Starting phenix.real_space_refine
on Thu Feb 13 20:48:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nf6_12296/02_2025/7nf6_12296.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nf6_12296/02_2025/7nf6_12296.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nf6_12296/02_2025/7nf6_12296.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nf6_12296/02_2025/7nf6_12296.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nf6_12296/02_2025/7nf6_12296.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nf6_12296/02_2025/7nf6_12296.cif"
  }
  resolution = 3.05
  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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       1      5.49       5
     S      49      5.16       5
     C    5754      2.51       5
     N    1417      2.21       5
     O    1595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8817
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 3506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3506
          Classifications: {'peptide': 455}
          Link IDs: {'PTRANS': 25, 'TRANS': 429}
    Chain: "A"
      Number of atoms: 5090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 623, 5090
          Classifications: {'peptide': 623}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 596}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 109
          Unusual residues: {' CA': 1, 'LBN': 1, 'NAG': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 5.90, per 1000 atoms: 0.67
  Number of scatterers: 8817
  At special positions: 0
  Unit cell: (87.8848, 95.5747, 139.517, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      49     16.00
     P       1     15.00
     O    1595      8.00
     N    1417      7.00
     C    5754      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS A 114 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 242 " - pdb=" SG  CYS A 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 571 " - pdb=" SG  CYS A 666 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 673 " - pdb=" SG  CYS A 685 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 703 " - " ASN A 513 "
      " NAG A 704 " - " ASN A 246 "
      " NAG A 705 " - " ASN A 228 "
      " NAG A 706 " - " ASN A 523 "
      " NAG C   1 " - " ASN A 332 "
      " NAG D   1 " - " ASN A 261 "
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2018

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      55.2% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 31 through 44
      removed outlier: 4.440A  pdb=" N   ILE B  39 " --> pdb=" O   GLY B  35 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY B  41 " --> pdb=" O   CYS B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 60
      removed outlier: 4.184A  pdb=" N   SER B  54 " --> pdb=" O   ILE B  50 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ASN B  58 " --> pdb=" O   SER B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 90
      removed outlier: 3.657A  pdb=" N   ILE B  67 " --> pdb=" O   GLY B  63 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   TRP B  69 " --> pdb=" O   CYS B  65 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU B  86 " --> pdb=" O   CYS B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 104
      removed outlier: 3.556A  pdb=" N   LEU B 100 " --> pdb=" O   GLU B  96 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA B 103 " --> pdb=" O   TYR B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 119
      removed outlier: 4.197A  pdb=" N   ALA B 109 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 137
      removed outlier: 3.708A  pdb=" N   SER B 133 " --> pdb=" O   CYS B 129 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU B 134 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   TYR B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 142
    Processing helix  chain 'B' and resid 147 through 169
      removed outlier: 3.506A  pdb=" N   ILE B 151 " --> pdb=" O   PRO B 147 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA B 155 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA B 167 " --> pdb=" O   SER B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 176
      removed outlier: 3.953A  pdb=" N   VAL B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 201
      removed outlier: 3.530A  pdb=" N   ALA B 182 " --> pdb=" O   ASN B 178 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   MET B 185 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL B 188 " --> pdb=" O   LYS B 184 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU B 199 " --> pdb=" O   GLY B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 231
      removed outlier: 3.585A  pdb=" N   SER B 222 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ASN B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ALA B 231 " --> pdb=" O   ASN B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 244
      removed outlier: 3.921A  pdb=" N   ILE B 241 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU B 243 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 258
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 259 through 276
      removed outlier: 3.586A  pdb=" N   MET B 270 " --> pdb=" O   CYS B 266 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   SER B 273 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE B 275 " --> pdb=" O   ASN B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 284
      removed outlier: 4.200A  pdb=" N   LEU B 284 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 298
      removed outlier: 3.647A  pdb=" N   ARG B 296 " --> pdb=" O   THR B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 323
      removed outlier: 3.501A  pdb=" N   ALA B 310 " --> pdb=" O   PRO B 306 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   THR B 323 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 334
      removed outlier: 4.182A  pdb=" N   LEU B 327 " --> pdb=" O   THR B 323 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   VAL B 328 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE B 329 " --> pdb=" O   GLY B 325 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL B 330 " --> pdb=" O   ARG B 326 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLU B 334 " --> pdb=" O   VAL B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 351 through 367
      removed outlier: 3.502A  pdb=" N   MET B 360 " --> pdb=" O   MET B 356 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE B 361 " --> pdb=" O   PHE B 357 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA B 362 " --> pdb=" O   HIS B 358 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ILE B 364 " --> pdb=" O   MET B 360 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE B 367 " --> pdb=" O   ILE B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 399
      removed outlier: 3.603A  pdb=" N   ASN B 376 " --> pdb=" O   ASN B 372 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR B 377 " --> pdb=" O   SER B 373 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA B 381 " --> pdb=" O   TYR B 377 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TRP B 383 " --> pdb=" O   SER B 379 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE B 385 " --> pdb=" O   ALA B 381 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE B 390 " --> pdb=" O   TYR B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 432
      removed outlier: 3.774A  pdb=" N   ILE B 415 " --> pdb=" O   ILE B 411 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 416 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE B 423 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      Proline residue:  B 428  - end of helix
    Processing helix  chain 'B' and resid 434 through 455
      removed outlier: 4.013A  pdb=" N   LEU B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR B 439 " --> pdb=" O   TRP B 435 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET B 444 " --> pdb=" O   CYS B 440 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   PHE B 452 " --> pdb=" O   LEU B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 478
      removed outlier: 3.781A  pdb=" N   GLN B 463 " --> pdb=" O   PHE B 459 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LYS B 464 " --> pdb=" O   GLY B 460 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE B 465 " --> pdb=" O   TRP B 461 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER B 466 " --> pdb=" O   ALA B 462 " (cutoff:3.500A)
      Proline residue:  B 468  - end of helix
      removed outlier: 3.829A  pdb=" N   MET B 471 " --> pdb=" O   LYS B 467 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   HIS B 472 " --> pdb=" O   PRO B 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 77
      removed outlier: 3.742A  pdb=" N   LEU A  73 " --> pdb=" O   PRO A  69 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLN A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   PHE A  76 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 111
      removed outlier: 3.648A  pdb=" N   GLU A  87 " --> pdb=" O   ARG A  83 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE A 105 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ILE A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 121
      removed outlier: 4.114A  pdb=" N   GLY A 121 " --> pdb=" O   TRP A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 131
      removed outlier: 3.975A  pdb=" N   PHE A 131 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 148
      removed outlier: 3.578A  pdb=" N   LYS A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 153
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 189 through 203
      removed outlier: 3.600A  pdb=" N   LYS A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 228
      removed outlier: 3.609A  pdb=" N   ASN A 228 " --> pdb=" O   GLN A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
      removed outlier: 3.762A  pdb=" N   THR A 234 " --> pdb=" O   GLY A 231 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASP A 235 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 306
      removed outlier: 3.890A  pdb=" N   GLN A 293 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS A 306 " --> pdb=" O   PHE A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 344
      No H-bonds generated for 'chain 'A' and resid 342 through 344'
    Processing helix  chain 'A' and resid 356 through 368
      removed outlier: 3.752A  pdb=" N   ILE A 360 " --> pdb=" O   GLY A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 398
      removed outlier: 3.522A  pdb=" N   VAL A 395 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 416
      removed outlier: 3.521A  pdb=" N   LYS A 415 " --> pdb=" O   TYR A 412 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 416 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 412 through 416'
    Processing helix  chain 'A' and resid 420 through 435
      removed outlier: 3.664A  pdb=" N   VAL A 427 " --> pdb=" O   SER A 423 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASN A 434 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 458 through 460
      No H-bonds generated for 'chain 'A' and resid 458 through 460'
    Processing helix  chain 'A' and resid 461 through 472
      removed outlier: 3.549A  pdb=" N   VAL A 469 " --> pdb=" O   MET A 465 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR A 471 " --> pdb=" O   MET A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 519
      removed outlier: 3.504A  pdb=" N   ALA A 517 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 542
    Processing helix  chain 'A' and resid 547 through 561
      removed outlier: 3.529A  pdb=" N   LEU A 557 " --> pdb=" O   GLN A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 590
      removed outlier: 3.857A  pdb=" N   ILE A 589 " --> pdb=" O   LEU A 586 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ASN A 590 " --> pdb=" O   ASP A 587 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 586 through 590'
    Processing helix  chain 'A' and resid 606 through 611
      removed outlier: 4.176A  pdb=" N   MET A 610 " --> pdb=" O   ASN A 606 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 344 through 345
    Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 409
      removed outlier: 6.762A  pdb=" N   MET A 381 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   PHE A 409 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   THR A 383 " --> pdb=" O   PHE A 409 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 310 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 170
      removed outlier: 7.137A  pdb=" N   LYS A 167 " --> pdb=" O   GLU A 178 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ALA A 176 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240
      removed outlier: 3.776A  pdb=" N   GLN A 272 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 245
    Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 330
      removed outlier: 4.135A  pdb=" N   ALA A 329 " --> pdb=" O   HIS A 347 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 632 through 634
      removed outlier: 3.623A  pdb=" N   ARG A 619 " --> pdb=" O   GLU A 649 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ILE A 647 " --> pdb=" O   ARG A 621 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   SER A 623 " --> pdb=" O   GLY A 645 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   GLY A 645 " --> pdb=" O   SER A 623 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 603 through 605
    Processing sheet with id=AA9, first strand: chain 'A' and resid 673 through 675

    371 hydrogen bonds defined for protein.
    1035 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.83

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1546
        1.33 -     1.45: 2438
        1.45 -     1.57: 4988
        1.57 -     1.70: 2
        1.70 -     1.82: 81
  Bond restraints: 9055
  Sorted by residual:
  bond pdb=" C9  LBN A 701 "
       pdb=" O2  LBN A 701 "
    ideal  model  delta    sigma   weight residual
    1.409  1.455 -0.046 2.00e-02 2.50e+03 5.35e+00
  bond pdb=" O2  LBN A 701 "
       pdb=" P1  LBN A 701 "
    ideal  model  delta    sigma   weight residual
    1.650  1.605  0.045 2.00e-02 2.50e+03 5.07e+00
  bond pdb=" C1  LBN A 701 "
       pdb=" O1  LBN A 701 "
    ideal  model  delta    sigma   weight residual
    1.410  1.453 -0.043 2.00e-02 2.50e+03 4.71e+00
  bond pdb=" C11 LBN A 701 "
       pdb=" C8  LBN A 701 "
    ideal  model  delta    sigma   weight residual
    1.530  1.493  0.037 2.00e-02 2.50e+03 3.50e+00
  bond pdb=" N   ALA A  66 "
       pdb=" CA  ALA A  66 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.024 1.29e-02 6.01e+03 3.34e+00
  ... (remaining 9050 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 12007
        1.95 -     3.90: 269
        3.90 -     5.86: 33
        5.86 -     7.81: 9
        7.81 -     9.76: 4
  Bond angle restraints: 12322
  Sorted by residual:
  angle pdb=" C   GLU B  96 "
        pdb=" N   TYR B  97 "
        pdb=" CA  TYR B  97 "
      ideal   model   delta    sigma   weight residual
     120.09  125.56   -5.47 1.25e+00 6.40e-01 1.92e+01
  angle pdb=" C   PHE A 173 "
        pdb=" N   ARG A 174 "
        pdb=" CA  ARG A 174 "
      ideal   model   delta    sigma   weight residual
     121.54  129.78   -8.24 1.91e+00 2.74e-01 1.86e+01
  angle pdb=" CA  TYR A  65 "
        pdb=" CB  TYR A  65 "
        pdb=" CG  TYR A  65 "
      ideal   model   delta    sigma   weight residual
     113.90  120.26   -6.36 1.80e+00 3.09e-01 1.25e+01
  angle pdb=" C   TYR A  65 "
        pdb=" N   ALA A  66 "
        pdb=" CA  ALA A  66 "
      ideal   model   delta    sigma   weight residual
     121.54  127.72   -6.18 1.91e+00 2.74e-01 1.05e+01
  angle pdb=" N   LYS A  70 "
        pdb=" CA  LYS A  70 "
        pdb=" C   LYS A  70 "
      ideal   model   delta    sigma   weight residual
     111.02  114.55   -3.53 1.22e+00 6.72e-01 8.35e+00
  ... (remaining 12317 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.26: 5112
       26.26 -    52.52: 361
       52.52 -    78.78: 42
       78.78 -   105.05: 9
      105.05 -   131.31: 4
  Dihedral angle restraints: 5528
    sinusoidal: 2383
      harmonic: 3145
  Sorted by residual:
  dihedral pdb=" CA  ARG A 174 "
           pdb=" C   ARG A 174 "
           pdb=" N   HIS A 175 "
           pdb=" CA  HIS A 175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.18   42.82     0      5.00e+00 4.00e-02 7.33e+01
  dihedral pdb=" CA  GLN A  79 "
           pdb=" C   GLN A  79 "
           pdb=" N   ALA A  80 "
           pdb=" CA  ALA A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.31  -27.69     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CA  TYR A  65 "
           pdb=" C   TYR A  65 "
           pdb=" N   ALA A  66 "
           pdb=" CA  ALA A  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.49  -22.51     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 5525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1314
       0.086 -    0.172: 82
       0.172 -    0.259: 1
       0.259 -    0.345: 2
       0.345 -    0.431: 1
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 4.30e+01
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 246 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.97   -0.43 2.00e-01 2.50e+01 4.64e+00
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 513 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.72    0.32 2.00e-01 2.50e+01 2.57e+00
  ... (remaining 1397 not shown)

  Planarity restraints: 1526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 523 "    0.233 2.00e-02 2.50e+03   3.33e-01 1.38e+03
        pdb=" CG  ASN A 523 "   -0.117 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 523 "    0.026 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 523 "   -0.559 2.00e-02 2.50e+03
        pdb=" C1  NAG A 706 "    0.416 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 513 "   -0.080 2.00e-02 2.50e+03   2.29e-01 6.58e+02
        pdb=" CG  ASN A 513 "   -0.062 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 513 "    0.228 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 513 "   -0.357 2.00e-02 2.50e+03
        pdb=" C1  NAG A 703 "    0.271 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 246 "   -0.037 2.00e-02 2.50e+03   1.67e-01 3.49e+02
        pdb=" CG  ASN A 246 "   -0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 246 "    0.154 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 246 "   -0.275 2.00e-02 2.50e+03
        pdb=" C1  NAG A 704 "    0.194 2.00e-02 2.50e+03
  ... (remaining 1523 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 177
        2.67 -     3.23: 8456
        3.23 -     3.79: 13271
        3.79 -     4.34: 19237
        4.34 -     4.90: 31117
  Nonbonded interactions: 72258
  Sorted by model distance:
  nonbonded pdb=" O   GLY B  47 "
            pdb=" OG  SER B  51 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OG  SER B 345 "
            pdb=" O   ARG B 348 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   LEU A 565 "
            pdb=" NH2 ARG A 584 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" OG1 THR A 471 "
            pdb=" OH  TYR A 582 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" NE2 GLN B 474 "
            pdb=" O   VAL B 479 "
     model   vdw
     2.281 3.120
  ... (remaining 72253 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     23.150
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
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      :  0.006   0.049   9055  Z= 0.396
  Angle     :  0.746   9.759  12322  Z= 0.416
  Chirality :  0.047   0.431   1400
  Planarity :  0.005   0.043   1520
  Dihedral  : 17.273 131.306   3498
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.03 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  8.17 %
    Allowed  : 22.27 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.80 (0.19), residues: 1074
  helix: -4.12 (0.12), residues: 486
  sheet: -2.26 (0.45), residues: 88
  loop : -2.20 (0.24), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 383 
 HIS   0.008   0.001   HIS A 175 
 PHE   0.023   0.001   PHE A 407 
 TYR   0.019   0.001   TYR A  65 
 ARG   0.002   0.000   ARG B 400 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 143
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
REVERT: B   71 MET cc_start: 0.7689 (ttt) cc_final: 0.7288 (ttt)
REVERT: B  233 ASP cc_start: 0.8265 (t70) cc_final: 0.7786 (t70)
REVERT: B  237 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7955 (mp10)
REVERT: B  244 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7166 (tm-30)
REVERT: B  338 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8751 (tp)
REVERT: B  356 MET cc_start: 0.6922 (mmm) cc_final: 0.6637 (mmt)
REVERT: B  360 MET cc_start: 0.7974 (ttp) cc_final: 0.7408 (tmm)
REVERT: B  436 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7395 (mm-30)
REVERT: B  471 MET cc_start: 0.7639 (pp-130) cc_final: 0.7432 (ppp)
REVERT: A  284 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8078 (m-30)
REVERT: A  377 ARG cc_start: 0.8259 (mtp85) cc_final: 0.8020 (mtp180)
REVERT: A  465 MET cc_start: 0.9099 (tpt) cc_final: 0.8816 (mmm)
REVERT: A  495 ASN cc_start: 0.8308 (t0) cc_final: 0.7849 (t0)
REVERT: A  524 HIS cc_start: 0.7906 (p90) cc_final: 0.7688 (p-80)
REVERT: A  574 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7777 (ppp-140)
REVERT: A  662 PHE cc_start: 0.8497 (m-80) cc_final: 0.7648 (m-80)
  outliers start: 77
  outliers final: 44
  residues processed: 206
  average time/residue: 0.2491
  time to fit residues: 68.0826
Evaluate side-chains
  171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 121
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  207 PHE
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  237 GLN
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  431 SER
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  670 ASN
Chi-restraints excluded: chain A residue  675 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0040
   chunk 83 optimal weight:    0.5980
   chunk 32 optimal weight:    8.9990
   chunk 50 optimal weight:    0.0980
   chunk 62 optimal weight:    0.0980
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.2992

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

Flipped N/Q/H residues before XYZ refinement:
B 148 GLN
B 203 ASN
B 251 ASN
B 372 ASN
B 456 HIS
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
A  79 GLN
A 146 GLN
A 156 ASN
A 181 GLN
A 220 HIS
A 224 GLN
A 282 GLN
A 293 GLN
A 301 GLN
A 335 GLN
A 345 GLN
A 366 GLN
A 370 GLN
A 403 GLN
A 442 ASN
A 510 GLN
A 544 GLN
A 561 ASN
A 575 ASN
A 606 ASN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.152105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.099620 restraints weight = 10522.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.51
r_work: 0.2864 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9055  Z= 0.189
  Angle     :  0.663   8.467  12322  Z= 0.341
  Chirality :  0.044   0.286   1400
  Planarity :  0.005   0.039   1520
  Dihedral  : 11.370 126.899   1600
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.10 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 23.22 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.79 (0.22), residues: 1074
  helix: -1.92 (0.19), residues: 507
  sheet: -1.93 (0.44), residues: 80
  loop : -1.59 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 383 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.014   0.001   PHE A 407 
 TYR   0.015   0.001   TYR A  65 
 ARG   0.006   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 133
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  205 ARG cc_start: 0.6881 (ttt90) cc_final: 0.6641 (ttm-80)
REVERT: B  233 ASP cc_start: 0.8458 (t70) cc_final: 0.7970 (t70)
REVERT: B  278 MET cc_start: 0.8923 (ptp) cc_final: 0.8574 (ptp)
REVERT: B  356 MET cc_start: 0.7496 (mmm) cc_final: 0.7037 (mmt)
REVERT: B  360 MET cc_start: 0.8440 (ttp) cc_final: 0.8045 (tmm)
REVERT: B  394 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7723 (mt)
REVERT: B  436 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7256 (mm-30)
REVERT: B  444 MET cc_start: 0.7869 (mpp) cc_final: 0.7340 (mtt)
REVERT: A  240 HIS cc_start: 0.8013 (t70) cc_final: 0.7715 (m90)
REVERT: A  243 ASN cc_start: 0.8062 (m-40) cc_final: 0.7314 (p0)
REVERT: A  245 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7574 (mp0)
REVERT: A  250 ILE cc_start: 0.8694 (pp) cc_final: 0.8129 (mp)
REVERT: A  284 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8890 (m-30)
REVERT: A  377 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8527 (mtp180)
REVERT: A  465 MET cc_start: 0.9199 (tpt) cc_final: 0.8982 (mmm)
REVERT: A  495 ASN cc_start: 0.8695 (t0) cc_final: 0.8224 (t0)
  outliers start: 51
  outliers final: 27
  residues processed: 173
  average time/residue: 0.2551
  time to fit residues: 58.8112
Evaluate side-chains
  149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  175 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  454 PHE
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  403 GLN
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  670 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0270
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
A 403 GLN
A 561 ASN
A 613 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.152291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.094174 restraints weight = 10962.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 2.80
r_work: 0.2808 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9055  Z= 0.247
  Angle     :  0.640   8.902  12322  Z= 0.325
  Chirality :  0.045   0.316   1400
  Planarity :  0.005   0.039   1520
  Dihedral  :  9.920 129.450   1548
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.10 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 22.69 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.81 (0.24), residues: 1074
  helix: -0.81 (0.22), residues: 506
  sheet: -1.68 (0.44), residues: 80
  loop : -1.42 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 383 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.019   0.001   PHE A 407 
 TYR   0.015   0.001   TYR A  65 
 ARG   0.006   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 122
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 GLU cc_start: 0.8576 (tp30) cc_final: 0.8054 (tp30)
REVERT: B  175 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5939 (m-80)
REVERT: B  233 ASP cc_start: 0.8527 (t70) cc_final: 0.7936 (t70)
REVERT: B  278 MET cc_start: 0.8901 (ptp) cc_final: 0.8489 (ptp)
REVERT: B  356 MET cc_start: 0.7457 (mmm) cc_final: 0.7045 (mmt)
REVERT: B  360 MET cc_start: 0.8494 (ttp) cc_final: 0.8151 (tmm)
REVERT: B  435 TRP cc_start: 0.7318 (m-90) cc_final: 0.6178 (m-10)
REVERT: B  436 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7164 (mm-30)
REVERT: B  444 MET cc_start: 0.7918 (mpp) cc_final: 0.7231 (mtt)
REVERT: A  240 HIS cc_start: 0.8135 (t70) cc_final: 0.7865 (t70)
REVERT: A  245 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7837 (mp0)
REVERT: A  273 CYS cc_start: 0.8729 (m) cc_final: 0.8522 (m)
REVERT: A  284 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8869 (m-30)
REVERT: A  377 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8647 (mtp180)
REVERT: A  465 MET cc_start: 0.9233 (tpt) cc_final: 0.9011 (mmm)
REVERT: A  546 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7701 (mtp180)
  outliers start: 52
  outliers final: 31
  residues processed: 161
  average time/residue: 0.2696
  time to fit residues: 56.6136
Evaluate side-chains
  145 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  175 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  379 SER
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  403 GLN
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  670 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0870
   chunk 16 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0970
   chunk 23 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
A 403 GLN
A 466 ASN
A 561 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.155356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.100256 restraints weight = 10811.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.63
r_work: 0.2851 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9055  Z= 0.198
  Angle     :  0.608   8.080  12322  Z= 0.306
  Chirality :  0.044   0.317   1400
  Planarity :  0.004   0.038   1520
  Dihedral  :  9.248 130.015   1539
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.10 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 23.44 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.22 (0.25), residues: 1074
  helix: -0.22 (0.24), residues: 506
  sheet: -1.57 (0.44), residues: 80
  loop : -1.22 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 383 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.016   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A  65 
 ARG   0.004   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 118
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 GLU cc_start: 0.8528 (tp30) cc_final: 0.8088 (tp30)
REVERT: B  175 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.6003 (m-80)
REVERT: B  233 ASP cc_start: 0.8497 (t70) cc_final: 0.7888 (t70)
REVERT: B  278 MET cc_start: 0.8792 (ptp) cc_final: 0.8513 (ptp)
REVERT: B  356 MET cc_start: 0.7419 (mmm) cc_final: 0.6997 (mmt)
REVERT: B  360 MET cc_start: 0.8377 (ttp) cc_final: 0.8039 (tmm)
REVERT: B  435 TRP cc_start: 0.7342 (m-90) cc_final: 0.6206 (m-10)
REVERT: B  436 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7179 (mm-30)
REVERT: B  444 MET cc_start: 0.7931 (mpp) cc_final: 0.7274 (mtt)
REVERT: A  240 HIS cc_start: 0.8213 (t70) cc_final: 0.7988 (t70)
REVERT: A  245 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7614 (mp0)
REVERT: A  284 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8956 (m-30)
REVERT: A  377 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8644 (mtp180)
REVERT: A  465 MET cc_start: 0.9140 (tpt) cc_final: 0.8935 (mmm)
REVERT: A  546 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7747 (mtp180)
  outliers start: 46
  outliers final: 27
  residues processed: 153
  average time/residue: 0.2272
  time to fit residues: 48.2369
Evaluate side-chains
  142 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  175 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  403 GLN
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  670 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
A 403 GLN
A 561 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.151204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.092770 restraints weight = 10601.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.52
r_work: 0.2834 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9055  Z= 0.275
  Angle     :  0.624   8.116  12322  Z= 0.313
  Chirality :  0.045   0.318   1400
  Planarity :  0.004   0.038   1520
  Dihedral  :  8.987 130.053   1536
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.28 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 23.75 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.06 (0.25), residues: 1074
  helix: -0.01 (0.24), residues: 502
  sheet: -1.62 (0.43), residues: 90
  loop : -1.17 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 383 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.026   0.001   PHE A 407 
 TYR   0.015   0.001   TYR A  65 
 ARG   0.003   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 109
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 GLU cc_start: 0.8527 (tp30) cc_final: 0.8114 (tp30)
REVERT: B  175 TYR cc_start: 0.6404 (OUTLIER) cc_final: 0.5979 (m-80)
REVERT: B  233 ASP cc_start: 0.8504 (t70) cc_final: 0.7896 (t70)
REVERT: B  356 MET cc_start: 0.7404 (mmm) cc_final: 0.6975 (mmt)
REVERT: B  360 MET cc_start: 0.8364 (ttp) cc_final: 0.8119 (tmm)
REVERT: B  435 TRP cc_start: 0.7349 (m-90) cc_final: 0.6210 (m-10)
REVERT: B  436 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7181 (mm-30)
REVERT: A  240 HIS cc_start: 0.8245 (t70) cc_final: 0.8023 (t70)
REVERT: A  284 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8863 (m-30)
REVERT: A  377 ARG cc_start: 0.8869 (mtp85) cc_final: 0.8649 (mtp180)
REVERT: A  418 LYS cc_start: 0.8933 (mttp) cc_final: 0.8704 (mmmt)
REVERT: A  465 MET cc_start: 0.9169 (tpt) cc_final: 0.8950 (mmm)
REVERT: A  546 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7759 (mtp180)
  outliers start: 46
  outliers final: 31
  residues processed: 145
  average time/residue: 0.2299
  time to fit residues: 45.3783
Evaluate side-chains
  138 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  175 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  403 GLN
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  670 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0070
   chunk 105 optimal weight:    0.3980
   chunk 100 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.3376

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

Flipped N/Q/H residues before XYZ refinement:
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
A 403 GLN
A 679 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.157000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.096193 restraints weight = 10726.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 2.67
r_work: 0.2860 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9055  Z= 0.171
  Angle     :  0.590   8.102  12322  Z= 0.296
  Chirality :  0.043   0.315   1400
  Planarity :  0.004   0.038   1520
  Dihedral  :  8.647 127.874   1535
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.10 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 24.50 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.26), residues: 1074
  helix:  0.27 (0.24), residues: 508
  sheet: -1.33 (0.45), residues: 80
  loop : -1.04 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 383 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.013   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A  65 
 ARG   0.003   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 116
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.8512 (tpt) cc_final: 0.8267 (tpt)
REVERT: B  102 GLU cc_start: 0.8559 (tp30) cc_final: 0.8173 (tp30)
REVERT: B  175 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5832 (m-80)
REVERT: B  233 ASP cc_start: 0.8496 (t70) cc_final: 0.7889 (t70)
REVERT: B  356 MET cc_start: 0.7457 (mmm) cc_final: 0.7040 (mmt)
REVERT: B  360 MET cc_start: 0.8345 (ttp) cc_final: 0.8116 (tmm)
REVERT: B  390 ILE cc_start: 0.8279 (mm) cc_final: 0.7991 (mm)
REVERT: B  405 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7844 (mtt90)
REVERT: B  435 TRP cc_start: 0.7179 (m-90) cc_final: 0.6090 (m-10)
REVERT: B  436 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7164 (mm-30)
REVERT: B  444 MET cc_start: 0.7957 (mpp) cc_final: 0.7186 (mtt)
REVERT: A  284 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8943 (m-30)
REVERT: A  377 ARG cc_start: 0.8855 (mtp85) cc_final: 0.8628 (mtp180)
REVERT: A  418 LYS cc_start: 0.8956 (mttp) cc_final: 0.8691 (mmmt)
REVERT: A  656 LEU cc_start: 0.8379 (mp) cc_final: 0.8164 (mp)
  outliers start: 40
  outliers final: 25
  residues processed: 148
  average time/residue: 0.2456
  time to fit residues: 49.5704
Evaluate side-chains
  139 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  175 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  405 ARG
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  670 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 102 optimal weight:    6.9990
   chunk 78 optimal weight:    0.2980
   chunk 4 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.154115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.094861 restraints weight = 10746.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 2.55
r_work: 0.2856 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9055  Z= 0.216
  Angle     :  0.605   7.974  12322  Z= 0.302
  Chirality :  0.044   0.318   1400
  Planarity :  0.004   0.038   1520
  Dihedral  :  8.291 125.828   1528
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.00 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 24.81 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1074
  helix:  0.37 (0.24), residues: 508
  sheet: -1.44 (0.44), residues: 90
  loop : -1.00 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 383 
 HIS   0.008   0.001   HIS A 175 
 PHE   0.020   0.001   PHE A 407 
 TYR   0.015   0.001   TYR A  65 
 ARG   0.004   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 114
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.8473 (tpt) cc_final: 0.8237 (tpt)
REVERT: B  102 GLU cc_start: 0.8528 (tp30) cc_final: 0.8148 (tp30)
REVERT: B  175 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5882 (m-80)
REVERT: B  233 ASP cc_start: 0.8486 (t70) cc_final: 0.7906 (t70)
REVERT: B  356 MET cc_start: 0.7468 (mmm) cc_final: 0.7055 (mmt)
REVERT: B  360 MET cc_start: 0.8369 (ttp) cc_final: 0.8113 (tmm)
REVERT: B  390 ILE cc_start: 0.8221 (mm) cc_final: 0.7965 (mm)
REVERT: B  435 TRP cc_start: 0.7171 (m-90) cc_final: 0.6065 (m-10)
REVERT: B  436 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7173 (mm-30)
REVERT: A  284 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8899 (m-30)
REVERT: A  377 ARG cc_start: 0.8878 (mtp85) cc_final: 0.8641 (mtp180)
REVERT: A  418 LYS cc_start: 0.8907 (mttp) cc_final: 0.8644 (mmmt)
REVERT: A  656 LEU cc_start: 0.8388 (mp) cc_final: 0.8177 (mp)
REVERT: A  679 ASN cc_start: 0.8495 (t0) cc_final: 0.8204 (t0)
  outliers start: 38
  outliers final: 28
  residues processed: 144
  average time/residue: 0.2244
  time to fit residues: 44.3367
Evaluate side-chains
  141 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 110
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  175 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  670 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0570
   chunk 44 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 49 optimal weight:    0.1980
   chunk 58 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0070
   overall best weight:    0.3516

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

Flipped N/Q/H residues before XYZ refinement:
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.155906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.097361 restraints weight = 10835.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.47
r_work: 0.2922 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9055  Z= 0.169
  Angle     :  0.584   8.006  12322  Z= 0.291
  Chirality :  0.043   0.316   1400
  Planarity :  0.004   0.037   1520
  Dihedral  :  8.172 121.821   1528
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.00 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 24.60 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.26), residues: 1074
  helix:  0.56 (0.24), residues: 509
  sheet: -1.29 (0.45), residues: 88
  loop : -0.98 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 383 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.018   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A  65 
 ARG   0.004   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 119
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.8484 (tpt) cc_final: 0.8208 (tpt)
REVERT: B  102 GLU cc_start: 0.8486 (tp30) cc_final: 0.8132 (tp30)
REVERT: B  175 TYR cc_start: 0.6235 (OUTLIER) cc_final: 0.5985 (m-80)
REVERT: B  233 ASP cc_start: 0.8468 (t70) cc_final: 0.7874 (t70)
REVERT: B  356 MET cc_start: 0.7404 (mmm) cc_final: 0.6996 (mmt)
REVERT: B  360 MET cc_start: 0.8388 (ttp) cc_final: 0.8122 (tmm)
REVERT: B  390 ILE cc_start: 0.8242 (mm) cc_final: 0.7960 (mm)
REVERT: B  405 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7839 (mtt90)
REVERT: B  435 TRP cc_start: 0.7227 (m-90) cc_final: 0.6147 (m-10)
REVERT: B  436 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7203 (mm-30)
REVERT: B  445 LEU cc_start: 0.7574 (mt) cc_final: 0.7334 (mm)
REVERT: A  377 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8629 (mtp180)
REVERT: A  418 LYS cc_start: 0.8879 (mttp) cc_final: 0.8663 (mmmt)
REVERT: A  546 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7784 (mtp180)
REVERT: A  656 LEU cc_start: 0.8437 (mp) cc_final: 0.8222 (mp)
REVERT: A  679 ASN cc_start: 0.8508 (t0) cc_final: 0.8235 (t0)
  outliers start: 37
  outliers final: 26
  residues processed: 147
  average time/residue: 0.2253
  time to fit residues: 45.6055
Evaluate side-chains
  142 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  175 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  405 ARG
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  546 ARG
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  670 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 38 optimal weight:    0.4980
   chunk 85 optimal weight:    0.1980
   chunk 20 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0870
   chunk 76 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0370
   chunk 96 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
A 561 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.156220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.102228 restraints weight = 10726.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 2.79
r_work: 0.2897 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9055  Z= 0.159
  Angle     :  0.580   8.075  12322  Z= 0.288
  Chirality :  0.043   0.315   1400
  Planarity :  0.004   0.037   1520
  Dihedral  :  8.012 116.891   1526
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.72 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 25.45 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.26), residues: 1074
  helix:  0.72 (0.24), residues: 508
  sheet: -1.27 (0.45), residues: 88
  loop : -0.95 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 383 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.017   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A  65 
 ARG   0.004   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.8490 (tpt) cc_final: 0.8190 (tpt)
REVERT: B  102 GLU cc_start: 0.8516 (tp30) cc_final: 0.8113 (tp30)
REVERT: B  175 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.6006 (m-80)
REVERT: B  233 ASP cc_start: 0.8490 (t70) cc_final: 0.7856 (t70)
REVERT: B  356 MET cc_start: 0.7432 (mmm) cc_final: 0.7015 (mmt)
REVERT: B  360 MET cc_start: 0.8370 (ttp) cc_final: 0.8101 (tmm)
REVERT: B  390 ILE cc_start: 0.8112 (mm) cc_final: 0.7859 (mm)
REVERT: B  405 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7833 (mtt90)
REVERT: B  435 TRP cc_start: 0.7016 (m-90) cc_final: 0.5913 (m-10)
REVERT: B  436 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7123 (mm-30)
REVERT: B  445 LEU cc_start: 0.7489 (mt) cc_final: 0.7248 (mm)
REVERT: A  377 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8628 (mtp180)
REVERT: A  418 LYS cc_start: 0.8876 (mttp) cc_final: 0.8628 (mmmt)
REVERT: A  679 ASN cc_start: 0.8518 (t0) cc_final: 0.8279 (t0)
  outliers start: 32
  outliers final: 25
  residues processed: 141
  average time/residue: 0.2463
  time to fit residues: 47.5834
Evaluate side-chains
  142 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  175 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  405 ARG
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  663 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 76 optimal weight:    0.1980
   chunk 80 optimal weight:    0.0770
   chunk 44 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.156031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.096791 restraints weight = 10754.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.55
r_work: 0.2885 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9055  Z= 0.183
  Angle     :  0.593   8.048  12322  Z= 0.296
  Chirality :  0.043   0.322   1400
  Planarity :  0.004   0.041   1520
  Dihedral  :  7.910 113.498   1524
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.00 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 25.87 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.26), residues: 1074
  helix:  0.79 (0.24), residues: 507
  sheet: -1.24 (0.45), residues: 88
  loop : -0.92 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 383 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.019   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A  65 
 ARG   0.005   0.000   ARG A 658 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.8355 (tpt) cc_final: 0.8125 (tpt)
REVERT: B  102 GLU cc_start: 0.8504 (tp30) cc_final: 0.8034 (tp30)
REVERT: B  233 ASP cc_start: 0.8452 (t70) cc_final: 0.7824 (t70)
REVERT: B  360 MET cc_start: 0.8350 (ttp) cc_final: 0.8064 (tmm)
REVERT: B  390 ILE cc_start: 0.8102 (mm) cc_final: 0.7864 (mm)
REVERT: B  405 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7809 (mtt90)
REVERT: B  435 TRP cc_start: 0.7090 (m-90) cc_final: 0.5952 (m-10)
REVERT: B  436 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7134 (mm-30)
REVERT: B  445 LEU cc_start: 0.7495 (mt) cc_final: 0.7271 (mm)
REVERT: A  377 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8616 (mtp180)
REVERT: A  418 LYS cc_start: 0.8869 (mttp) cc_final: 0.8616 (mmmt)
REVERT: A  546 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7467 (mtp180)
REVERT: A  679 ASN cc_start: 0.8518 (t0) cc_final: 0.8268 (t0)
  outliers start: 29
  outliers final: 24
  residues processed: 136
  average time/residue: 0.2382
  time to fit residues: 43.8728
Evaluate side-chains
  142 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  348 ARG
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  405 ARG
Chi-restraints excluded: chain B residue  436 GLU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  426 GLU
Chi-restraints excluded: chain A residue  433 GLU
Chi-restraints excluded: chain A residue  493 ASN
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  546 ARG
Chi-restraints excluded: chain A residue  563 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 98 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 85 optimal weight:    0.1980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.154258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.094702 restraints weight = 10777.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.56
r_work: 0.2853 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2689 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9055  Z= 0.251
  Angle     :  0.620   8.147  12322  Z= 0.309
  Chirality :  0.045   0.320   1400
  Planarity :  0.004   0.043   1520
  Dihedral  :  7.953 110.849   1524
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.28 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 25.56 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.26), residues: 1074
  helix:  0.72 (0.24), residues: 507
  sheet: -1.26 (0.46), residues: 88
  loop : -0.91 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 443 
 HIS   0.009   0.001   HIS A 175 
 PHE   0.022   0.001   PHE A 407 
 TYR   0.016   0.001   TYR A  65 
 ARG   0.004   0.000   ARG A 658 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6191.39 seconds
wall clock time: 110 minutes 23.70 seconds (6623.70 seconds total)