Starting phenix.real_space_refine
on Sat Aug 23 00:37:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wam_37397/08_2025/8wam_37397.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wam_37397/08_2025/8wam_37397.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wam_37397/08_2025/8wam_37397.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wam_37397/08_2025/8wam_37397.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wam_37397/08_2025/8wam_37397.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wam_37397/08_2025/8wam_37397.map"
  }
  resolution = 3.23
  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=  -0.002 sd=   0.071
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    5612      2.51       5
     N    1448      2.21       5
     O    1528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  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: 8650
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4293
          Classifications: {'peptide': 551}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 532}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4293
          Classifications: {'peptide': 551}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 532}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.44, per 1000 atoms: 0.28
  Number of scatterers: 8650
  At special positions: 0
  Unit cell: (97.455, 77.745, 124.83, 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    1528      8.00
     N    1448      7.00
     C    5612      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: 0.96
  Conformation dependent library (CDL) restraints added in 258.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2024

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      65.1% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 135 through 140
    Processing helix  chain 'A' and resid 156 through 169
    Processing helix  chain 'A' and resid 174 through 189
      removed outlier: 3.511A  pdb=" N   LYS A 178 " --> pdb=" O   THR A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 222
      removed outlier: 3.671A  pdb=" N   LYS A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ARG A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLU A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 255
    Processing helix  chain 'A' and resid 268 through 274
      removed outlier: 3.810A  pdb=" N   MET A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 4.474A  pdb=" N   ALA A 297 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 321
    Processing helix  chain 'A' and resid 338 through 357
      removed outlier: 4.228A  pdb=" N   ALA A 350 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      Proline residue:  A 351  - end of helix
    Processing helix  chain 'A' and resid 379 through 402
      removed outlier: 3.577A  pdb=" N   ILE A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 425
      removed outlier: 4.106A  pdb=" N   ILE A 411 " --> pdb=" O   ASP A 407 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ALA A 416 " --> pdb=" O   PHE A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 456
      removed outlier: 3.790A  pdb=" N   GLY A 438 " --> pdb=" O   HIS A 434 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU A 439 " --> pdb=" O   ASP A 435 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 440 " --> pdb=" O   ARG A 436 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      removed outlier: 3.671A  pdb=" N   VAL A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 473
      removed outlier: 3.551A  pdb=" N   GLU A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   ALA A 464 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   ILE A 465 " --> pdb=" O   GLN A 461 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A 467 " --> pdb=" O   ARG A 463 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ARG A 468 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   SER A 472 " --> pdb=" O   ARG A 468 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY A 473 " --> pdb=" O   GLU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 493
      removed outlier: 3.665A  pdb=" N   TYR A 480 " --> pdb=" O   THR A 476 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   MET A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU A 493 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.844A  pdb=" N   ALA A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   TRP A 505 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 541
      removed outlier: 3.593A  pdb=" N   ILE A 541 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 562
      removed outlier: 3.945A  pdb=" N   THR A 549 " --> pdb=" O   LYS A 545 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ILE A 550 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 579
      removed outlier: 3.973A  pdb=" N   VAL A 574 " --> pdb=" O   SER A 571 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   TRP A 575 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   MET A 576 " --> pdb=" O   MET A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 595
      removed outlier: 4.223A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 605
      removed outlier: 4.004A  pdb=" N   MET A 603 " --> pdb=" O   GLU A 599 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU A 604 " --> pdb=" O   ILE A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 630
    Processing helix  chain 'A' and resid 634 through 660
      removed outlier: 3.590A  pdb=" N   ARG A 650 " --> pdb=" O   PHE A 646 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE A 660 " --> pdb=" O   ALA A 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 115
    Processing helix  chain 'B' and resid 135 through 140
    Processing helix  chain 'B' and resid 156 through 169
    Processing helix  chain 'B' and resid 174 through 189
    Processing helix  chain 'B' and resid 208 through 222
      removed outlier: 3.724A  pdb=" N   LYS B 213 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ARG B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU B 220 " --> pdb=" O   SER B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 255
    Processing helix  chain 'B' and resid 268 through 274
      removed outlier: 3.854A  pdb=" N   MET B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 303
      removed outlier: 3.619A  pdb=" N   PHE B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 321
      removed outlier: 3.525A  pdb=" N   PHE B 315 " --> pdb=" O   ASN B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 358
      removed outlier: 4.391A  pdb=" N   ALA B 350 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      Proline residue:  B 351  - end of helix
      removed outlier: 3.942A  pdb=" N   GLU B 358 " --> pdb=" O   LYS B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 402
      removed outlier: 3.656A  pdb=" N   ILE B 383 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 425
      removed outlier: 4.468A  pdb=" N   ILE B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA B 416 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 455
      removed outlier: 3.754A  pdb=" N   GLY B 438 " --> pdb=" O   HIS B 434 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU B 439 " --> pdb=" O   ASP B 435 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 440 " --> pdb=" O   ARG B 436 " (cutoff:3.500A)
      Proline residue:  B 451  - end of helix
    Processing helix  chain 'B' and resid 457 through 473
      removed outlier: 3.854A  pdb=" N   GLU B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   ALA B 464 " --> pdb=" O   PRO B 460 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   ILE B 465 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR B 467 " --> pdb=" O   ARG B 463 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ARG B 468 " --> pdb=" O   ALA B 464 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER B 472 " --> pdb=" O   ARG B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 493
      removed outlier: 3.719A  pdb=" N   TYR B 480 " --> pdb=" O   THR B 476 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU B 489 " --> pdb=" O   VAL B 485 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   MET B 491 " --> pdb=" O   GLY B 487 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B 493 " --> pdb=" O   LEU B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 507
      removed outlier: 3.838A  pdb=" N   ALA B 497 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   PHE B 502 " --> pdb=" O   SER B 498 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   TRP B 505 " --> pdb=" O   THR B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 541
      removed outlier: 3.513A  pdb=" N   ILE B 541 " --> pdb=" O   LEU B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 561
      removed outlier: 3.717A  pdb=" N   THR B 549 " --> pdb=" O   LYS B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 579
    Processing helix  chain 'B' and resid 580 through 595
      removed outlier: 4.015A  pdb=" N   TYR B 584 " --> pdb=" O   SER B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 605
    Processing helix  chain 'B' and resid 621 through 630
    Processing helix  chain 'B' and resid 634 through 660
      removed outlier: 3.614A  pdb=" N   ARG B 650 " --> pdb=" O   PHE B 646 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE B 660 " --> pdb=" O   ALA B 656 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 91
      removed outlier: 3.599A  pdb=" N   LEU A  84 " --> pdb=" O   TYR A  47 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY A  86 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   VAL A  45 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   THR A  88 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL A  43 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   MET A  90 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LYS A  41 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145
      removed outlier: 6.124A  pdb=" N   MET A  97 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LEU A 280 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 91
      removed outlier: 3.567A  pdb=" N   LEU B  84 " --> pdb=" O   TYR B  47 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY B  86 " --> pdb=" O   VAL B  45 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   VAL B  45 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   THR B  88 " --> pdb=" O   VAL B  43 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL B  43 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET B  90 " --> pdb=" O   LYS B  41 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LYS B  41 " --> pdb=" O   MET B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145
      removed outlier: 6.271A  pdb=" N   GLY B 143 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   MET B  97 " --> pdb=" O   THR B 262 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   VAL B 278 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU B 280 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)

    481 hydrogen bonds defined for protein.
    1410 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: 1.48

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2689
        1.34 -     1.46: 1657
        1.46 -     1.58: 4386
        1.58 -     1.69: 10
        1.69 -     1.81: 88
  Bond restraints: 8830
  Sorted by residual:
  bond pdb=" CA  PHE A 646 "
       pdb=" C   PHE A 646 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.30e-02 5.92e+03 1.13e+00
  bond pdb=" CA  PHE A 647 "
       pdb=" C   PHE A 647 "
    ideal  model  delta    sigma   weight residual
    1.524  1.536 -0.012 1.27e-02 6.20e+03 8.79e-01
  bond pdb=" C   GLU B 599 "
       pdb=" O   GLU B 599 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.011 1.26e-02 6.30e+03 7.70e-01
  bond pdb=" C   ILE B 383 "
       pdb=" O   ILE B 383 "
    ideal  model  delta    sigma   weight residual
    1.237  1.246 -0.009 1.13e-02 7.83e+03 6.73e-01
  bond pdb=" CE1 PHE A 646 "
       pdb=" CZ  PHE A 646 "
    ideal  model  delta    sigma   weight residual
    1.382  1.404 -0.022 3.00e-02 1.11e+03 5.17e-01
  ... (remaining 8825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 11759
        1.28 -     2.55: 155
        2.55 -     3.83: 43
        3.83 -     5.10: 19
        5.10 -     6.38: 4
  Bond angle restraints: 11980
  Sorted by residual:
  angle pdb=" CA  GLU B 492 "
        pdb=" CB  GLU B 492 "
        pdb=" CG  GLU B 492 "
      ideal   model   delta    sigma   weight residual
     114.10  120.48   -6.38 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" C   VAL B  43 "
        pdb=" N   ASP B  44 "
        pdb=" CA  ASP B  44 "
      ideal   model   delta    sigma   weight residual
     122.46  125.78   -3.32 1.41e+00 5.03e-01 5.56e+00
  angle pdb=" C   VAL A  43 "
        pdb=" N   ASP A  44 "
        pdb=" CA  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     122.46  125.72   -3.26 1.41e+00 5.03e-01 5.35e+00
  angle pdb=" N   PHE A 647 "
        pdb=" CA  PHE A 647 "
        pdb=" C   PHE A 647 "
      ideal   model   delta    sigma   weight residual
     111.07  112.96   -1.89 1.07e+00 8.73e-01 3.12e+00
  angle pdb=" C   PHE A 646 "
        pdb=" CA  PHE A 646 "
        pdb=" CB  PHE A 646 "
      ideal   model   delta    sigma   weight residual
     110.79  113.68   -2.89 1.66e+00 3.63e-01 3.04e+00
  ... (remaining 11975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4369
       17.92 -    35.84: 637
       35.84 -    53.77: 186
       53.77 -    71.69: 25
       71.69 -    89.61: 7
  Dihedral angle restraints: 5224
    sinusoidal: 2072
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" CA  TRP B 447 "
           pdb=" C   TRP B 447 "
           pdb=" N   GLY B 448 "
           pdb=" CA  GLY B 448 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.29   16.71     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CG  ARG A 171 "
           pdb=" CD  ARG A 171 "
           pdb=" NE  ARG A 171 "
           pdb=" CZ  ARG A 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.33   44.67     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CA  ASP A  44 "
           pdb=" CB  ASP A  44 "
           pdb=" CG  ASP A  44 "
           pdb=" OD1 ASP A  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.64   55.64     1      2.00e+01 2.50e-03 1.05e+01
  ... (remaining 5221 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 898
       0.026 -    0.052: 303
       0.052 -    0.078: 145
       0.078 -    0.104: 56
       0.104 -    0.130: 18
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" CA  ILE B 129 "
            pdb=" N   ILE B 129 "
            pdb=" C   ILE B 129 "
            pdb=" CB  ILE B 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  ILE A 129 "
            pdb=" N   ILE A 129 "
            pdb=" C   ILE A 129 "
            pdb=" CB  ILE A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  chirality pdb=" CA  VAL A 261 "
            pdb=" N   VAL A 261 "
            pdb=" C   VAL A 261 "
            pdb=" CB  VAL A 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.68e-01
  ... (remaining 1417 not shown)

  Planarity restraints: 1460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 646 "    0.014 2.00e-02 2.50e+03   1.53e-02 4.08e+00
        pdb=" CG  PHE A 646 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 646 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 646 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 646 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 646 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 646 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 492 "    0.009 2.00e-02 2.50e+03   1.90e-02 3.60e+00
        pdb=" C   GLU B 492 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   GLU B 492 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU B 493 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 305 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO A 306 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 306 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 306 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1457 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 899
        2.75 -     3.29: 8168
        3.29 -     3.82: 14286
        3.82 -     4.36: 15239
        4.36 -     4.90: 27932
  Nonbonded interactions: 66524
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 108 "
            pdb=" OD2 ASP A 231 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   GLU B 599 "
            pdb=" NE  ARG B 602 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O   SER B 596 "
            pdb=" OG  SER B 596 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" OG1 THR A 240 "
            pdb=" OD1 ASN B 321 "
     model   vdw
     2.400 3.040
  nonbonded pdb=" O   SER B 548 "
            pdb=" OG1 THR B 552 "
     model   vdw
     2.405 3.040
  ... (remaining 66519 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:                  0.010
  Normalize map: mean=0, sd=1:             1.270
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.930
  Find NCS groups from input model:        0.140
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
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      :  0.002   0.022   8830  Z= 0.095
  Angle     :  0.450   6.377  11980  Z= 0.230
  Chirality :  0.036   0.130   1420
  Planarity :  0.003   0.047   1460
  Dihedral  : 17.901  89.612   3200
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 27.09 %
    Favored  : 72.81 %
  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:  1.70 (0.26), residues: 1082
  helix:  2.22 (0.21), residues: 638
  sheet:  1.47 (0.62), residues: 80
  loop : -1.00 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 293 
 TYR   0.004   0.001   TYR A 430 
 PHE   0.021   0.001   PHE A 647 
 TRP   0.015   0.001   TRP B 505 
 HIS   0.002   0.000   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00176 ( 8830)
  covalent geometry    : angle       0.45025 (11980)
  hydrogen bonds       : bond        0.12619 (  481)
  hydrogen bonds       : angle       4.72009 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.331 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 112
  average time/residue: 0.1139
  time to fit residues: 17.2238
Evaluate side-chains
  110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0670
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.8126

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

Flipped N/Q/H residues before XYZ refinement:
** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 484 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.185410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.147167 restraints weight = 10813.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 2.45
r_work: 0.3583 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8830  Z= 0.214
  Angle     :  0.597   6.752  11980  Z= 0.302
  Chirality :  0.043   0.152   1420
  Planarity :  0.004   0.040   1460
  Dihedral  :  9.867  86.337   1265
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 24.95 %
    Favored  : 72.27 %
  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:  1.18 (0.26), residues: 1082
  helix:  1.64 (0.20), residues: 662
  sheet:  1.04 (0.59), residues: 80
  loop : -0.98 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 602 
 TYR   0.017   0.002   TYR B 594 
 PHE   0.023   0.002   PHE A 499 
 TRP   0.013   0.002   TRP A 447 
 HIS   0.005   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 8830)
  covalent geometry    : angle       0.59711 (11980)
  hydrogen bonds       : bond        0.05195 (  481)
  hydrogen bonds       : angle       3.85717 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7641 (tpt) cc_final: 0.7096 (tpt)
REVERT: A  170 PRO cc_start: 0.6753 (Cg_exo) cc_final: 0.6546 (Cg_endo)
REVERT: A  310 MET cc_start: 0.4406 (ppp) cc_final: 0.3504 (ppp)
REVERT: A  573 MET cc_start: 0.7619 (mmt) cc_final: 0.7182 (mmt)
REVERT: B  265 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.6720 (t-170)
  outliers start: 26
  outliers final: 16
  residues processed: 131
  average time/residue: 0.1170
  time to fit residues: 20.3149
Evaluate side-chains
  125 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  660 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 232 GLN
A 454 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.187713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.150141 restraints weight = 10689.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.40
r_work: 0.3623 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8830  Z= 0.125
  Angle     :  0.484   5.844  11980  Z= 0.245
  Chirality :  0.038   0.134   1420
  Planarity :  0.003   0.041   1460
  Dihedral  :  9.406  89.634   1262
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 25.37 %
    Favored  : 72.81 %
  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:  1.36 (0.26), residues: 1082
  helix:  1.81 (0.21), residues: 662
  sheet:  1.01 (0.58), residues: 80
  loop : -0.96 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 293 
 TYR   0.010   0.001   TYR B 594 
 PHE   0.013   0.001   PHE A 499 
 TRP   0.012   0.001   TRP A 447 
 HIS   0.003   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8830)
  covalent geometry    : angle       0.48421 (11980)
  hydrogen bonds       : bond        0.04110 (  481)
  hydrogen bonds       : angle       3.63397 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7596 (tpt) cc_final: 0.7174 (tpt)
REVERT: A  310 MET cc_start: 0.4664 (ppp) cc_final: 0.3731 (ppp)
REVERT: A  573 MET cc_start: 0.7578 (mmt) cc_final: 0.7095 (mmt)
REVERT: A  603 MET cc_start: 0.5111 (mpp) cc_final: 0.4019 (mtt)
REVERT: B  196 ASN cc_start: 0.8235 (t0) cc_final: 0.7892 (t0)
REVERT: B  265 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6668 (t-170)
  outliers start: 17
  outliers final: 12
  residues processed: 127
  average time/residue: 0.1228
  time to fit residues: 20.5224
Evaluate side-chains
  119 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  133 LYS
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  286 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  660 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 72 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.183287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.145206 restraints weight = 10962.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.43
r_work: 0.3559 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8830  Z= 0.198
  Angle     :  0.572   6.681  11980  Z= 0.289
  Chirality :  0.041   0.143   1420
  Planarity :  0.004   0.039   1460
  Dihedral  :  9.297  89.848   1262
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.16 %
    Favored  : 71.20 %
  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:  1.00 (0.26), residues: 1082
  helix:  1.51 (0.20), residues: 662
  sheet:  0.53 (0.57), residues: 82
  loop : -0.96 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 293 
 TYR   0.022   0.002   TYR B 594 
 PHE   0.020   0.002   PHE A 499 
 TRP   0.014   0.002   TRP A 447 
 HIS   0.004   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 8830)
  covalent geometry    : angle       0.57221 (11980)
  hydrogen bonds       : bond        0.04974 (  481)
  hydrogen bonds       : angle       3.71772 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7818 (tpt) cc_final: 0.7322 (ttm)
REVERT: A  196 ASN cc_start: 0.8151 (t0) cc_final: 0.7849 (t0)
REVERT: A  310 MET cc_start: 0.4573 (ppp) cc_final: 0.3638 (ppp)
REVERT: A  603 MET cc_start: 0.5242 (mpp) cc_final: 0.4149 (mtt)
REVERT: B  196 ASN cc_start: 0.8241 (t0) cc_final: 0.7893 (t0)
REVERT: B  224 ASN cc_start: 0.7594 (m-40) cc_final: 0.7279 (p0)
REVERT: B  265 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.6757 (t-170)
REVERT: B  528 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7876 (mp)
  outliers start: 34
  outliers final: 23
  residues processed: 143
  average time/residue: 0.1302
  time to fit residues: 24.1264
Evaluate side-chains
  137 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  133 LYS
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  660 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.183689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.145130 restraints weight = 11058.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.52
r_work: 0.3548 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8830  Z= 0.198
  Angle     :  0.573   6.662  11980  Z= 0.290
  Chirality :  0.042   0.142   1420
  Planarity :  0.004   0.040   1460
  Dihedral  :  9.191  86.995   1262
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 24.20 %
    Favored  : 70.99 %
  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:  0.81 (0.25), residues: 1082
  helix:  1.38 (0.20), residues: 662
  sheet:  0.40 (0.57), residues: 82
  loop : -1.08 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 168 
 TYR   0.022   0.002   TYR B 594 
 PHE   0.018   0.002   PHE A 499 
 TRP   0.015   0.002   TRP A 447 
 HIS   0.007   0.001   HIS A 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 8830)
  covalent geometry    : angle       0.57316 (11980)
  hydrogen bonds       : bond        0.04968 (  481)
  hydrogen bonds       : angle       3.71576 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 116
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7690 (tpt) cc_final: 0.7338 (ttm)
REVERT: A  196 ASN cc_start: 0.8160 (t0) cc_final: 0.7831 (t0)
REVERT: A  310 MET cc_start: 0.4714 (ppp) cc_final: 0.3701 (ppp)
REVERT: A  397 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7079 (mp)
REVERT: A  492 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6699 (tp30)
REVERT: A  573 MET cc_start: 0.7565 (mmt) cc_final: 0.6981 (mmt)
REVERT: A  603 MET cc_start: 0.5534 (mpp) cc_final: 0.4963 (tmm)
REVERT: A  623 ARG cc_start: 0.5730 (OUTLIER) cc_final: 0.5408 (ptp-170)
REVERT: B  168 ARG cc_start: 0.8256 (tpp80) cc_final: 0.8020 (tpp80)
REVERT: B  196 ASN cc_start: 0.8339 (t0) cc_final: 0.7992 (t0)
REVERT: B  224 ASN cc_start: 0.7971 (m-40) cc_final: 0.7351 (p0)
REVERT: B  265 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.6822 (t-170)
REVERT: B  462 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6833 (mp0)
REVERT: B  528 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7830 (mp)
  outliers start: 45
  outliers final: 29
  residues processed: 153
  average time/residue: 0.1288
  time to fit residues: 25.4596
Evaluate side-chains
  147 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 112
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  133 LYS
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  576 MET
Chi-restraints excluded: chain B residue  600 ILE
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  660 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.183775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.145092 restraints weight = 11013.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.46
r_work: 0.3546 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
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   0.038   8830  Z= 0.182
  Angle     :  0.561   6.611  11980  Z= 0.284
  Chirality :  0.041   0.137   1420
  Planarity :  0.004   0.041   1460
  Dihedral  :  9.121  86.768   1262
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 25.37 %
    Favored  : 70.77 %
  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:  0.80 (0.25), residues: 1082
  helix:  1.39 (0.20), residues: 660
  sheet:  0.25 (0.55), residues: 82
  loop : -1.07 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 293 
 TYR   0.017   0.002   TYR B 594 
 PHE   0.017   0.002   PHE B 499 
 TRP   0.019   0.002   TRP A 505 
 HIS   0.004   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8830)
  covalent geometry    : angle       0.56136 (11980)
  hydrogen bonds       : bond        0.04791 (  481)
  hydrogen bonds       : angle       3.70324 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 114
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7704 (tpt) cc_final: 0.7351 (ttm)
REVERT: A  196 ASN cc_start: 0.8253 (t0) cc_final: 0.7926 (t0)
REVERT: A  310 MET cc_start: 0.4708 (ppp) cc_final: 0.3739 (ppp)
REVERT: A  492 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6714 (tp30)
REVERT: A  573 MET cc_start: 0.7589 (mmt) cc_final: 0.7084 (mmt)
REVERT: A  603 MET cc_start: 0.5649 (mpp) cc_final: 0.5099 (tmm)
REVERT: A  623 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5504 (ptp-170)
REVERT: B  168 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8042 (tpp80)
REVERT: B  196 ASN cc_start: 0.8354 (t0) cc_final: 0.7988 (t0)
REVERT: B  224 ASN cc_start: 0.7728 (m-40) cc_final: 0.7195 (p0)
REVERT: B  265 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.6714 (t-170)
REVERT: B  462 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6750 (mp0)
REVERT: B  528 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7798 (mp)
  outliers start: 36
  outliers final: 27
  residues processed: 143
  average time/residue: 0.1263
  time to fit residues: 23.4827
Evaluate side-chains
  142 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  133 LYS
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  576 MET
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  660 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.185356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.146689 restraints weight = 11034.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.46
r_work: 0.3573 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8830  Z= 0.140
  Angle     :  0.517   6.146  11980  Z= 0.261
  Chirality :  0.039   0.132   1420
  Planarity :  0.004   0.041   1460
  Dihedral  :  8.967  85.778   1262
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.80 %
    Favored  : 70.56 %
  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:  0.94 (0.26), residues: 1082
  helix:  1.54 (0.20), residues: 662
  sheet:  0.28 (0.55), residues: 82
  loop : -1.10 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 293 
 TYR   0.013   0.001   TYR B 594 
 PHE   0.013   0.001   PHE A 441 
 TRP   0.025   0.002   TRP A 505 
 HIS   0.003   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8830)
  covalent geometry    : angle       0.51680 (11980)
  hydrogen bonds       : bond        0.04177 (  481)
  hydrogen bonds       : angle       3.60092 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7698 (tpt) cc_final: 0.7407 (ttm)
REVERT: A  196 ASN cc_start: 0.8217 (t0) cc_final: 0.7736 (t0)
REVERT: A  265 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6899 (t-90)
REVERT: A  310 MET cc_start: 0.4820 (ppp) cc_final: 0.3849 (ppp)
REVERT: A  492 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6767 (tp30)
REVERT: A  573 MET cc_start: 0.7525 (mmt) cc_final: 0.6917 (mmt)
REVERT: A  603 MET cc_start: 0.5819 (mpp) cc_final: 0.5231 (tmm)
REVERT: B  168 ARG cc_start: 0.8273 (tpp80) cc_final: 0.8022 (tpp80)
REVERT: B  196 ASN cc_start: 0.8316 (t0) cc_final: 0.7947 (t0)
REVERT: B  224 ASN cc_start: 0.7688 (m-40) cc_final: 0.7219 (p0)
REVERT: B  265 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.6730 (t-170)
REVERT: B  310 MET cc_start: 0.4645 (ppp) cc_final: 0.3802 (ppp)
REVERT: B  462 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6768 (mp0)
REVERT: B  528 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7845 (mp)
  outliers start: 34
  outliers final: 25
  residues processed: 145
  average time/residue: 0.1204
  time to fit residues: 22.9855
Evaluate side-chains
  143 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  133 LYS
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  576 MET
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  660 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0670
   chunk 41 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.186941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.148703 restraints weight = 10942.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.47
r_work: 0.3588 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8830  Z= 0.118
  Angle     :  0.498   6.751  11980  Z= 0.251
  Chirality :  0.038   0.128   1420
  Planarity :  0.003   0.043   1460
  Dihedral  :  8.842  85.236   1262
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 25.37 %
    Favored  : 71.09 %
  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:  1.07 (0.26), residues: 1082
  helix:  1.66 (0.20), residues: 660
  sheet:  0.34 (0.55), residues: 82
  loop : -1.10 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 293 
 TYR   0.010   0.001   TYR B 594 
 PHE   0.012   0.001   PHE A 441 
 TRP   0.026   0.002   TRP A 505 
 HIS   0.003   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8830)
  covalent geometry    : angle       0.49770 (11980)
  hydrogen bonds       : bond        0.03846 (  481)
  hydrogen bonds       : angle       3.52262 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7707 (tpt) cc_final: 0.7408 (ttm)
REVERT: A  196 ASN cc_start: 0.8176 (t0) cc_final: 0.7803 (t0)
REVERT: A  265 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6887 (t-90)
REVERT: A  270 ARG cc_start: 0.7735 (mmm160) cc_final: 0.7492 (mmp80)
REVERT: A  310 MET cc_start: 0.4821 (ppp) cc_final: 0.3882 (ppp)
REVERT: A  397 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6998 (mp)
REVERT: A  492 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6642 (tp30)
REVERT: A  603 MET cc_start: 0.5869 (mpp) cc_final: 0.5225 (tmm)
REVERT: B  168 ARG cc_start: 0.8293 (tpp80) cc_final: 0.8050 (tpp80)
REVERT: B  196 ASN cc_start: 0.8323 (t0) cc_final: 0.7930 (t0)
REVERT: B  224 ASN cc_start: 0.7596 (m-40) cc_final: 0.7190 (p0)
REVERT: B  265 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.6565 (t-170)
REVERT: B  270 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7533 (mmp80)
REVERT: B  310 MET cc_start: 0.4590 (ppp) cc_final: 0.3710 (ppp)
REVERT: B  462 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.6795 (mp0)
REVERT: B  528 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7781 (mp)
  outliers start: 33
  outliers final: 23
  residues processed: 149
  average time/residue: 0.1196
  time to fit residues: 23.4713
Evaluate side-chains
  142 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  133 LYS
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.186713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.148263 restraints weight = 10946.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.48
r_work: 0.3582 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8830  Z= 0.121
  Angle     :  0.499   6.676  11980  Z= 0.252
  Chirality :  0.038   0.133   1420
  Planarity :  0.003   0.044   1460
  Dihedral  :  8.781  85.058   1262
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 25.48 %
    Favored  : 71.20 %
  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:  1.12 (0.26), residues: 1082
  helix:  1.70 (0.20), residues: 660
  sheet:  0.33 (0.55), residues: 82
  loop : -1.07 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 293 
 TYR   0.010   0.001   TYR B 594 
 PHE   0.012   0.001   PHE B 275 
 TRP   0.028   0.002   TRP A 505 
 HIS   0.002   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8830)
  covalent geometry    : angle       0.49925 (11980)
  hydrogen bonds       : bond        0.03777 (  481)
  hydrogen bonds       : angle       3.51207 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7702 (tpt) cc_final: 0.7395 (ttm)
REVERT: A  196 ASN cc_start: 0.8188 (t0) cc_final: 0.7827 (t0)
REVERT: A  265 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6903 (t-90)
REVERT: A  270 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7475 (mmp80)
REVERT: A  310 MET cc_start: 0.4832 (ppp) cc_final: 0.3890 (ppp)
REVERT: A  397 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.7013 (mp)
REVERT: A  402 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.6790 (mmm-85)
REVERT: A  492 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6640 (tp30)
REVERT: A  603 MET cc_start: 0.5878 (mpp) cc_final: 0.5234 (tmm)
REVERT: B  168 ARG cc_start: 0.8282 (tpp80) cc_final: 0.8038 (tpp80)
REVERT: B  196 ASN cc_start: 0.8319 (t0) cc_final: 0.7932 (t0)
REVERT: B  224 ASN cc_start: 0.7563 (m-40) cc_final: 0.7279 (p0)
REVERT: B  265 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.6545 (t-170)
REVERT: B  310 MET cc_start: 0.4607 (ppp) cc_final: 0.3717 (ppp)
REVERT: B  462 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6770 (mp0)
REVERT: B  528 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7785 (mp)
  outliers start: 31
  outliers final: 25
  residues processed: 144
  average time/residue: 0.1223
  time to fit residues: 23.1219
Evaluate side-chains
  144 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  133 LYS
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  660 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 36 optimal weight:    0.2980
   chunk 78 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN
B 389 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.187286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.149012 restraints weight = 10940.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.48
r_work: 0.3593 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8830  Z= 0.115
  Angle     :  0.494   6.821  11980  Z= 0.249
  Chirality :  0.038   0.146   1420
  Planarity :  0.003   0.046   1460
  Dihedral  :  8.727  85.346   1262
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 26.02 %
    Favored  : 70.66 %
  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:  1.17 (0.26), residues: 1082
  helix:  1.76 (0.20), residues: 660
  sheet:  0.36 (0.56), residues: 82
  loop : -1.10 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 270 
 TYR   0.010   0.001   TYR B 594 
 PHE   0.015   0.001   PHE B 275 
 TRP   0.025   0.002   TRP A 505 
 HIS   0.002   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8830)
  covalent geometry    : angle       0.49367 (11980)
  hydrogen bonds       : bond        0.03624 (  481)
  hydrogen bonds       : angle       3.46817 ( 1410)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7681 (tpt) cc_final: 0.7363 (ttm)
REVERT: A  196 ASN cc_start: 0.8178 (t0) cc_final: 0.7818 (t0)
REVERT: A  265 HIS cc_start: 0.7125 (OUTLIER) cc_final: 0.6839 (t-90)
REVERT: A  310 MET cc_start: 0.4834 (ppp) cc_final: 0.3898 (ppp)
REVERT: A  397 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6938 (mp)
REVERT: A  402 ARG cc_start: 0.7008 (mmm-85) cc_final: 0.6789 (mmm-85)
REVERT: A  492 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6594 (tp30)
REVERT: A  603 MET cc_start: 0.5827 (mpp) cc_final: 0.5175 (tmm)
REVERT: B  196 ASN cc_start: 0.8327 (t0) cc_final: 0.7949 (t0)
REVERT: B  224 ASN cc_start: 0.7512 (m-40) cc_final: 0.7268 (p0)
REVERT: B  265 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.6617 (t-170)
REVERT: B  310 MET cc_start: 0.4707 (ppp) cc_final: 0.3925 (ppp)
REVERT: B  462 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6717 (mp0)
REVERT: B  528 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7738 (mp)
  outliers start: 31
  outliers final: 24
  residues processed: 140
  average time/residue: 0.1233
  time to fit residues: 22.6103
Evaluate side-chains
  140 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  133 LYS
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  492 GLU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  184 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  652 LEU
Chi-restraints excluded: chain B residue  660 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 105 optimal weight:    0.0030
   chunk 43 optimal weight:    0.7980
   chunk 85 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.188216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.150163 restraints weight = 10837.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.43
r_work: 0.3605 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8830  Z= 0.108
  Angle     :  0.491   6.677  11980  Z= 0.247
  Chirality :  0.038   0.141   1420
  Planarity :  0.004   0.050   1460
  Dihedral  :  8.681  85.774   1262
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 26.55 %
    Favored  : 70.56 %
  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:  1.21 (0.26), residues: 1082
  helix:  1.83 (0.21), residues: 660
  sheet:  0.21 (0.55), residues: 80
  loop : -1.12 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 270 
 TYR   0.008   0.001   TYR B 594 
 PHE   0.012   0.001   PHE B 275 
 TRP   0.022   0.002   TRP B 505 
 HIS   0.002   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8830)
  covalent geometry    : angle       0.49067 (11980)
  hydrogen bonds       : bond        0.03454 (  481)
  hydrogen bonds       : angle       3.42370 ( 1410)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2004.54 seconds
wall clock time: 35 minutes 14.06 seconds (2114.06 seconds total)