Starting phenix.real_space_refine
on Fri Aug 22 22:26:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w6g_37322/08_2025/8w6g_37322.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w6g_37322/08_2025/8w6g_37322.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w6g_37322/08_2025/8w6g_37322.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w6g_37322/08_2025/8w6g_37322.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w6g_37322/08_2025/8w6g_37322.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w6g_37322/08_2025/8w6g_37322.map"
  }
  resolution = 3.3
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      58      5.16       5
     C    5582      2.51       5
     N    1280      2.21       5
     O    1392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 8314
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4049
          Classifications: {'peptide': 527}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 33, 'TRANS': 493}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 108
          Unusual residues: {'3PH': 1, 'VIJ': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.82, per 1000 atoms: 0.34
  Number of scatterers: 8314
  At special positions: 0
  Unit cell: (98.917, 107.613, 90.221, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     P       2     15.00
     O    1392      8.00
     N    1280      7.00
     C    5582      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: 0.42
  Conformation dependent library (CDL) restraints added in 331.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1976

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 2 sheets defined
      71.9% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
      removed outlier: 4.022A  pdb=" N   TRP A   9 " --> pdb=" O   TRP A   5 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA A  10 " --> pdb=" O   GLN A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 24
      removed outlier: 3.658A  pdb=" N   ILE A  16 " --> pdb=" O   ARG A  12 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL A  17 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
      Proline residue:  A  21  - end of helix
    Processing helix  chain 'A' and resid 25 through 31
      removed outlier: 3.619A  pdb=" N   VAL A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 51
      removed outlier: 3.568A  pdb=" N   CYS A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A  41 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   CYS A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 60
      removed outlier: 3.535A  pdb=" N   ALA A  60 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.899A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 103
      removed outlier: 3.710A  pdb=" N   LEU A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TRP A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 117
      removed outlier: 3.568A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE A 116 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 136
      removed outlier: 3.565A  pdb=" N   LEU A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 162
      Proline residue:  A 150  - end of helix
      removed outlier: 3.564A  pdb=" N   LEU A 156 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 232
      removed outlier: 3.721A  pdb=" N   SER A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A 225 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   CYS A 226 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER A 230 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 241 through 254
      removed outlier: 3.695A  pdb=" N   VAL A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 246 " --> pdb=" O   PRO A 242 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLN A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASN A 251 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 290
      removed outlier: 3.755A  pdb=" N   SER A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      Proline residue:  A 272  - end of helix
    Processing helix  chain 'A' and resid 304 through 321
      removed outlier: 4.087A  pdb=" N   VAL A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 345
      removed outlier: 3.627A  pdb=" N   ILE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR A 345 " --> pdb=" O   LEU A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 358
    Processing helix  chain 'A' and resid 369 through 381
      removed outlier: 3.630A  pdb=" N   VAL A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 417
      removed outlier: 3.663A  pdb=" N   GLN A 415 " --> pdb=" O   LYS A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 438
      removed outlier: 3.865A  pdb=" N   VAL A 422 " --> pdb=" O   PRO A 418 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 423 " --> pdb=" O   TRP A 419 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TYR A 429 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER A 435 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 447 through 453
      Proline residue:  A 450  - end of helix
      removed outlier: 4.309A  pdb=" N   SER A 453 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 447 through 453'
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 471
    Processing helix  chain 'A' and resid 475 through 492
      removed outlier: 3.569A  pdb=" N   ILE A 482 " --> pdb=" O   ALA A 478 " (cutoff:3.500A)
      Proline residue:  A 485  - end of helix
    Processing helix  chain 'A' and resid 502 through 508
    Processing helix  chain 'A' and resid 509 through 511
      No H-bonds generated for 'chain 'A' and resid 509 through 511'
    Processing helix  chain 'A' and resid 520 through 525
      removed outlier: 3.623A  pdb=" N   ILE A 524 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL A 525 " --> pdb=" O   PRO A 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 520 through 525'
    Processing helix  chain 'A' and resid 532 through 555
      removed outlier: 3.642A  pdb=" N   PHE A 541 " --> pdb=" O   ALA A 537 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   LEU A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU A 543 " --> pdb=" O   ALA A 539 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ILE A 545 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 11
      removed outlier: 4.021A  pdb=" N   TRP B   9 " --> pdb=" O   TRP B   5 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 24
      removed outlier: 3.657A  pdb=" N   ILE B  16 " --> pdb=" O   ARG B  12 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL B  17 " --> pdb=" O   SER B  13 " (cutoff:3.500A)
      Proline residue:  B  21  - end of helix
    Processing helix  chain 'B' and resid 25 through 31
      removed outlier: 3.618A  pdb=" N   VAL B  31 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 51
      removed outlier: 3.567A  pdb=" N   CYS B  38 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA B  41 " --> pdb=" O   TYR B  37 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   CYS B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 60
      removed outlier: 3.535A  pdb=" N   ALA B  60 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.899A  pdb=" N   VAL B  80 " --> pdb=" O   SER B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 103
      removed outlier: 3.709A  pdb=" N   LEU B  88 " --> pdb=" O   LYS B  84 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA B  99 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TRP B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
      removed outlier: 3.569A  pdb=" N   LEU B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE B 116 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 136
      removed outlier: 3.564A  pdb=" N   LEU B 124 " --> pdb=" O   ARG B 120 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 162
      Proline residue:  B 150  - end of helix
      removed outlier: 3.563A  pdb=" N   LEU B 156 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 232
      removed outlier: 3.722A  pdb=" N   SER B 222 " --> pdb=" O   THR B 218 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL B 225 " --> pdb=" O   MET B 221 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   CYS B 226 " --> pdb=" O   SER B 222 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER B 230 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 241 through 254
      removed outlier: 3.694A  pdb=" N   VAL B 245 " --> pdb=" O   ALA B 241 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU B 246 " --> pdb=" O   PRO B 242 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLN B 247 " --> pdb=" O   ASN B 243 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASN B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 290
      removed outlier: 3.755A  pdb=" N   SER B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      Proline residue:  B 272  - end of helix
    Processing helix  chain 'B' and resid 304 through 321
      removed outlier: 4.087A  pdb=" N   VAL B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE B 315 " --> pdb=" O   ALA B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 345
      removed outlier: 3.628A  pdb=" N   ILE B 334 " --> pdb=" O   LYS B 330 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 358
    Processing helix  chain 'B' and resid 369 through 381
      removed outlier: 3.629A  pdb=" N   VAL B 373 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 417
      removed outlier: 3.662A  pdb=" N   GLN B 415 " --> pdb=" O   LYS B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 438
      removed outlier: 3.865A  pdb=" N   VAL B 422 " --> pdb=" O   PRO B 418 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU B 423 " --> pdb=" O   TRP B 419 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY B 428 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TYR B 429 " --> pdb=" O   LEU B 425 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER B 435 " --> pdb=" O   LEU B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 446
    Processing helix  chain 'B' and resid 447 through 453
      Proline residue:  B 450  - end of helix
      removed outlier: 4.309A  pdb=" N   SER B 453 " --> pdb=" O   PRO B 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 447 through 453'
    Processing helix  chain 'B' and resid 455 through 457
      No H-bonds generated for 'chain 'B' and resid 455 through 457'
    Processing helix  chain 'B' and resid 458 through 471
    Processing helix  chain 'B' and resid 475 through 492
      removed outlier: 3.570A  pdb=" N   ILE B 482 " --> pdb=" O   ALA B 478 " (cutoff:3.500A)
      Proline residue:  B 485  - end of helix
    Processing helix  chain 'B' and resid 502 through 508
    Processing helix  chain 'B' and resid 509 through 511
      No H-bonds generated for 'chain 'B' and resid 509 through 511'
    Processing helix  chain 'B' and resid 520 through 525
      removed outlier: 3.622A  pdb=" N   ILE B 524 " --> pdb=" O   PRO B 520 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL B 525 " --> pdb=" O   PRO B 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 520 through 525'
    Processing helix  chain 'B' and resid 532 through 555
      removed outlier: 3.642A  pdb=" N   PHE B 541 " --> pdb=" O   ALA B 537 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   LEU B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU B 543 " --> pdb=" O   ALA B 539 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ILE B 545 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU B 553 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 393
      removed outlier: 3.582A  pdb=" N   THR A 392 " --> pdb=" O   LYS A 402 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 392 through 393
      removed outlier: 3.581A  pdb=" N   THR B 392 " --> pdb=" O   LYS B 402 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1188 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: 0.95

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1236
        1.31 -     1.43: 2250
        1.43 -     1.56: 4958
        1.56 -     1.68: 4
        1.68 -     1.81: 96
  Bond restraints: 8544
  Sorted by residual:
  bond pdb=" C   THR B 449 "
       pdb=" N   PRO B 450 "
    ideal  model  delta    sigma   weight residual
    1.334  1.375 -0.041 8.40e-03 1.42e+04 2.40e+01
  bond pdb=" O11 3PH A 603 "
       pdb=" P   3PH A 603 "
    ideal  model  delta    sigma   weight residual
    1.703  1.609  0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" C20 VIJ A 601 "
       pdb=" N04 VIJ A 601 "
    ideal  model  delta    sigma   weight residual
    1.353  1.446 -0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" O11 3PH B 603 "
       pdb=" P   3PH B 603 "
    ideal  model  delta    sigma   weight residual
    1.703  1.610  0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C20 VIJ B 601 "
       pdb=" N04 VIJ B 601 "
    ideal  model  delta    sigma   weight residual
    1.353  1.445 -0.092 2.00e-02 2.50e+03 2.13e+01
  ... (remaining 8539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.48: 11477
        3.48 -     6.95: 163
        6.95 -    10.43: 22
       10.43 -    13.90: 0
       13.90 -    17.38: 2
  Bond angle restraints: 11664
  Sorted by residual:
  angle pdb=" CA  LEU B 322 "
        pdb=" CB  LEU B 322 "
        pdb=" CG  LEU B 322 "
      ideal   model   delta    sigma   weight residual
     116.30  133.68  -17.38 3.50e+00 8.16e-02 2.47e+01
  angle pdb=" CA  LEU A 322 "
        pdb=" CB  LEU A 322 "
        pdb=" CG  LEU A 322 "
      ideal   model   delta    sigma   weight residual
     116.30  133.63  -17.33 3.50e+00 8.16e-02 2.45e+01
  angle pdb=" C   PRO A 455 "
        pdb=" N   ALA A 456 "
        pdb=" CA  ALA A 456 "
      ideal   model   delta    sigma   weight residual
     120.06  125.80   -5.74 1.19e+00 7.06e-01 2.33e+01
  angle pdb=" C   PRO B 455 "
        pdb=" N   ALA B 456 "
        pdb=" CA  ALA B 456 "
      ideal   model   delta    sigma   weight residual
     120.06  125.78   -5.72 1.19e+00 7.06e-01 2.31e+01
  angle pdb=" N   PRO B 520 "
        pdb=" CA  PRO B 520 "
        pdb=" C   PRO B 520 "
      ideal   model   delta    sigma   weight residual
     110.70  116.37   -5.67 1.22e+00 6.72e-01 2.16e+01
  ... (remaining 11659 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 4605
       16.97 -    33.94: 411
       33.94 -    50.91: 76
       50.91 -    67.88: 12
       67.88 -    84.85: 6
  Dihedral angle restraints: 5110
    sinusoidal: 2066
      harmonic: 3044
  Sorted by residual:
  dihedral pdb=" CA  PRO B 398 "
           pdb=" C   PRO B 398 "
           pdb=" N   GLY B 399 "
           pdb=" CA  GLY B 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  126.99   53.01     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  PRO A 398 "
           pdb=" C   PRO A 398 "
           pdb=" N   GLY A 399 "
           pdb=" CA  GLY A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.02   52.98     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  PRO B 520 "
           pdb=" C   PRO B 520 "
           pdb=" N   PRO B 521 "
           pdb=" CA  PRO B 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  ... (remaining 5107 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1112
       0.060 -    0.120: 204
       0.120 -    0.180: 60
       0.180 -    0.240: 8
       0.240 -    0.301: 2
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  ASN A 397 "
            pdb=" N   ASN A 397 "
            pdb=" C   ASN A 397 "
            pdb=" CB  ASN A 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  ASN B 397 "
            pdb=" N   ASN B 397 "
            pdb=" C   ASN B 397 "
            pdb=" CB  ASN B 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" C2  3PH B 603 "
            pdb=" C1  3PH B 603 "
            pdb=" C3  3PH B 603 "
            pdb=" O21 3PH B 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.55    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1383 not shown)

  Planarity restraints: 1406
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  25 "    0.062 5.00e-02 4.00e+02   9.23e-02 1.36e+01
        pdb=" N   PRO B  26 "   -0.160 5.00e-02 4.00e+02
        pdb=" CA  PRO B  26 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B  26 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  25 "   -0.062 5.00e-02 4.00e+02   9.23e-02 1.36e+01
        pdb=" N   PRO A  26 "    0.160 5.00e-02 4.00e+02
        pdb=" CA  PRO A  26 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A  26 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 520 "   -0.053 5.00e-02 4.00e+02   8.00e-02 1.02e+01
        pdb=" N   PRO B 521 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO B 521 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 521 "   -0.045 5.00e-02 4.00e+02
  ... (remaining 1403 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2708
        2.83 -     3.35: 7270
        3.35 -     3.87: 12413
        3.87 -     4.38: 15270
        4.38 -     4.90: 26439
  Nonbonded interactions: 64100
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 460 "
            pdb=" OG  SER A 464 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   ALA B 460 "
            pdb=" OG  SER B 464 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   ILE A 524 "
            pdb=" OG  SER A 527 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   ILE B 524 "
            pdb=" OG  SER B 527 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" NH2 ARG A 108 "
            pdb=" O   GLY A 323 "
     model   vdw
     2.351 3.120
  ... (remaining 64095 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             2.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.500
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
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      :  0.008   0.094   8544  Z= 0.353
  Angle     :  1.063  17.379  11664  Z= 0.566
  Chirality :  0.055   0.301   1386
  Planarity :  0.010   0.092   1406
  Dihedral  : 13.355  84.845   3134
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -6.99 (0.15), residues: 1046
  helix: -4.76 (0.06), residues: 692
  sheet:  None (None), residues: 0
  loop : -3.90 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 538 
 TYR   0.010   0.001   TYR A  40 
 PHE   0.019   0.002   PHE B 351 
 TRP   0.028   0.003   TRP A 558 
 HIS   0.006   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00815 ( 8544)
  covalent geometry    : angle       1.06296 (11664)
  hydrogen bonds       : bond        0.34437 (  400)
  hydrogen bonds       : angle       9.98072 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  295 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.8228 (mtp85)
REVERT: A  514 MET cc_start: 0.8977 (mtm) cc_final: 0.8691 (mtp)
REVERT: B  514 MET cc_start: 0.8973 (mtm) cc_final: 0.8685 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0929
  time to fit residues: 13.9037
Evaluate side-chains
  87 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 243 ASN
A 356 ASN
A 556 ASN
B 243 ASN
B 356 ASN
B 556 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.095799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.079694 restraints weight = 13155.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.08
r_work: 0.2739 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2618 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8544  Z= 0.170
  Angle     :  0.713  12.099  11664  Z= 0.361
  Chirality :  0.044   0.159   1386
  Planarity :  0.007   0.071   1406
  Dihedral  :  7.891  48.879   1342
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  8.03 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.98 (0.22), residues: 1046
  helix: -2.10 (0.16), residues: 696
  sheet:  None (None), residues: 0
  loop : -3.54 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 320 
 TYR   0.010   0.001   TYR A  11 
 PHE   0.013   0.002   PHE B 376 
 TRP   0.023   0.001   TRP A 558 
 HIS   0.002   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8544)
  covalent geometry    : angle       0.71298 (11664)
  hydrogen bonds       : bond        0.05992 (  400)
  hydrogen bonds       : angle       4.43635 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  295 ARG cc_start: 0.8803 (mtp-110) cc_final: 0.8550 (mtp85)
REVERT: A  514 MET cc_start: 0.9242 (mtm) cc_final: 0.9010 (mtp)
REVERT: B  514 MET cc_start: 0.9232 (mtm) cc_final: 0.9019 (mtp)
  outliers start: 11
  outliers final: 7
  residues processed: 99
  average time/residue: 0.0859
  time to fit residues: 11.7771
Evaluate side-chains
  92 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  495 CYS
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0050
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.097657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.081454 restraints weight = 12859.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.05
r_work: 0.2776 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8544  Z= 0.129
  Angle     :  0.619  11.874  11664  Z= 0.305
  Chirality :  0.041   0.150   1386
  Planarity :  0.006   0.064   1406
  Dihedral  :  7.735  50.581   1342
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  9.29 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -2.21 (0.25), residues: 1046
  helix: -0.53 (0.19), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.49 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 320 
 TYR   0.007   0.001   TYR A  11 
 PHE   0.013   0.001   PHE B 292 
 TRP   0.020   0.001   TRP A 558 
 HIS   0.001   0.000   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8544)
  covalent geometry    : angle       0.61886 (11664)
  hydrogen bonds       : bond        0.04367 (  400)
  hydrogen bonds       : angle       3.84058 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  295 ARG cc_start: 0.8827 (mtp-110) cc_final: 0.8592 (mtp85)
  outliers start: 8
  outliers final: 5
  residues processed: 94
  average time/residue: 0.0806
  time to fit residues: 10.5696
Evaluate side-chains
  92 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  495 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0970
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0980
   chunk 60 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.098691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.082459 restraints weight = 13138.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 2.06
r_work: 0.2790 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2671 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8544  Z= 0.118
  Angle     :  0.595  11.193  11664  Z= 0.292
  Chirality :  0.041   0.147   1386
  Planarity :  0.006   0.065   1406
  Dihedral  :  7.588  51.684   1342
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.86 %
    Favored  : 88.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -1.35 (0.27), residues: 1046
  helix:  0.17 (0.20), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.29 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 320 
 TYR   0.007   0.001   TYR B  11 
 PHE   0.013   0.001   PHE B 292 
 TRP   0.017   0.001   TRP A 558 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8544)
  covalent geometry    : angle       0.59488 (11664)
  hydrogen bonds       : bond        0.03685 (  400)
  hydrogen bonds       : angle       3.60000 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.281 
Fit side-chains
  outliers start: 13
  outliers final: 5
  residues processed: 98
  average time/residue: 0.0850
  time to fit residues: 11.4827
Evaluate side-chains
  90 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  495 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 81 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.095727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.079425 restraints weight = 13045.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.2808 rms_B_bonded: 2.15
r_work: 0.2700 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2582 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8544  Z= 0.180
  Angle     :  0.650  13.936  11664  Z= 0.315
  Chirality :  0.043   0.147   1386
  Planarity :  0.006   0.065   1406
  Dihedral  :  7.805  50.677   1342
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.86 %
    Favored  : 88.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.27), residues: 1046
  helix:  0.49 (0.20), residues: 712
  sheet:  None (None), residues: 0
  loop : -3.17 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 320 
 TYR   0.005   0.001   TYR A  40 
 PHE   0.013   0.001   PHE B 292 
 TRP   0.020   0.001   TRP A 558 
 HIS   0.002   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8544)
  covalent geometry    : angle       0.65048 (11664)
  hydrogen bonds       : bond        0.04172 (  400)
  hydrogen bonds       : angle       3.66086 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  344 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7263 (t80)
REVERT: B  344 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7272 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 92
  average time/residue: 0.0907
  time to fit residues: 11.5385
Evaluate side-chains
  96 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  495 CYS
Chi-restraints excluded: chain B residue  542 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 92 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 308 GLN
B 308 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.097453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.081142 restraints weight = 12784.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.13
r_work: 0.2728 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2611 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8544  Z= 0.132
  Angle     :  0.613  13.419  11664  Z= 0.298
  Chirality :  0.042   0.148   1386
  Planarity :  0.005   0.063   1406
  Dihedral  :  7.761  51.786   1342
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.78 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.27), residues: 1046
  helix:  0.87 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -3.07 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 437 
 TYR   0.007   0.001   TYR B  11 
 PHE   0.013   0.001   PHE B 292 
 TRP   0.018   0.001   TRP B 558 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8544)
  covalent geometry    : angle       0.61274 (11664)
  hydrogen bonds       : bond        0.03628 (  400)
  hydrogen bonds       : angle       3.53932 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  344 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7236 (t80)
REVERT: B  344 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7245 (t80)
REVERT: B  437 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7927 (tpp80)
  outliers start: 14
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0767
  time to fit residues: 9.6909
Evaluate side-chains
  94 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  495 CYS
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 85 optimal weight:    0.1980
   chunk 21 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0470
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
B 286 GLN
B 297 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.098988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.082488 restraints weight = 12925.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.17
r_work: 0.2770 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8544  Z= 0.118
  Angle     :  0.595  12.845  11664  Z= 0.289
  Chirality :  0.041   0.147   1386
  Planarity :  0.005   0.064   1406
  Dihedral  :  7.630  52.809   1342
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.89 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.08 (0.28), residues: 1046
  helix:  1.24 (0.21), residues: 702
  sheet:  None (None), residues: 0
  loop : -2.94 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 437 
 TYR   0.007   0.001   TYR A  11 
 PHE   0.012   0.001   PHE B 292 
 TRP   0.015   0.001   TRP B 558 
 HIS   0.001   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8544)
  covalent geometry    : angle       0.59481 (11664)
  hydrogen bonds       : bond        0.03264 (  400)
  hydrogen bonds       : angle       3.40923 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  344 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7235 (t80)
REVERT: A  437 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7788 (tpp80)
REVERT: B  344 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7301 (t80)
REVERT: B  437 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7688 (tpp80)
  outliers start: 14
  outliers final: 7
  residues processed: 100
  average time/residue: 0.0919
  time to fit residues: 12.6902
Evaluate side-chains
  94 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  495 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0770
   chunk 19 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
B 286 GLN
B 297 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.097946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.081327 restraints weight = 12805.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 2.16
r_work: 0.2765 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8544  Z= 0.122
  Angle     :  0.593  12.864  11664  Z= 0.288
  Chirality :  0.042   0.147   1386
  Planarity :  0.005   0.065   1406
  Dihedral  :  7.621  52.609   1342
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.24 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.16 (0.28), residues: 1046
  helix:  1.45 (0.21), residues: 702
  sheet:  None (None), residues: 0
  loop : -2.91 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 320 
 TYR   0.005   0.001   TYR A  11 
 PHE   0.013   0.001   PHE A 292 
 TRP   0.016   0.001   TRP B 558 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8544)
  covalent geometry    : angle       0.59315 (11664)
  hydrogen bonds       : bond        0.03296 (  400)
  hydrogen bonds       : angle       3.39277 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  344 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7305 (t80)
REVERT: A  437 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7854 (tpp80)
REVERT: B  344 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7306 (t80)
  outliers start: 14
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0987
  time to fit residues: 12.5151
Evaluate side-chains
  93 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  495 CYS
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 78 optimal weight:    0.4980
   chunk 63 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    0.3980
   chunk 52 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 286 GLN
B 297 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.099026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.082532 restraints weight = 12749.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.15
r_work: 0.2771 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8544  Z= 0.121
  Angle     :  0.597  12.689  11664  Z= 0.291
  Chirality :  0.041   0.146   1386
  Planarity :  0.005   0.065   1406
  Dihedral  :  7.610  52.714   1342
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.70 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.35 (0.28), residues: 1046
  helix:  1.63 (0.21), residues: 700
  sheet:  None (None), residues: 0
  loop : -2.90 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 320 
 TYR   0.006   0.001   TYR B  11 
 PHE   0.013   0.001   PHE B 292 
 TRP   0.016   0.001   TRP B 558 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8544)
  covalent geometry    : angle       0.59702 (11664)
  hydrogen bonds       : bond        0.03237 (  400)
  hydrogen bonds       : angle       3.36223 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  344 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7305 (t80)
REVERT: A  437 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7799 (mmm-85)
REVERT: B  344 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7301 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0887
  time to fit residues: 11.2120
Evaluate side-chains
  94 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  495 CYS
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 100 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.098683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.082085 restraints weight = 12808.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 2.15
r_work: 0.2764 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8544  Z= 0.127
  Angle     :  0.600  12.755  11664  Z= 0.292
  Chirality :  0.042   0.149   1386
  Planarity :  0.005   0.065   1406
  Dihedral  :  7.651  52.353   1342
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.70 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.49 (0.28), residues: 1046
  helix:  1.73 (0.21), residues: 700
  sheet:  None (None), residues: 0
  loop : -2.83 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 320 
 TYR   0.005   0.001   TYR A  40 
 PHE   0.013   0.001   PHE A 292 
 TRP   0.016   0.001   TRP B 558 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8544)
  covalent geometry    : angle       0.60016 (11664)
  hydrogen bonds       : bond        0.03329 (  400)
  hydrogen bonds       : angle       3.36496 ( 1188)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  344 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7344 (t80)
REVERT: A  437 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7736 (tpp80)
REVERT: B  344 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7295 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0866
  time to fit residues: 11.1823
Evaluate side-chains
  92 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  495 CYS
Chi-restraints excluded: chain A residue  558 TRP
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  495 CYS
Chi-restraints excluded: chain B residue  558 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 24 optimal weight:    0.0010
   chunk 102 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 96 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0020
   chunk 103 optimal weight:    0.0060
   chunk 74 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0070
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.1428

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
A 297 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.102660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.086084 restraints weight = 12678.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 2.15
r_work: 0.2812 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8544  Z= 0.104
  Angle     :  0.574  12.153  11664  Z= 0.280
  Chirality :  0.040   0.148   1386
  Planarity :  0.005   0.064   1406
  Dihedral  :  7.460  54.885   1342
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 12.84 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.82 (0.29), residues: 1046
  helix:  1.94 (0.21), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.52 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 437 
 TYR   0.008   0.001   TYR B  11 
 PHE   0.012   0.001   PHE A 292 
 TRP   0.011   0.001   TRP B 558 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8544)
  covalent geometry    : angle       0.57384 (11664)
  hydrogen bonds       : bond        0.02529 (  400)
  hydrogen bonds       : angle       3.17157 ( 1188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1608.60 seconds
wall clock time: 28 minutes 12.55 seconds (1692.55 seconds total)