVERT: D  439 GLN cc_start: 0.8823 (tt0) cc_final: 0.8274 (pm20)
REVERT: D  488 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8554 (mm-30)
REVERT: A  207 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8157 (mp0)
REVERT: A  296 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8402 (mmtm)
REVERT: A  410 MET cc_start: 0.9451 (mtp) cc_final: 0.9226 (mtm)
REVERT: A  421 MET cc_start: 0.9096 (mtp) cc_final: 0.8871 (mtm)
REVERT: A  461 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7577 (mtpt)
REVERT: A  561 MET cc_start: 0.8276 (mmt) cc_final: 0.7871 (mmm)
REVERT: A  563 GLU cc_start: 0.8262 (pt0) cc_final: 0.7937 (pm20)
REVERT: A  587 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8373 (ttp-110)
REVERT: A  605 MET cc_start: 0.9122 (mtp) cc_final: 0.8874 (mtt)
REVERT: B  142 ASP cc_start: 0.8731 (t0) cc_final: 0.8394 (t0)
REVERT: C   14 MET cc_start: 0.9099 (ttp) cc_final: 0.8894 (ttp)
REVERT: C   62 THR cc_start: 0.8808 (p) cc_final: 0.8579 (m)
REVERT: C   99 LYS cc_start: 0.8777 (mttm) cc_final: 0.8384 (mmtt)
REVERT: C  105 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7041 (mp10)
REVERT: E  128 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8808 (tp)
REVERT: E  143 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7666 (ttm-80)
REVERT: F    1 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6734 (tpp)
REVERT: G   92 TYR cc_start: 0.9218 (t80) cc_final: 0.8962 (t80)
REVERT: e    8 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7471 (t0)
  outliers start: 21
  outliers final: 12
  residues processed: 226
  average time/residue: 1.5322
  time to fit residues: 377.8924
Evaluate side-chains
  228 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 210
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  276 LEU
Chi-restraints excluded: chain D residue  462 LEU
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain C residue  105 GLN
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue  128 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain G residue    4 VAL
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue  110 MET
Chi-restraints excluded: chain e residue    8 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 117 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 169 optimal weight:    1.9990
   chunk 151 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0070
   chunk 175 optimal weight:    0.2980
   chunk 164 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 164 GLN
A 683 GLN
C  50 GLN
E   8 ASN
** E  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.104504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.076349 restraints weight = 107245.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 2.85
r_work: 0.2663 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2552 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  16137  Z= 0.148
  Angle     :  0.545   8.251  21939  Z= 0.295
  Chirality :  0.041   0.210   2633
  Planarity :  0.004   0.043   2637
  Dihedral  :  7.306  68.275   2268
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.14 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.19), residues: 2010
  helix:  2.14 (0.13), residues: 1529
  sheet:  0.05 (0.72), residues: 48
  loop :  0.09 (0.32), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 101 
 HIS   0.007   0.001   HIS D 333 
 PHE   0.036   0.002   PHE A 352 
 TYR   0.024   0.002   TYR C  92 
 ARG   0.006   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05578 ( 1213)
  hydrogen bonds       : angle       4.26920 ( 3611)
  covalent geometry    : bond        0.00317 (16137)
  covalent geometry    : angle       0.54472 (21939)

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

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

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4020 Ramachandran restraints generated.
    2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 210
  time to evaluate  : 1.797 
Fit side-chains
REVERT: D   24 LYS cc_start: 0.8627 (mmmm) cc_final: 0.8404 (mppt)
REVERT: D  103 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8004 (mm-30)
REVERT: D  311 MET cc_start: 0.9351 (mtt) cc_final: 0.9000 (mtt)
REVERT: D  439 GLN cc_start: 0.8839 (tt0) cc_final: 0.8312 (pm20)
REVERT: D  488 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8546 (mm-30)
REVERT: A  207 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8162 (mp0)
REVERT: A  296 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8409 (mmtm)
REVERT: A  410 MET cc_start: 0.9457 (mtp) cc_final: 0.9235 (mtm)
REVERT: A  421 MET cc_start: 0.9097 (mtp) cc_final: 0.8868 (mtm)
REVERT: A  461 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7554 (mtpt)
REVERT: A  561 MET cc_start: 0.8281 (mmt) cc_final: 0.7903 (mmm)
REVERT: A  563 GLU cc_start: 0.8264 (pt0) cc_final: 0.7939 (pm20)
REVERT: A  587 ARG cc_start: 0.8637 (mtm110) cc_final: 0.8370 (ttp-110)
REVERT: A  605 MET cc_start: 0.9120 (mtp) cc_final: 0.8880 (mtt)
REVERT: B   59 ASP cc_start: 0.8587 (p0) cc_final: 0.8362 (p0)
REVERT: B  142 ASP cc_start: 0.8760 (t0) cc_final: 0.8384 (t0)
REVERT: C   14 MET cc_start: 0.9085 (ttp) cc_final: 0.8882 (ttp)
REVERT: C   62 THR cc_start: 0.8804 (p) cc_final: 0.8584 (m)
REVERT: C   99 LYS cc_start: 0.8785 (mttm) cc_final: 0.8400 (mmtt)
REVERT: C  105 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7126 (mp10)
REVERT: E  128 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8830 (tp)
REVERT: E  143 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7665 (ttm-80)
REVERT: G   92 TYR cc_start: 0.9213 (t80) cc_final: 0.8982 (t80)
  outliers start: 19
  outliers final: 14
  residues processed: 223
  average time/residue: 1.6070
  time to fit residues: 391.6714
Evaluate side-chains
  227 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 209
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  103 GLU
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   92 TYR
Chi-restraints excluded: chain C residue   96 LYS
Chi-restraints excluded: chain C residue  105 GLN
Chi-restraints excluded: chain E residue    8 ASN
Chi-restraints excluded: chain E residue   13 VAL
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue  128 ILE
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain G residue    4 VAL
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue  110 MET
Chi-restraints excluded: chain e residue    8 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 149 optimal weight:    0.1980
   chunk 170 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 189 optimal weight:    0.8980
   chunk 148 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:
E   8 ASN
** E  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 137 ASN
E 146 HIS
e   8 ASN
e  17 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.103956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.075926 restraints weight = 96591.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 2.73
r_work: 0.2654 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2545 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2527
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2527 r_free = 0.2527    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2527 r_free = 0.2527    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  16137  Z= 0.165
  Angle     :  0.560   8.170  21939  Z= 0.305
  Chirality :  0.042   0.212   2633
  Planarity :  0.004   0.043   2637
  Dihedral  :  7.315  67.092   2268
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.38 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.68 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.18), residues: 2010
  helix:  2.10 (0.13), residues: 1527
  sheet:  0.06 (0.72), residues: 48
  loop :  0.04 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP E 101 
 HIS   0.007   0.001   HIS A 349 
 PHE   0.035   0.002   PHE A 352 
 TYR   0.024   0.002   TYR C  92 
 ARG   0.009   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05798 ( 1213)
  hydrogen bonds       : angle       4.31482 ( 3611)
  covalent geometry    : bond        0.00367 (16137)
  covalent geometry    : angle       0.55975 (21939)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16952.19 seconds
wall clock time: 289 minutes 28.88 seconds (17368.88 seconds total)