Starting phenix.real_space_refine
on Sat Aug 23 01:34:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p27_17358/08_2025/8p27_17358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p27_17358/08_2025/8p27_17358.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p27_17358/08_2025/8p27_17358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p27_17358/08_2025/8p27_17358.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p27_17358/08_2025/8p27_17358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p27_17358/08_2025/8p27_17358.map"
  }
  resolution = 2.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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
     P       6      5.49       5
     Mg      2      5.21       5
     S      54      5.16       5
     C    5564      2.51       5
     N    1517      2.21       5
     O    1667      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8810
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 544, 4372
          Classifications: {'peptide': 544}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 523}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 4376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4376
          Classifications: {'peptide': 545}
          Incomplete info: {'backbone_only': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 524}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 31
          Unusual residues: {' MG': 1, 'DTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 31
          Unusual residues: {' MG': 1, 'DTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.67, per 1000 atoms: 0.19
  Number of scatterers: 8810
  At special positions: 0
  Unit cell: (101.509, 104.112, 96.3036, 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)
     S      54     16.00
     P       6     15.00
     Mg      2     11.99
     O    1667      8.00
     N    1517      7.00
     C    5564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 221.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2032

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 6 sheets defined
      50.5% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 142
      removed outlier: 3.714A  pdb=" N   MET A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      Proline residue:  A 136  - end of helix
    Processing helix  chain 'A' and resid 144 through 152
      removed outlier: 3.768A  pdb=" N   ALA A 150 " --> pdb=" O   ASP A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 164
    Processing helix  chain 'A' and resid 175 through 182
      removed outlier: 4.140A  pdb=" N   ILE A 179 " --> pdb=" O   PRO A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 211
    Processing helix  chain 'A' and resid 212 through 214
      No H-bonds generated for 'chain 'A' and resid 212 through 214'
    Processing helix  chain 'A' and resid 223 through 247
      Proline residue:  A 230  - end of helix
      removed outlier: 3.763A  pdb=" N   ARG A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LYS A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   THR A 247 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 283 through 299
    Processing helix  chain 'A' and resid 322 through 334
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 3.945A  pdb=" N   GLN A 338 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 334 through 339'
    Processing helix  chain 'A' and resid 367 through 382
      removed outlier: 3.833A  pdb=" N   ARG A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.703A  pdb=" N   GLU A 410 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 450
      removed outlier: 4.123A  pdb=" N   LEU A 446 " --> pdb=" O   ASN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 486
      removed outlier: 3.698A  pdb=" N   ARG A 459 " --> pdb=" O   ASN A 455 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   PHE A 463 " --> pdb=" O   ARG A 459 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   PHE A 464 " --> pdb=" O   ILE A 460 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA A 465 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ASN A 469 " --> pdb=" O   ALA A 465 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE A 470 " --> pdb=" O   LYS A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 500
    Processing helix  chain 'A' and resid 516 through 520
      removed outlier: 4.030A  pdb=" N   HIS A 519 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 534
      removed outlier: 3.515A  pdb=" N   CYS A 532 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 550
      removed outlier: 3.608A  pdb=" N   LEU A 550 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 570
      removed outlier: 3.772A  pdb=" N   THR A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   MET A 558 " --> pdb=" O   ILE A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 596
      removed outlier: 3.726A  pdb=" N   LYS A 589 " --> pdb=" O   GLY A 585 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LYS A 590 " --> pdb=" O   LYS A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 629
      removed outlier: 3.724A  pdb=" N   LYS A 624 " --> pdb=" O   THR A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 635
      removed outlier: 4.384A  pdb=" N   LEU A 634 " --> pdb=" O   PRO A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 666
      removed outlier: 3.560A  pdb=" N   TYR A 666 " --> pdb=" O   MET A 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 142
      removed outlier: 3.671A  pdb=" N   PHE B 129 " --> pdb=" O   MET B 125 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      Proline residue:  B 136  - end of helix
      removed outlier: 3.528A  pdb=" N   ASP B 140 " --> pdb=" O   PRO B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 152
      removed outlier: 3.789A  pdb=" N   MET B 152 " --> pdb=" O   ARG B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 3.553A  pdb=" N   TYR B 163 " --> pdb=" O   ASP B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 182
      removed outlier: 3.698A  pdb=" N   HIS B 182 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 212
    Processing helix  chain 'B' and resid 213 through 215
      No H-bonds generated for 'chain 'B' and resid 213 through 215'
    Processing helix  chain 'B' and resid 223 through 229
      removed outlier: 3.634A  pdb=" N   LEU B 228 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 241
      removed outlier: 3.810A  pdb=" N   ARG B 233 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 299
      removed outlier: 3.833A  pdb=" N   LEU B 276 " --> pdb=" O   GLY B 272 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   HIS B 279 " --> pdb=" O   ARG B 275 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA B 280 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR B 284 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ASN B 286 " --> pdb=" O   ASN B 282 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 334
      removed outlier: 3.572A  pdb=" N   ILE B 328 " --> pdb=" O   GLU B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.660A  pdb=" N   GLN B 338 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 334 through 339'
    Processing helix  chain 'B' and resid 367 through 382
      removed outlier: 3.515A  pdb=" N   ALA B 374 " --> pdb=" O   LEU B 370 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   CYS B 375 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LYS B 376 " --> pdb=" O   LYS B 372 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ARG B 380 " --> pdb=" O   LYS B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 3.702A  pdb=" N   GLU B 410 " --> pdb=" O   TYR B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 450
      removed outlier: 4.097A  pdb=" N   LEU B 446 " --> pdb=" O   ASN B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 486
      removed outlier: 3.669A  pdb=" N   ARG B 459 " --> pdb=" O   ASN B 455 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ALA B 465 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASN B 469 " --> pdb=" O   ALA B 465 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ILE B 470 " --> pdb=" O   LYS B 466 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG B 481 " --> pdb=" O   GLN B 477 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   PHE B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 493
      removed outlier: 3.639A  pdb=" N   PHE B 493 " --> pdb=" O   ALA B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 520
      removed outlier: 3.892A  pdb=" N   HIS B 519 " --> pdb=" O   VAL B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 534
      removed outlier: 3.523A  pdb=" N   CYS B 532 " --> pdb=" O   GLY B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 570
      removed outlier: 3.567A  pdb=" N   LEU B 552 " --> pdb=" O   GLN B 548 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS B 553 " --> pdb=" O   GLU B 549 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ILE B 555 " --> pdb=" O   GLY B 551 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   MET B 558 " --> pdb=" O   ILE B 554 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ASN B 563 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU B 564 " --> pdb=" O   ASP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 593
      removed outlier: 3.597A  pdb=" N   LYS B 590 " --> pdb=" O   LYS B 586 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LYS B 593 " --> pdb=" O   LYS B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 629
      removed outlier: 3.812A  pdb=" N   ILE B 627 " --> pdb=" O   LYS B 623 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 635
      removed outlier: 4.329A  pdb=" N   LEU B 634 " --> pdb=" O   PRO B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 666
      removed outlier: 4.289A  pdb=" N   VAL B 659 " --> pdb=" O   VAL B 655 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL B 660 " --> pdb=" O   ILE B 656 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR B 666 " --> pdb=" O   MET B 662 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158
      removed outlier: 5.152A  pdb=" N   ASN A 435 " --> pdb=" O   THR A 521 " (cutoff:3.500A)
      removed outlier: 8.649A  pdb=" N   GLY A 523 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   SER A 437 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   GLY A 525 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   SER A 439 " --> pdb=" O   GLY A 525 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE A 526 " --> pdb=" O   LEU A 576 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158
      removed outlier: 3.658A  pdb=" N   CYS A 171 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL A 172 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   GLN A 219 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   ASN A 316 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ILE A 221 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   SER A 313 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   ILE A 352 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ILE A 315 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   LYS A 354 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   TYR A 317 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   GLN A 351 " --> pdb=" O   ASN A 385 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   LEU A 387 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   TRP A 353 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186
    Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158
      removed outlier: 7.896A  pdb=" N   GLY B 523 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   PHE B 438 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.663A  pdb=" N   CYS B 171 " --> pdb=" O   ASN B 435 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL B 172 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN B 316 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   SER B 313 " --> pdb=" O   ILE B 350 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   ILE B 352 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE B 315 " --> pdb=" O   ILE B 352 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   LYS B 354 " --> pdb=" O   ILE B 315 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TYR B 317 " --> pdb=" O   LYS B 354 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   GLN B 351 " --> pdb=" O   ASN B 385 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   LEU B 387 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   TRP B 353 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   VAL B 643 " --> pdb=" O   ASN B 674 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 186

    315 hydrogen bonds defined for protein.
    906 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: 1.13

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2901
        1.34 -     1.46: 1587
        1.46 -     1.57: 4420
        1.57 -     1.69: 10
        1.69 -     1.81: 90
  Bond restraints: 9008
  Sorted by residual:
  bond pdb=" CA  SER B 304 "
       pdb=" C   SER B 304 "
    ideal  model  delta    sigma   weight residual
    1.528  1.516  0.011 1.37e-02 5.33e+03 6.93e-01
  bond pdb=" C4' DTP B 801 "
       pdb=" O4' DTP B 801 "
    ideal  model  delta    sigma   weight residual
    1.444  1.436  0.008 1.10e-02 8.26e+03 5.41e-01
  bond pdb=" CB  GLU A 277 "
       pdb=" CG  GLU A 277 "
    ideal  model  delta    sigma   weight residual
    1.520  1.499  0.021 3.00e-02 1.11e+03 4.84e-01
  bond pdb=" CG  PRO B 175 "
       pdb=" CD  PRO B 175 "
    ideal  model  delta    sigma   weight residual
    1.503  1.480  0.023 3.40e-02 8.65e+02 4.72e-01
  bond pdb=" CA  LYS A 135 "
       pdb=" C   LYS A 135 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.008 1.23e-02 6.61e+03 4.36e-01
  ... (remaining 9003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 11889
        1.43 -     2.86: 230
        2.86 -     4.28: 39
        4.28 -     5.71: 20
        5.71 -     7.14: 1
  Bond angle restraints: 12179
  Sorted by residual:
  angle pdb=" N   GLU A 514 "
        pdb=" CA  GLU A 514 "
        pdb=" C   GLU A 514 "
      ideal   model   delta    sigma   weight residual
     114.75  110.29    4.46 1.26e+00 6.30e-01 1.25e+01
  angle pdb=" N   ALA A 535 "
        pdb=" CA  ALA A 535 "
        pdb=" C   ALA A 535 "
      ideal   model   delta    sigma   weight residual
     114.16  110.17    3.99 1.48e+00 4.57e-01 7.26e+00
  angle pdb=" CA  GLU A 514 "
        pdb=" C   GLU A 514 "
        pdb=" N   SER A 515 "
      ideal   model   delta    sigma   weight residual
     119.80  116.34    3.46 1.34e+00 5.57e-01 6.67e+00
  angle pdb=" C   ALA A 391 "
        pdb=" N   THR A 392 "
        pdb=" CA  THR A 392 "
      ideal   model   delta    sigma   weight residual
     121.54  125.85   -4.31 1.91e+00 2.74e-01 5.10e+00
  angle pdb=" CA  TYR A 231 "
        pdb=" CB  TYR A 231 "
        pdb=" CG  TYR A 231 "
      ideal   model   delta    sigma   weight residual
     113.90  109.85    4.05 1.80e+00 3.09e-01 5.07e+00
  ... (remaining 12174 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.53: 4922
       15.53 -    31.07: 358
       31.07 -    46.60: 101
       46.60 -    62.14: 33
       62.14 -    77.67: 5
  Dihedral angle restraints: 5419
    sinusoidal: 2250
      harmonic: 3169
  Sorted by residual:
  dihedral pdb=" CA  VAL A 534 "
           pdb=" C   VAL A 534 "
           pdb=" N   ALA A 535 "
           pdb=" CA  ALA A 535 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.85   27.15     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  ASP B 390 "
           pdb=" C   ASP B 390 "
           pdb=" N   ALA B 391 "
           pdb=" CA  ALA B 391 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.84   25.16     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CA  VAL B 534 "
           pdb=" C   VAL B 534 "
           pdb=" N   ALA B 535 "
           pdb=" CA  ALA B 535 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.07   24.93     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 5416 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 704
       0.030 -    0.061: 392
       0.061 -    0.091: 133
       0.091 -    0.122: 59
       0.122 -    0.152: 12
  Chirality restraints: 1300
  Sorted by residual:
  chirality pdb=" CA  ILE A 524 "
            pdb=" N   ILE A 524 "
            pdb=" C   ILE A 524 "
            pdb=" CB  ILE A 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.77e-01
  chirality pdb=" CA  ILE B 598 "
            pdb=" N   ILE B 598 "
            pdb=" C   ILE B 598 "
            pdb=" CB  ILE B 598 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  VAL A 613 "
            pdb=" N   VAL A 613 "
            pdb=" C   VAL A 613 "
            pdb=" CB  VAL A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1297 not shown)

  Planarity restraints: 1573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 495 "    0.011 2.00e-02 2.50e+03   2.29e-02 5.25e+00
        pdb=" C   LEU A 495 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   LEU A 495 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 496 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 192 "   -0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO A 193 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 193 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 193 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 362 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 363 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 363 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 363 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1570 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 44
        2.53 -     3.12: 6427
        3.12 -     3.71: 12905
        3.71 -     4.31: 18190
        4.31 -     4.90: 31234
  Nonbonded interactions: 68800
  Sorted by model distance:
  nonbonded pdb=" O3B DTP A 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.936 2.170
  nonbonded pdb="MG    MG A 802 "
            pdb=" O2B DTP B 801 "
     model   vdw
     1.985 2.170
  nonbonded pdb="MG    MG A 802 "
            pdb=" O3B DTP B 801 "
     model   vdw
     1.985 2.170
  nonbonded pdb=" O2B DTP A 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.135 2.170
  nonbonded pdb=" O2A DTP A 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.156 2.170
  ... (remaining 68795 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 'A'
  selection = (chain 'B' and (resid 120 through 304 or resid 311 through 802))
}

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:             7.270
  Set stop_for_unknowns flag:              0.010
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.270
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  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:7.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9008  Z= 0.160
  Angle     :  0.551   7.141  12179  Z= 0.298
  Chirality :  0.045   0.152   1300
  Planarity :  0.004   0.035   1573
  Dihedral  : 12.492  77.670   3387
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  :  6.70 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.25), residues: 1077
  helix: -0.91 (0.23), residues: 504
  sheet:  1.09 (0.51), residues: 108
  loop : -2.50 (0.25), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 196 
 TYR   0.017   0.002   TYR A 231 
 PHE   0.015   0.002   PHE A 224 
 TRP   0.008   0.001   TRP B 399 
 HIS   0.005   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9008)
  covalent geometry    : angle       0.55089 (12179)
  hydrogen bonds       : bond        0.27265 (  311)
  hydrogen bonds       : angle       7.81989 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 240
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7543 (mt-10)
REVERT: A  293 GLU cc_start: 0.7909 (tt0) cc_final: 0.7629 (tt0)
REVERT: A  330 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7342 (ttp-110)
REVERT: A  451 MET cc_start: 0.7642 (mtm) cc_final: 0.7387 (mtp)
REVERT: A  540 HIS cc_start: 0.7885 (p-80) cc_final: 0.7437 (p90)
REVERT: A  564 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6486 (mp0)
REVERT: B  249 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.5327 (mp0)
REVERT: B  277 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6110 (mm-30)
REVERT: B  278 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5919 (tm-30)
REVERT: B  424 ARG cc_start: 0.7491 (mtt90) cc_final: 0.7206 (mtt-85)
REVERT: B  478 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6776 (mt)
REVERT: B  534 VAL cc_start: 0.8319 (t) cc_final: 0.8109 (p)
REVERT: B  545 GLU cc_start: 0.6883 (tp30) cc_final: 0.6506 (tp30)
REVERT: B  560 ASP cc_start: 0.7821 (m-30) cc_final: 0.7604 (m-30)
  outliers start: 51
  outliers final: 25
  residues processed: 276
  average time/residue: 0.5492
  time to fit residues: 161.9255
Evaluate side-chains
  236 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 206
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  249 GLU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  478 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  639 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0470
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A 157 HIS
A 278 GLN
A 367 ASN
A 609 ASN
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 ASN
B 367 ASN
B 626 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.139334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.130422 restraints weight = 12042.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.62
r_work: 0.3700 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3579 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9008  Z= 0.186
  Angle     :  0.617   6.692  12179  Z= 0.335
  Chirality :  0.047   0.150   1300
  Planarity :  0.005   0.049   1573
  Dihedral  :  9.981  71.120   1308
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 13.19 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.25), residues: 1077
  helix: -0.50 (0.23), residues: 504
  sheet:  1.31 (0.49), residues: 107
  loop : -2.59 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 287 
 TYR   0.018   0.002   TYR A 231 
 PHE   0.018   0.002   PHE A 184 
 TRP   0.010   0.001   TRP B 399 
 HIS   0.008   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9008)
  covalent geometry    : angle       0.61662 (12179)
  hydrogen bonds       : bond        0.06483 (  311)
  hydrogen bonds       : angle       5.34593 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 208
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.7455 (mt) cc_final: 0.7169 (mt)
REVERT: A  278 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.5709 (tt0)
REVERT: A  283 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8171 (mtpp)
REVERT: A  330 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7676 (ttp-110)
REVERT: A  451 MET cc_start: 0.7792 (mtm) cc_final: 0.7460 (mtp)
REVERT: B  120 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7051 (m-30)
REVERT: B  277 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.5960 (mm-30)
REVERT: B  278 GLN cc_start: 0.6194 (OUTLIER) cc_final: 0.5690 (tp-100)
REVERT: B  424 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7452 (mtt-85)
REVERT: B  478 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6962 (mt)
REVERT: B  489 MET cc_start: 0.7873 (mmt) cc_final: 0.7218 (mmt)
REVERT: B  545 GLU cc_start: 0.7091 (tp30) cc_final: 0.6828 (tp30)
REVERT: B  560 ASP cc_start: 0.7774 (m-30) cc_final: 0.7436 (m-30)
  outliers start: 58
  outliers final: 26
  residues processed: 248
  average time/residue: 0.5683
  time to fit residues: 150.7943
Evaluate side-chains
  227 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 196
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  278 GLN
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  539 LYS
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  225 ASP
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  478 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  639 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 14 optimal weight:    0.0770
   chunk 81 optimal weight:    0.0040
   chunk 22 optimal weight:    0.2980
   chunk 36 optimal weight:    0.0770
   chunk 21 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 97 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 69 optimal weight:    0.4980
   overall best weight:    0.1708

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

Flipped N/Q/H residues before XYZ refinement:
A 385 ASN
A 395 GLN
A 609 ASN
A 652 ASN
B 297 HIS
B 626 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.141992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.133385 restraints weight = 11971.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 1.56
r_work: 0.3738 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3618 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9008  Z= 0.113
  Angle     :  0.534   9.629  12179  Z= 0.284
  Chirality :  0.044   0.144   1300
  Planarity :  0.004   0.048   1573
  Dihedral  :  9.060  68.380   1294
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 16.28 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.25), residues: 1077
  helix: -0.11 (0.24), residues: 508
  sheet:  1.42 (0.49), residues: 108
  loop : -2.52 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 380 
 TYR   0.015   0.001   TYR B 231 
 PHE   0.017   0.001   PHE A 184 
 TRP   0.007   0.001   TRP B 399 
 HIS   0.006   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9008)
  covalent geometry    : angle       0.53388 (12179)
  hydrogen bonds       : bond        0.04650 (  311)
  hydrogen bonds       : angle       4.89042 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 202
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.7332 (mt) cc_final: 0.7076 (mt)
REVERT: A  271 GLN cc_start: 0.7553 (mp10) cc_final: 0.7117 (mp10)
REVERT: A  451 MET cc_start: 0.7668 (mtm) cc_final: 0.7432 (mtp)
REVERT: A  505 GLU cc_start: 0.6934 (pp20) cc_final: 0.6543 (pp20)
REVERT: B  268 ASP cc_start: 0.7455 (t0) cc_final: 0.7177 (t0)
REVERT: B  277 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5883 (mm-30)
REVERT: B  278 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.5953 (tp-100)
REVERT: B  330 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7320 (ttm170)
REVERT: B  380 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7262 (tpt-90)
REVERT: B  424 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7409 (mtt-85)
REVERT: B  560 ASP cc_start: 0.7703 (m-30) cc_final: 0.7492 (m-30)
  outliers start: 51
  outliers final: 23
  residues processed: 234
  average time/residue: 0.5603
  time to fit residues: 140.5089
Evaluate side-chains
  215 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 188
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  225 ASP
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain B residue  380 ARG
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  656 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 395 GLN
A 570 HIS
A 609 ASN
A 652 ASN
B 216 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.136223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.127525 restraints weight = 12089.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 1.56
r_work: 0.3670 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   9008  Z= 0.307
  Angle     :  0.714   7.175  12179  Z= 0.385
  Chirality :  0.052   0.152   1300
  Planarity :  0.005   0.051   1573
  Dihedral  :  9.422  76.545   1284
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 17.23 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.79 (0.24), residues: 1077
  helix: -0.35 (0.23), residues: 499
  sheet:  1.38 (0.53), residues: 89
  loop : -2.65 (0.24), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 400 
 TYR   0.023   0.003   TYR A 337 
 PHE   0.020   0.003   PHE A 184 
 TRP   0.013   0.002   TRP B 399 
 HIS   0.011   0.002   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00734 ( 9008)
  covalent geometry    : angle       0.71385 (12179)
  hydrogen bonds       : bond        0.07022 (  311)
  hydrogen bonds       : angle       5.36660 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 194
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  241 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6871 (mtmm)
REVERT: A  451 MET cc_start: 0.7924 (mtm) cc_final: 0.7701 (mtp)
REVERT: A  505 GLU cc_start: 0.7272 (pp20) cc_final: 0.6843 (pp20)
REVERT: B  177 ASP cc_start: 0.7408 (p0) cc_final: 0.7181 (m-30)
REVERT: B  249 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.4084 (mp0)
REVERT: B  277 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6376 (mm-30)
REVERT: B  278 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5997 (tp-100)
REVERT: B  329 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7057 (mtm)
REVERT: B  560 ASP cc_start: 0.7877 (m-30) cc_final: 0.7349 (m-30)
REVERT: B  564 GLU cc_start: 0.7884 (mp0) cc_final: 0.7653 (mp0)
  outliers start: 64
  outliers final: 30
  residues processed: 231
  average time/residue: 0.5803
  time to fit residues: 143.1019
Evaluate side-chains
  225 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 190
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  249 GLU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  329 MET
Chi-restraints excluded: chain B residue  380 ARG
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  639 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 100 optimal weight:    0.4980
   chunk 68 optimal weight:    0.2980
   chunk 37 optimal weight:    0.0270
   chunk 8 optimal weight:    0.8980
   chunk 98 optimal weight:    0.2980
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.3438

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
A 395 GLN
A 609 ASN
A 652 ASN
B 626 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.139745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.131005 restraints weight = 11994.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 1.57
r_work: 0.3714 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3597 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9008  Z= 0.145
  Angle     :  0.573   6.720  12179  Z= 0.309
  Chirality :  0.045   0.141   1300
  Planarity :  0.004   0.051   1573
  Dihedral  :  9.065  75.049   1282
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 19.26 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.25), residues: 1077
  helix: -0.07 (0.24), residues: 502
  sheet:  1.29 (0.54), residues: 91
  loop : -2.53 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 424 
 TYR   0.023   0.001   TYR A 337 
 PHE   0.018   0.002   PHE A 184 
 TRP   0.010   0.001   TRP B 399 
 HIS   0.007   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9008)
  covalent geometry    : angle       0.57282 (12179)
  hydrogen bonds       : bond        0.05148 (  311)
  hydrogen bonds       : angle       5.01592 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 198
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7144 (mt)
REVERT: A  451 MET cc_start: 0.7759 (mtm) cc_final: 0.7513 (mtp)
REVERT: A  505 GLU cc_start: 0.7127 (pp20) cc_final: 0.6702 (pp20)
REVERT: B  169 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7748 (mt)
REVERT: B  244 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.4596 (pp20)
REVERT: B  254 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7251 (mt)
REVERT: B  277 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.5719 (mp0)
REVERT: B  278 GLN cc_start: 0.6337 (OUTLIER) cc_final: 0.6059 (tp-100)
  outliers start: 55
  outliers final: 28
  residues processed: 232
  average time/residue: 0.5802
  time to fit residues: 143.8659
Evaluate side-chains
  230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  380 ARG
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  549 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0060
   chunk 78 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 395 GLN
A 609 ASN
A 652 ASN
B 188 HIS
B 626 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.138247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.129618 restraints weight = 12019.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.54
r_work: 0.3698 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3578 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9008  Z= 0.203
  Angle     :  0.627  11.066  12179  Z= 0.336
  Chirality :  0.048   0.140   1300
  Planarity :  0.005   0.050   1573
  Dihedral  :  9.197  77.139   1282
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 19.89 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.61 (0.25), residues: 1077
  helix: -0.15 (0.24), residues: 502
  sheet:  1.43 (0.53), residues: 89
  loop : -2.64 (0.24), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 424 
 TYR   0.022   0.002   TYR B 231 
 PHE   0.019   0.002   PHE A 184 
 TRP   0.011   0.001   TRP B 399 
 HIS   0.008   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 9008)
  covalent geometry    : angle       0.62747 (12179)
  hydrogen bonds       : bond        0.05806 (  311)
  hydrogen bonds       : angle       5.08401 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 198
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7182 (mt)
REVERT: A  342 ASN cc_start: 0.7626 (t0) cc_final: 0.7314 (t0)
REVERT: A  451 MET cc_start: 0.7846 (mtm) cc_final: 0.7629 (mtp)
REVERT: A  505 GLU cc_start: 0.7261 (pp20) cc_final: 0.6839 (pp20)
REVERT: B  152 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6539 (pmm)
REVERT: B  249 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.4123 (mp0)
REVERT: B  254 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7256 (mt)
REVERT: B  277 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.5754 (mp0)
REVERT: B  278 GLN cc_start: 0.6435 (OUTLIER) cc_final: 0.4880 (tm-30)
REVERT: B  560 ASP cc_start: 0.7842 (m-30) cc_final: 0.7178 (m-30)
REVERT: B  564 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7431 (mp0)
  outliers start: 58
  outliers final: 38
  residues processed: 232
  average time/residue: 0.5287
  time to fit residues: 130.9046
Evaluate side-chains
  239 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 194
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  545 GLU
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  152 MET
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  249 GLU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  380 ARG
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  564 GLU
Chi-restraints excluded: chain B residue  639 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0000
   chunk 94 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 395 GLN
A 609 ASN
A 652 ASN
B 188 HIS
B 626 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.137905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.129150 restraints weight = 12035.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 1.58
r_work: 0.3692 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9008  Z= 0.209
  Angle     :  0.633   6.800  12179  Z= 0.341
  Chirality :  0.049   0.167   1300
  Planarity :  0.005   0.050   1573
  Dihedral  :  9.242  78.358   1282
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 20.21 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.25), residues: 1077
  helix: -0.17 (0.24), residues: 500
  sheet:  1.48 (0.53), residues: 87
  loop : -2.62 (0.24), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 424 
 TYR   0.022   0.002   TYR A 337 
 PHE   0.019   0.002   PHE A 184 
 TRP   0.012   0.001   TRP B 399 
 HIS   0.008   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 9008)
  covalent geometry    : angle       0.63349 (12179)
  hydrogen bonds       : bond        0.05868 (  311)
  hydrogen bonds       : angle       5.08364 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 198
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7207 (mt)
REVERT: A  342 ASN cc_start: 0.7685 (t0) cc_final: 0.7376 (t0)
REVERT: A  451 MET cc_start: 0.7857 (mtm) cc_final: 0.7636 (mtp)
REVERT: A  505 GLU cc_start: 0.7307 (pp20) cc_final: 0.6889 (pp20)
REVERT: B  177 ASP cc_start: 0.7387 (p0) cc_final: 0.7165 (m-30)
REVERT: B  249 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.4208 (mp0)
REVERT: B  254 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7298 (mt)
REVERT: B  277 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.5805 (mp0)
REVERT: B  278 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.6165 (tp-100)
REVERT: B  380 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7524 (tpt-90)
REVERT: B  564 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7387 (mp0)
REVERT: B  576 LEU cc_start: 0.8527 (tp) cc_final: 0.8301 (tp)
  outliers start: 62
  outliers final: 43
  residues processed: 235
  average time/residue: 0.5231
  time to fit residues: 131.5444
Evaluate side-chains
  243 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 193
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  454 GLU
Chi-restraints excluded: chain A residue  457 LYS
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  545 GLU
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  652 ASN
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  249 GLU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  380 ARG
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  549 GLU
Chi-restraints excluded: chain B residue  564 GLU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  639 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 2 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 98 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0770
   chunk 78 optimal weight:    0.5980
   chunk 55 optimal weight:    0.2980
   chunk 48 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 395 GLN
A 609 ASN
A 652 ASN
B 188 HIS
B 626 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.139675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.130879 restraints weight = 12085.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 1.57
r_work: 0.3713 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9008  Z= 0.155
  Angle     :  0.587   6.517  12179  Z= 0.316
  Chirality :  0.046   0.161   1300
  Planarity :  0.004   0.052   1573
  Dihedral  :  9.038  77.217   1282
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 21.17 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.25), residues: 1077
  helix:  0.02 (0.24), residues: 499
  sheet:  1.54 (0.53), residues: 88
  loop : -2.57 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 400 
 TYR   0.021   0.001   TYR A 337 
 PHE   0.019   0.002   PHE A 184 
 TRP   0.011   0.001   TRP B 399 
 HIS   0.006   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9008)
  covalent geometry    : angle       0.58664 (12179)
  hydrogen bonds       : bond        0.05155 (  311)
  hydrogen bonds       : angle       4.95502 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 198
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7170 (mt)
REVERT: A  342 ASN cc_start: 0.7648 (t0) cc_final: 0.7314 (t0)
REVERT: A  451 MET cc_start: 0.7741 (mtm) cc_final: 0.7472 (mtp)
REVERT: A  505 GLU cc_start: 0.7236 (pp20) cc_final: 0.6846 (pp20)
REVERT: B  169 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7701 (mp)
REVERT: B  244 GLU cc_start: 0.4919 (OUTLIER) cc_final: 0.4604 (pp20)
REVERT: B  249 GLU cc_start: 0.5568 (OUTLIER) cc_final: 0.4246 (mp0)
REVERT: B  254 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7227 (mt)
REVERT: B  277 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6272 (mm-30)
REVERT: B  278 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.6147 (tp-100)
REVERT: B  545 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6825 (mm-30)
REVERT: B  564 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7474 (mp0)
REVERT: B  576 LEU cc_start: 0.8522 (tp) cc_final: 0.8287 (tp)
  outliers start: 57
  outliers final: 33
  residues processed: 230
  average time/residue: 0.5183
  time to fit residues: 127.5595
Evaluate side-chains
  235 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 193
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  545 GLU
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  249 GLU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  380 ARG
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  549 GLU
Chi-restraints excluded: chain B residue  564 GLU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  607 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0970
   chunk 56 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   chunk 78 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 395 GLN
A 609 ASN
A 652 ASN
B 213 ASN
B 626 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.137873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.129036 restraints weight = 11965.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 1.58
r_work: 0.3690 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   9008  Z= 0.217
  Angle     :  0.650   6.759  12179  Z= 0.350
  Chirality :  0.049   0.159   1300
  Planarity :  0.005   0.049   1573
  Dihedral  :  9.069  78.939   1278
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.19 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 21.91 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.25), residues: 1077
  helix: -0.10 (0.23), residues: 500
  sheet:  1.61 (0.53), residues: 86
  loop : -2.60 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 424 
 TYR   0.021   0.002   TYR A 337 
 PHE   0.019   0.002   PHE A 184 
 TRP   0.012   0.002   TRP B 399 
 HIS   0.008   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 9008)
  covalent geometry    : angle       0.65047 (12179)
  hydrogen bonds       : bond        0.05926 (  311)
  hydrogen bonds       : angle       5.10594 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 194
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 ASN cc_start: 0.7679 (t0) cc_final: 0.7363 (t0)
REVERT: A  451 MET cc_start: 0.7839 (mtm) cc_final: 0.7581 (mtp)
REVERT: A  657 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7417 (mt-10)
REVERT: B  249 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.4247 (mp0)
REVERT: B  254 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7292 (mt)
REVERT: B  277 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5710 (mp0)
REVERT: B  278 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.6152 (tp-100)
REVERT: B  564 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7437 (mp0)
REVERT: B  576 LEU cc_start: 0.8522 (tp) cc_final: 0.8302 (tp)
  outliers start: 54
  outliers final: 41
  residues processed: 224
  average time/residue: 0.4972
  time to fit residues: 119.1437
Evaluate side-chains
  235 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 189
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  545 GLU
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  652 ASN
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  249 GLU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  549 GLU
Chi-restraints excluded: chain B residue  564 GLU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  639 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    0.0060
   chunk 80 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 105 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 101 optimal weight:    0.0020
   chunk 79 optimal weight:    0.7980
   chunk 90 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.2804

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 395 GLN
A 609 ASN
A 652 ASN
B 213 ASN
B 626 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.140504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.131695 restraints weight = 11900.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 1.58
r_work: 0.3723 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3606 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9008  Z= 0.137
  Angle     :  0.585   7.364  12179  Z= 0.313
  Chirality :  0.046   0.179   1300
  Planarity :  0.004   0.052   1573
  Dihedral  :  8.805  76.581   1278
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 22.87 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.25), residues: 1077
  helix:  0.10 (0.24), residues: 500
  sheet:  1.52 (0.53), residues: 88
  loop : -2.54 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 380 
 TYR   0.020   0.001   TYR A 337 
 PHE   0.017   0.001   PHE A 184 
 TRP   0.010   0.001   TRP B 399 
 HIS   0.005   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9008)
  covalent geometry    : angle       0.58473 (12179)
  hydrogen bonds       : bond        0.04880 (  311)
  hydrogen bonds       : angle       4.92859 (  906)

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

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

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2154 Ramachandran restraints generated.
    1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 194
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.7428 (mt) cc_final: 0.7142 (mt)
REVERT: A  241 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6937 (mtmm)
REVERT: A  342 ASN cc_start: 0.7619 (t0) cc_final: 0.7293 (t0)
REVERT: A  451 MET cc_start: 0.7696 (mtm) cc_final: 0.7473 (mtp)
REVERT: A  657 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7417 (mt-10)
REVERT: B  169 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7655 (mp)
REVERT: B  249 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.4225 (mp0)
REVERT: B  545 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6797 (mm-30)
REVERT: B  564 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7475 (mp0)
REVERT: B  576 LEU cc_start: 0.8508 (tp) cc_final: 0.8304 (tp)
  outliers start: 46
  outliers final: 30
  residues processed: 226
  average time/residue: 0.4925
  time to fit residues: 118.9671
Evaluate side-chains
  228 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 193
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 LYS
Chi-restraints excluded: chain A residue  279 HIS
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  545 GLU
Chi-restraints excluded: chain A residue  639 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  249 GLU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  383 PHE
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  549 GLU
Chi-restraints excluded: chain B residue  564 GLU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  607 TYR
Chi-restraints excluded: chain B residue  639 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    0.2980
   chunk 91 optimal weight:    0.6980
   chunk 88 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 82 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 76 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 395 GLN
A 609 ASN
A 652 ASN
B 213 ASN
B 278 GLN
B 626 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.139214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.130535 restraints weight = 11941.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 1.55
r_work: 0.3709 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9008  Z= 0.180
  Angle     :  0.620   6.854  12179  Z= 0.332
  Chirality :  0.047   0.158   1300
  Planarity :  0.005   0.048   1573
  Dihedral  :  8.301  77.659   1272
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 23.30 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.25), residues: 1077
  helix:  0.07 (0.24), residues: 499
  sheet:  1.55 (0.54), residues: 87
  loop : -2.55 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 424 
 TYR   0.021   0.002   TYR A 337 
 PHE   0.017   0.002   PHE A 184 
 TRP   0.010   0.001   TRP B 399 
 HIS   0.007   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 9008)
  covalent geometry    : angle       0.61991 (12179)
  hydrogen bonds       : bond        0.05410 (  311)
  hydrogen bonds       : angle       5.04120 (  906)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3615.89 seconds
wall clock time: 62 minutes 30.06 seconds (3750.06 seconds total)