Starting phenix.real_space_refine
on Sat Aug 23 13:04:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pwl_17994/08_2025/8pwl_17994.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pwl_17994/08_2025/8pwl_17994.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pwl_17994/08_2025/8pwl_17994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pwl_17994/08_2025/8pwl_17994.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pwl_17994/08_2025/8pwl_17994.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pwl_17994/08_2025/8pwl_17994.cif"
  }
  resolution = 4.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.080
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: 4
    Type Number    sf(0)   Gaussians
     S      91      5.16       5
     C    7769      2.51       5
     N    2132      2.21       5
     O    2274      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 12266
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 830, 6603
          Classifications: {'peptide': 830}
          Link IDs: {'PTRANS': 38, 'TRANS': 791}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 711, 5663
          Classifications: {'peptide': 711}
          Link IDs: {'PTRANS': 29, 'TRANS': 681}
          Chain breaks: 2
  Time building chain proxies: 2.86, per 1000 atoms: 0.23
  Number of scatterers: 12266
  At special positions: 0
  Unit cell: (79.23, 136.776, 168.468, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      91     16.00
     O    2274      8.00
     N    2132      7.00
     C    7769      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: 0.84
  Conformation dependent library (CDL) restraints added in 571.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2918

  Finding SS restraints...
    Secondary structure from input PDB file:
      85 helices and 8 sheets defined
      66.9% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 4.311A  pdb=" N   GLU A   6 " --> pdb=" O   GLU A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 32
    Processing helix  chain 'A' and resid 35 through 40
      removed outlier: 3.853A  pdb=" N   ALA A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 52
    Processing helix  chain 'A' and resid 67 through 76
      removed outlier: 3.704A  pdb=" N   ILE A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 88
      removed outlier: 3.674A  pdb=" N   GLY A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 108
    Processing helix  chain 'A' and resid 110 through 120
    Processing helix  chain 'A' and resid 133 through 142
      removed outlier: 3.886A  pdb=" N   ASN A 141 " --> pdb=" O   TRP A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 153
      removed outlier: 3.592A  pdb=" N   ASP A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN A 152 " --> pdb=" O   HIS A 148 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   HIS A 153 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 175
      removed outlier: 3.562A  pdb=" N   VAL A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 186
    Processing helix  chain 'A' and resid 199 through 208
      removed outlier: 3.919A  pdb=" N   PHE A 203 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 219
    Processing helix  chain 'A' and resid 231 through 238
    Processing helix  chain 'A' and resid 241 through 252
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 4.251A  pdb=" N   GLN A 257 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 282
      removed outlier: 3.776A  pdb=" N   GLN A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL A 276 " --> pdb=" O   MET A 272 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 307
      removed outlier: 3.664A  pdb=" N   GLU A 297 " --> pdb=" O   THR A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 334
      removed outlier: 3.572A  pdb=" N   LYS A 318 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLY A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 383
      removed outlier: 3.627A  pdb=" N   LYS A 358 " --> pdb=" O   SER A 354 " (cutoff:3.500A)
      Proline residue:  A 359  - end of helix
      removed outlier: 3.558A  pdb=" N   LEU A 362 " --> pdb=" O   LYS A 358 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 465
      removed outlier: 3.563A  pdb=" N   MET A 461 " --> pdb=" O   GLN A 457 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   CYS A 462 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   CYS A 463 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 483
      removed outlier: 3.607A  pdb=" N   PHE A 479 " --> pdb=" O   ARG A 475 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   HIS A 483 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
      removed outlier: 3.733A  pdb=" N   PHE A 490 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 491 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 501
      removed outlier: 4.469A  pdb=" N   ASP A 500 " --> pdb=" O   LYS A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 508 through 515
      removed outlier: 3.623A  pdb=" N   ARG A 514 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 520
    Processing helix  chain 'A' and resid 525 through 537
      removed outlier: 3.826A  pdb=" N   GLU A 529 " --> pdb=" O   LYS A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 560
      No H-bonds generated for 'chain 'A' and resid 558 through 560'
    Processing helix  chain 'A' and resid 561 through 573
    Processing helix  chain 'A' and resid 574 through 581
    Processing helix  chain 'A' and resid 593 through 609
      removed outlier: 3.788A  pdb=" N   VAL A 597 " --> pdb=" O   GLY A 593 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL A 609 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 3.578A  pdb=" N   VAL A 633 " --> pdb=" O   ASN A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 654
    Processing helix  chain 'A' and resid 663 through 672
      removed outlier: 3.653A  pdb=" N   TYR A 667 " --> pdb=" O   THR A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 684
      removed outlier: 3.613A  pdb=" N   VAL A 680 " --> pdb=" O   ASN A 676 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A 683 " --> pdb=" O   ASP A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 695
    Processing helix  chain 'A' and resid 736 through 751
    Processing helix  chain 'A' and resid 753 through 766
    Processing helix  chain 'A' and resid 769 through 774
    Processing helix  chain 'A' and resid 777 through 787
    Processing helix  chain 'A' and resid 792 through 799
    Processing helix  chain 'A' and resid 810 through 823
      removed outlier: 3.850A  pdb=" N   GLN A 814 " --> pdb=" O   ASP A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 836
    Processing helix  chain 'A' and resid 887 through 901
    Processing helix  chain 'B' and resid 3 through 17
    Processing helix  chain 'B' and resid 26 through 39
      Proline residue:  B  36  - end of helix
    Processing helix  chain 'B' and resid 42 through 52
    Processing helix  chain 'B' and resid 67 through 76
    Processing helix  chain 'B' and resid 78 through 87
      removed outlier: 3.559A  pdb=" N   VAL B  82 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 109
      removed outlier: 3.621A  pdb=" N   LEU B 104 " --> pdb=" O   THR B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 120
    Processing helix  chain 'B' and resid 133 through 142
      removed outlier: 4.000A  pdb=" N   TRP B 137 " --> pdb=" O   THR B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 152
    Processing helix  chain 'B' and resid 166 through 175
    Processing helix  chain 'B' and resid 176 through 186
      removed outlier: 3.593A  pdb=" N   VAL B 180 " --> pdb=" O   HIS B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 208
      removed outlier: 3.613A  pdb=" N   PHE B 203 " --> pdb=" O   THR B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 219
    Processing helix  chain 'B' and resid 231 through 240
      removed outlier: 3.771A  pdb=" N   LEU B 235 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 252
    Processing helix  chain 'B' and resid 254 through 262
    Processing helix  chain 'B' and resid 269 through 280
      removed outlier: 3.871A  pdb=" N   VAL B 276 " --> pdb=" O   MET B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 309
      removed outlier: 3.662A  pdb=" N   GLU B 297 " --> pdb=" O   THR B 293 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL B 298 " --> pdb=" O   SER B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 334
      removed outlier: 3.627A  pdb=" N   PHE B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 383
      Proline residue:  B 359  - end of helix
      removed outlier: 4.130A  pdb=" N   TRP B 364 " --> pdb=" O   LEU B 360 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 465
      removed outlier: 3.842A  pdb=" N   MET B 461 " --> pdb=" O   GLN B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 483
      removed outlier: 3.701A  pdb=" N   ILE B 477 " --> pdb=" O   SER B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 494
      removed outlier: 4.055A  pdb=" N   LEU B 487 " --> pdb=" O   HIS B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 501
      removed outlier: 3.983A  pdb=" N   ASP B 500 " --> pdb=" O   LYS B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 507
      removed outlier: 3.674A  pdb=" N   LEU B 506 " --> pdb=" O   HIS B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 520
      removed outlier: 3.664A  pdb=" N   SER B 513 " --> pdb=" O   PRO B 509 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ARG B 514 " --> pdb=" O   GLU B 510 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   HIS B 517 " --> pdb=" O   SER B 513 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ILE B 518 " --> pdb=" O   ARG B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 536
      removed outlier: 3.523A  pdb=" N   HIS B 536 " --> pdb=" O   TYR B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 573
    Processing helix  chain 'B' and resid 574 through 581
      removed outlier: 3.602A  pdb=" N   LEU B 578 " --> pdb=" O   ASN B 574 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLN B 580 " --> pdb=" O   ALA B 576 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY B 581 " --> pdb=" O   LYS B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 593 through 610
      removed outlier: 3.506A  pdb=" N   VAL B 597 " --> pdb=" O   GLY B 593 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASN B 610 " --> pdb=" O   ASN B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 611 through 614
    Processing helix  chain 'B' and resid 636 through 654
    Processing helix  chain 'B' and resid 663 through 672
    Processing helix  chain 'B' and resid 676 through 682
      removed outlier: 3.732A  pdb=" N   VAL B 680 " --> pdb=" O   ASN B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 696
      removed outlier: 3.505A  pdb=" N   ALA B 688 " --> pdb=" O   ASP B 684 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASP B 696 " --> pdb=" O   GLN B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 737 through 751
    Processing helix  chain 'B' and resid 753 through 766
      removed outlier: 3.540A  pdb=" N   MET B 766 " --> pdb=" O   GLN B 762 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 769 through 774
    Processing helix  chain 'B' and resid 777 through 787
    Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557
      removed outlier: 5.799A  pdb=" N   LEU A 555 " --> pdb=" O   ARG A 585 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 618
    Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 714
    Processing sheet with id=AA4, first strand: chain 'A' and resid 850 through 851
    Processing sheet with id=AA5, first strand: chain 'A' and resid 859 through 863
      removed outlier: 3.550A  pdb=" N   THR A 872 " --> pdb=" O   LYS A 881 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 554 through 557
      removed outlier: 6.063A  pdb=" N   LEU B 555 " --> pdb=" O   ARG B 585 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 616 through 618
    Processing sheet with id=AA8, first strand: chain 'B' and resid 710 through 714

    641 hydrogen bonds defined for protein.
    1887 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 1.17 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: 4104
        1.34 -     1.46: 2639
        1.46 -     1.58: 5644
        1.58 -     1.69: 0
        1.69 -     1.81: 140
  Bond restraints: 12527
  Sorted by residual:
  bond pdb=" CA  THR A 351 "
       pdb=" C   THR A 351 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.26e-02 6.30e+03 6.73e-01
  bond pdb=" CB  MET A   5 "
       pdb=" CG  MET A   5 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 6.04e-01
  bond pdb=" C   MET A  35 "
       pdb=" N   PRO A  36 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.010 1.36e-02 5.41e+03 5.94e-01
  bond pdb=" C   THR A 351 "
       pdb=" N   PRO A 352 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.19e-02 7.06e+03 5.82e-01
  bond pdb=" CB  ASP A 500 "
       pdb=" CG  ASP A 500 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 2.50e-02 1.60e+03 5.80e-01
  ... (remaining 12522 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 16656
        1.51 -     3.02: 240
        3.02 -     4.53: 44
        4.53 -     6.03: 27
        6.03 -     7.54: 8
  Bond angle restraints: 16975
  Sorted by residual:
  angle pdb=" CA  MET A   1 "
        pdb=" CB  MET A   1 "
        pdb=" CG  MET A   1 "
      ideal   model   delta    sigma   weight residual
     114.10  119.35   -5.25 2.00e+00 2.50e-01 6.89e+00
  angle pdb=" C   MET A   1 "
        pdb=" CA  MET A   1 "
        pdb=" CB  MET A   1 "
      ideal   model   delta    sigma   weight residual
     110.10  115.03   -4.93 1.90e+00 2.77e-01 6.73e+00
  angle pdb=" CB  MET A   1 "
        pdb=" CG  MET A   1 "
        pdb=" SD  MET A   1 "
      ideal   model   delta    sigma   weight residual
     112.70  120.24   -7.54 3.00e+00 1.11e-01 6.32e+00
  angle pdb=" CB  MET A   5 "
        pdb=" CG  MET A   5 "
        pdb=" SD  MET A   5 "
      ideal   model   delta    sigma   weight residual
     112.70  120.11   -7.41 3.00e+00 1.11e-01 6.09e+00
  angle pdb=" N   THR A 351 "
        pdb=" CA  THR A 351 "
        pdb=" C   THR A 351 "
      ideal   model   delta    sigma   weight residual
     109.81  115.15   -5.34 2.21e+00 2.05e-01 5.83e+00
  ... (remaining 16970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 6772
       16.25 -    32.50: 606
       32.50 -    48.75: 155
       48.75 -    65.01: 25
       65.01 -    81.26: 10
  Dihedral angle restraints: 7568
    sinusoidal: 3069
      harmonic: 4499
  Sorted by residual:
  dihedral pdb=" CA  TRP B 370 "
           pdb=" C   TRP B 370 "
           pdb=" N   LEU B 371 "
           pdb=" CA  LEU B 371 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.95   19.05     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  LYS A 358 "
           pdb=" C   LYS A 358 "
           pdb=" N   PRO A 359 "
           pdb=" CA  PRO A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.53   18.47     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  MET A 749 "
           pdb=" C   MET A 749 "
           pdb=" N   THR A 750 "
           pdb=" CA  THR A 750 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.24  -17.76     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 7565 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1266
       0.032 -    0.063: 487
       0.063 -    0.095: 102
       0.095 -    0.127: 48
       0.127 -    0.158: 2
  Chirality restraints: 1905
  Sorted by residual:
  chirality pdb=" CG  LEU A 371 "
            pdb=" CB  LEU A 371 "
            pdb=" CD1 LEU A 371 "
            pdb=" CD2 LEU A 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  THR A 351 "
            pdb=" N   THR A 351 "
            pdb=" C   THR A 351 "
            pdb=" CB  THR A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.78e-01
  chirality pdb=" CA  ILE B 768 "
            pdb=" N   ILE B 768 "
            pdb=" C   ILE B 768 "
            pdb=" CB  ILE B 768 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 1902 not shown)

  Planarity restraints: 2206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 358 "   -0.034 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO A 359 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 359 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 359 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 100 "   -0.029 5.00e-02 4.00e+02   4.35e-02 3.02e+00
        pdb=" N   PRO B 101 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 101 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 101 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 199 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.72e+00
        pdb=" N   PRO A 200 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 200 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 200 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2203 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2656
        2.78 -     3.31: 12751
        3.31 -     3.84: 20609
        3.84 -     4.37: 24398
        4.37 -     4.90: 38856
  Nonbonded interactions: 99270
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 500 "
            pdb=" N   HIS A 501 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" NH2 ARG B 527 "
            pdb=" O   LEU B 775 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" O   ALA B  18 "
            pdb=" NE  ARG B  19 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OG1 THR A 144 "
            pdb=" OG1 THR A 178 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" O   GLU A 821 "
            pdb=" NH2 ARG A 828 "
     model   vdw
     2.362 3.120
  ... (remaining 99265 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 335 or resid 353 through 787))
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.020
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6642
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   0.025  12527  Z= 0.085
  Angle     :  0.510   7.543  16975  Z= 0.243
  Chirality :  0.037   0.158   1905
  Planarity :  0.003   0.051   2206
  Dihedral  : 13.554  81.257   4650
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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: -0.12 (0.21), residues: 1529
  helix: -0.02 (0.17), residues: 951
  sheet:  1.37 (0.60), residues: 81
  loop : -0.14 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 451 
 TYR   0.016   0.001   TYR B 632 
 PHE   0.014   0.001   PHE B 476 
 TRP   0.019   0.001   TRP A 364 
 HIS   0.006   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00177 (12527)
  covalent geometry    : angle       0.50985 (16975)
  hydrogen bonds       : bond        0.25582 (  641)
  hydrogen bonds       : angle       7.12460 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.8134 (ttt) cc_final: 0.7601 (ttt)
REVERT: B  447 MET cc_start: 0.6652 (ppp) cc_final: 0.6400 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0885
  time to fit residues: 24.1421
Evaluate side-chains
  137 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   30.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:   10.0000
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 250 GLN
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
B 483 HIS
B 659 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.070156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.043795 restraints weight = 71241.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.045166 restraints weight = 55145.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.046200 restraints weight = 45586.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.046981 restraints weight = 39456.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.047593 restraints weight = 35360.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089  12527  Z= 0.264
  Angle     :  0.698   7.611  16975  Z= 0.373
  Chirality :  0.042   0.160   1905
  Planarity :  0.005   0.052   2206
  Dihedral  :  4.072  21.987   1659
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.47 %
    Favored  : 94.38 %
  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:  0.19 (0.21), residues: 1529
  helix:  0.19 (0.16), residues: 975
  sheet:  1.27 (0.65), residues: 71
  loop :  0.15 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 325 
 TYR   0.016   0.002   TYR A 120 
 PHE   0.026   0.003   PHE B 641 
 TRP   0.025   0.003   TRP B 137 
 HIS   0.012   0.002   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (12527)
  covalent geometry    : angle       0.69849 (16975)
  hydrogen bonds       : bond        0.05040 (  641)
  hydrogen bonds       : angle       5.03906 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6011 (tmm) cc_final: 0.5271 (tmm)
REVERT: A  169 HIS cc_start: 0.9157 (m90) cc_final: 0.8941 (m170)
REVERT: A  250 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8993 (pp30)
REVERT: A  516 MET cc_start: 0.9479 (tpp) cc_final: 0.9170 (tpp)
REVERT: A  766 MET cc_start: 0.9328 (mtm) cc_final: 0.8944 (mpp)
REVERT: B   35 MET cc_start: 0.9365 (mmp) cc_final: 0.8917 (mmm)
REVERT: B   39 MET cc_start: 0.9236 (mpp) cc_final: 0.8409 (mpp)
REVERT: B  370 TRP cc_start: 0.9309 (m-90) cc_final: 0.9012 (m100)
REVERT: B  476 PHE cc_start: 0.9170 (p90) cc_final: 0.8884 (p90)
REVERT: B  512 MET cc_start: 0.9308 (ptp) cc_final: 0.8879 (ptp)
REVERT: B  693 TRP cc_start: 0.9800 (t60) cc_final: 0.9470 (t60)
  outliers start: 2
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0985
  time to fit residues: 24.9834
Evaluate side-chains
  130 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 134 optimal weight:   30.0000
   chunk 139 optimal weight:    6.9990
   chunk 125 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 148 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 150 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 122 optimal weight:    0.0050
   chunk 39 optimal weight:    7.9990
   chunk 129 optimal weight:    0.7980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
B 483 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.074629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.047796 restraints weight = 68332.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.049361 restraints weight = 52195.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.050516 restraints weight = 42672.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.051404 restraints weight = 36594.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.052092 restraints weight = 32479.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12527  Z= 0.112
  Angle     :  0.571   9.309  16975  Z= 0.286
  Chirality :  0.040   0.140   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.908  19.631   1659
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.77 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.21), residues: 1529
  helix:  0.35 (0.16), residues: 974
  sheet:  1.11 (0.59), residues: 81
  loop :  0.03 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 451 
 TYR   0.022   0.001   TYR A 120 
 PHE   0.029   0.002   PHE B 760 
 TRP   0.009   0.001   TRP B 693 
 HIS   0.017   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (12527)
  covalent geometry    : angle       0.57053 (16975)
  hydrogen bonds       : bond        0.04300 (  641)
  hydrogen bonds       : angle       4.59017 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5647 (tmm) cc_final: 0.4739 (tmm)
REVERT: A  515 PHE cc_start: 0.9522 (m-80) cc_final: 0.9266 (m-80)
REVERT: A  516 MET cc_start: 0.9470 (tpp) cc_final: 0.9185 (tpp)
REVERT: A  766 MET cc_start: 0.9324 (mtm) cc_final: 0.9034 (mtt)
REVERT: B  163 MET cc_start: 0.9165 (tpt) cc_final: 0.8852 (tpp)
REVERT: B  297 GLU cc_start: 0.9184 (mp0) cc_final: 0.8871 (mp0)
REVERT: B  370 TRP cc_start: 0.9373 (m-90) cc_final: 0.9061 (m100)
REVERT: B  476 PHE cc_start: 0.9083 (p90) cc_final: 0.8743 (p90)
REVERT: B  512 MET cc_start: 0.9194 (ptp) cc_final: 0.8989 (ptp)
  outliers start: 1
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0876
  time to fit residues: 23.3664
Evaluate side-chains
  137 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 153 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 125 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 37 optimal weight:    2.9990
   chunk 102 optimal weight:    9.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.073891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.047424 restraints weight = 67998.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.048939 restraints weight = 52320.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.050011 restraints weight = 42836.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.050902 restraints weight = 36919.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.051594 restraints weight = 32787.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12527  Z= 0.112
  Angle     :  0.545   8.250  16975  Z= 0.276
  Chirality :  0.039   0.161   1905
  Planarity :  0.004   0.049   2206
  Dihedral  :  3.876  19.298   1659
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  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:  0.46 (0.21), residues: 1529
  helix:  0.49 (0.16), residues: 977
  sheet:  0.98 (0.59), residues: 81
  loop :  0.08 (0.30), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.014   0.001   TYR B 460 
 PHE   0.024   0.001   PHE B 760 
 TRP   0.008   0.001   TRP B 370 
 HIS   0.014   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (12527)
  covalent geometry    : angle       0.54469 (16975)
  hydrogen bonds       : bond        0.03735 (  641)
  hydrogen bonds       : angle       4.45415 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5625 (tmm) cc_final: 0.4626 (tmm)
REVERT: A   66 ARG cc_start: 0.9212 (ptt-90) cc_final: 0.8733 (ptm160)
REVERT: A  169 HIS cc_start: 0.9272 (m90) cc_final: 0.9032 (m170)
REVERT: A  317 MET cc_start: 0.9151 (mtt) cc_final: 0.8914 (ptp)
REVERT: A  515 PHE cc_start: 0.9545 (m-80) cc_final: 0.9266 (m-80)
REVERT: A  516 MET cc_start: 0.9468 (tpp) cc_final: 0.9166 (tpp)
REVERT: A  670 ILE cc_start: 0.9815 (tp) cc_final: 0.9558 (pt)
REVERT: A  766 MET cc_start: 0.9327 (mtm) cc_final: 0.8945 (mpp)
REVERT: B  163 MET cc_start: 0.9222 (tpt) cc_final: 0.8893 (tpp)
REVERT: B  370 TRP cc_start: 0.9356 (m-90) cc_final: 0.9072 (m100)
REVERT: B  476 PHE cc_start: 0.9079 (p90) cc_final: 0.8724 (p90)
REVERT: B  512 MET cc_start: 0.9182 (ptp) cc_final: 0.8921 (ptp)
REVERT: B  632 TYR cc_start: 0.9068 (t80) cc_final: 0.8857 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0922
  time to fit residues: 24.3587
Evaluate side-chains
  132 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
A 257 GLN
A 539 GLN
B  70 HIS
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.074389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.047859 restraints weight = 69326.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.049357 restraints weight = 53024.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.050493 restraints weight = 43503.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.051347 restraints weight = 37351.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.052035 restraints weight = 33178.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.085  12527  Z= 0.112
  Angle     :  0.557   8.217  16975  Z= 0.277
  Chirality :  0.042   0.627   1905
  Planarity :  0.004   0.049   2206
  Dihedral  :  3.898  19.071   1659
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  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:  0.52 (0.22), residues: 1529
  helix:  0.55 (0.17), residues: 976
  sheet:  0.86 (0.59), residues: 81
  loop :  0.11 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 475 
 TYR   0.021   0.001   TYR A 120 
 PHE   0.019   0.001   PHE B 760 
 TRP   0.009   0.001   TRP B 370 
 HIS   0.014   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (12527)
  covalent geometry    : angle       0.55675 (16975)
  hydrogen bonds       : bond        0.03636 (  641)
  hydrogen bonds       : angle       4.45016 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5573 (tmm) cc_final: 0.4471 (tmm)
REVERT: A  317 MET cc_start: 0.9104 (mtt) cc_final: 0.8889 (mmt)
REVERT: A  467 MET cc_start: 0.7899 (ptp) cc_final: 0.7608 (ptt)
REVERT: A  515 PHE cc_start: 0.9544 (m-80) cc_final: 0.9268 (m-80)
REVERT: A  516 MET cc_start: 0.9465 (tpp) cc_final: 0.9164 (tpp)
REVERT: A  670 ILE cc_start: 0.9824 (tp) cc_final: 0.9533 (pt)
REVERT: A  766 MET cc_start: 0.9317 (mtm) cc_final: 0.8921 (mpp)
REVERT: B  163 MET cc_start: 0.9226 (tpt) cc_final: 0.8913 (tpp)
REVERT: B  297 GLU cc_start: 0.9178 (mp0) cc_final: 0.8808 (mp0)
REVERT: B  370 TRP cc_start: 0.9356 (m-90) cc_final: 0.9070 (m100)
REVERT: B  447 MET cc_start: 0.8303 (ppp) cc_final: 0.8076 (ppp)
REVERT: B  476 PHE cc_start: 0.9091 (p90) cc_final: 0.8729 (p90)
REVERT: B  512 MET cc_start: 0.9125 (ptp) cc_final: 0.8823 (ptm)
REVERT: B  632 TYR cc_start: 0.9060 (t80) cc_final: 0.8849 (t80)
REVERT: B  693 TRP cc_start: 0.9770 (t60) cc_final: 0.9568 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0920
  time to fit residues: 24.2542
Evaluate side-chains
  129 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 135 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 88 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 114 optimal weight:    4.9990
   chunk 149 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 151 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
A 110 GLN
B  70 HIS
B 165 GLN
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.072663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.046222 restraints weight = 69689.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.047626 restraints weight = 53736.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.048643 restraints weight = 44161.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.049446 restraints weight = 38205.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.050096 restraints weight = 34170.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12527  Z= 0.139
  Angle     :  0.574   8.152  16975  Z= 0.290
  Chirality :  0.041   0.453   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.955  19.359   1659
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  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:  0.55 (0.22), residues: 1529
  helix:  0.57 (0.17), residues: 967
  sheet:  0.74 (0.60), residues: 79
  loop :  0.16 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 325 
 TYR   0.013   0.002   TYR B 288 
 PHE   0.023   0.002   PHE A 490 
 TRP   0.013   0.001   TRP B 370 
 HIS   0.014   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12527)
  covalent geometry    : angle       0.57403 (16975)
  hydrogen bonds       : bond        0.03506 (  641)
  hydrogen bonds       : angle       4.46624 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5765 (tmm) cc_final: 0.4355 (tmm)
REVERT: A  272 MET cc_start: 0.8890 (ttt) cc_final: 0.8517 (ttt)
REVERT: A  317 MET cc_start: 0.9169 (mtt) cc_final: 0.8942 (mtt)
REVERT: A  364 TRP cc_start: 0.7808 (m100) cc_final: 0.6960 (m100)
REVERT: A  467 MET cc_start: 0.7899 (ptp) cc_final: 0.7562 (ptt)
REVERT: A  515 PHE cc_start: 0.9565 (m-80) cc_final: 0.9259 (m-80)
REVERT: A  516 MET cc_start: 0.9515 (tpp) cc_final: 0.9187 (tpp)
REVERT: A  670 ILE cc_start: 0.9841 (tp) cc_final: 0.9541 (pt)
REVERT: A  766 MET cc_start: 0.9296 (mtm) cc_final: 0.8923 (mpp)
REVERT: B  163 MET cc_start: 0.9312 (tpt) cc_final: 0.9029 (tpp)
REVERT: B  262 MET cc_start: 0.9110 (mmp) cc_final: 0.8867 (mmm)
REVERT: B  297 GLU cc_start: 0.9086 (mp0) cc_final: 0.8778 (mp0)
REVERT: B  370 TRP cc_start: 0.9334 (m-90) cc_final: 0.9083 (m100)
REVERT: B  476 PHE cc_start: 0.9126 (p90) cc_final: 0.8777 (p90)
REVERT: B  512 MET cc_start: 0.9154 (ptp) cc_final: 0.8841 (ptm)
REVERT: B  693 TRP cc_start: 0.9769 (t60) cc_final: 0.9568 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0695
  time to fit residues: 18.2630
Evaluate side-chains
  127 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 56 optimal weight:    0.4980
   chunk 79 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   chunk 149 optimal weight:    5.9990
   chunk 122 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
B  70 HIS
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.074022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.047427 restraints weight = 69251.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.048916 restraints weight = 53118.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.050044 restraints weight = 43509.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.050911 restraints weight = 37405.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.051408 restraints weight = 33312.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061  12527  Z= 0.111
  Angle     :  0.584  13.667  16975  Z= 0.285
  Chirality :  0.040   0.331   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.933  19.089   1659
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  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:  0.63 (0.22), residues: 1529
  helix:  0.62 (0.17), residues: 975
  sheet:  0.74 (0.60), residues: 79
  loop :  0.22 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 451 
 TYR   0.013   0.001   TYR B 288 
 PHE   0.020   0.001   PHE A 490 
 TRP   0.012   0.001   TRP B 370 
 HIS   0.013   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (12527)
  covalent geometry    : angle       0.58432 (16975)
  hydrogen bonds       : bond        0.03372 (  641)
  hydrogen bonds       : angle       4.37564 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6418 (tmm) cc_final: 0.6000 (tmm)
REVERT: A  317 MET cc_start: 0.9170 (mtt) cc_final: 0.8880 (mmt)
REVERT: A  364 TRP cc_start: 0.7731 (m100) cc_final: 0.6987 (m100)
REVERT: A  467 MET cc_start: 0.7876 (ptp) cc_final: 0.7571 (ptt)
REVERT: A  515 PHE cc_start: 0.9552 (m-80) cc_final: 0.9247 (m-80)
REVERT: A  516 MET cc_start: 0.9492 (tpp) cc_final: 0.9166 (tpp)
REVERT: A  670 ILE cc_start: 0.9842 (tp) cc_final: 0.9539 (pt)
REVERT: A  766 MET cc_start: 0.9288 (mtm) cc_final: 0.8899 (mpp)
REVERT: B  163 MET cc_start: 0.9264 (tpt) cc_final: 0.9019 (tpp)
REVERT: B  297 GLU cc_start: 0.9052 (mp0) cc_final: 0.8721 (mp0)
REVERT: B  370 TRP cc_start: 0.9350 (m-90) cc_final: 0.9089 (m100)
REVERT: B  447 MET cc_start: 0.8295 (ppp) cc_final: 0.8061 (ppp)
REVERT: B  476 PHE cc_start: 0.9106 (p90) cc_final: 0.8744 (p90)
REVERT: B  512 MET cc_start: 0.9112 (ptp) cc_final: 0.8792 (ptm)
REVERT: B  632 TYR cc_start: 0.9092 (t80) cc_final: 0.8863 (t80)
REVERT: B  693 TRP cc_start: 0.9764 (t60) cc_final: 0.9553 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0710
  time to fit residues: 18.7661
Evaluate side-chains
  130 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 42 optimal weight:    0.0270
   chunk 21 optimal weight:    3.9990
   chunk 136 optimal weight:    0.2980
   chunk 152 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 149 optimal weight:    6.9990
   chunk 81 optimal weight:    8.9990
   chunk 73 optimal weight:    8.9990
   chunk 69 optimal weight:    0.3980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 174 ASN
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.075011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.047986 restraints weight = 68184.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.049537 restraints weight = 52364.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.050659 restraints weight = 42928.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.051558 restraints weight = 36963.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.052254 restraints weight = 32942.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  12527  Z= 0.103
  Angle     :  0.572   8.466  16975  Z= 0.280
  Chirality :  0.040   0.174   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.899  21.164   1659
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  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:  0.66 (0.22), residues: 1529
  helix:  0.65 (0.17), residues: 975
  sheet:  0.81 (0.60), residues: 79
  loop :  0.22 (0.31), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 751 
 TYR   0.013   0.001   TYR A 288 
 PHE   0.030   0.001   PHE B 760 
 TRP   0.021   0.001   TRP B 370 
 HIS   0.014   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (12527)
  covalent geometry    : angle       0.57152 (16975)
  hydrogen bonds       : bond        0.03294 (  641)
  hydrogen bonds       : angle       4.30259 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6719 (tmm) cc_final: 0.6108 (tmm)
REVERT: A  272 MET cc_start: 0.8844 (ttt) cc_final: 0.8490 (ttt)
REVERT: A  317 MET cc_start: 0.9173 (mtt) cc_final: 0.8904 (mmt)
REVERT: A  364 TRP cc_start: 0.7789 (m100) cc_final: 0.7101 (m100)
REVERT: A  467 MET cc_start: 0.7887 (ptp) cc_final: 0.7621 (ptt)
REVERT: A  515 PHE cc_start: 0.9544 (m-80) cc_final: 0.9258 (m-80)
REVERT: A  516 MET cc_start: 0.9478 (tpp) cc_final: 0.9164 (tpp)
REVERT: A  670 ILE cc_start: 0.9830 (tp) cc_final: 0.9532 (pt)
REVERT: A  766 MET cc_start: 0.9307 (mtm) cc_final: 0.8907 (mpp)
REVERT: B  163 MET cc_start: 0.9280 (tpt) cc_final: 0.9020 (tpp)
REVERT: B  297 GLU cc_start: 0.8997 (mp0) cc_final: 0.8687 (mp0)
REVERT: B  370 TRP cc_start: 0.9374 (m-90) cc_final: 0.9124 (m100)
REVERT: B  476 PHE cc_start: 0.9118 (p90) cc_final: 0.8745 (p90)
REVERT: B  512 MET cc_start: 0.9100 (ptp) cc_final: 0.8778 (ptm)
REVERT: B  632 TYR cc_start: 0.9099 (t80) cc_final: 0.8858 (t80)
REVERT: B  693 TRP cc_start: 0.9759 (t60) cc_final: 0.9538 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0770
  time to fit residues: 20.7130
Evaluate side-chains
  137 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    0.9990
   chunk 144 optimal weight:    3.9990
   chunk 151 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0050
   chunk 99 optimal weight:    0.7980
   chunk 121 optimal weight:    5.9990
   chunk 128 optimal weight:    4.9990
   chunk 117 optimal weight:    0.4980
   chunk 10 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.075408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.048299 restraints weight = 67236.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.049820 restraints weight = 51691.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.050975 restraints weight = 42359.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.051891 restraints weight = 36387.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.052374 restraints weight = 32322.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12527  Z= 0.099
  Angle     :  0.564   7.752  16975  Z= 0.276
  Chirality :  0.039   0.159   1905
  Planarity :  0.004   0.050   2206
  Dihedral  :  3.851  21.116   1659
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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:  0.71 (0.22), residues: 1529
  helix:  0.68 (0.17), residues: 979
  sheet:  0.78 (0.60), residues: 79
  loop :  0.27 (0.31), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 451 
 TYR   0.013   0.001   TYR B 288 
 PHE   0.033   0.001   PHE B 760 
 TRP   0.016   0.001   TRP B 370 
 HIS   0.013   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (12527)
  covalent geometry    : angle       0.56409 (16975)
  hydrogen bonds       : bond        0.03175 (  641)
  hydrogen bonds       : angle       4.24914 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6582 (tmm) cc_final: 0.5969 (tmm)
REVERT: A  116 LYS cc_start: 0.9247 (tmtt) cc_final: 0.9023 (mmtt)
REVERT: A  169 HIS cc_start: 0.9222 (m90) cc_final: 0.8974 (m170)
REVERT: A  272 MET cc_start: 0.8865 (ttt) cc_final: 0.8498 (ttt)
REVERT: A  317 MET cc_start: 0.9182 (mtt) cc_final: 0.8931 (mmt)
REVERT: A  364 TRP cc_start: 0.7809 (m100) cc_final: 0.7192 (m100)
REVERT: A  467 MET cc_start: 0.7885 (ptp) cc_final: 0.7564 (ptt)
REVERT: A  515 PHE cc_start: 0.9553 (m-80) cc_final: 0.9268 (m-80)
REVERT: A  516 MET cc_start: 0.9487 (tpp) cc_final: 0.9174 (tpp)
REVERT: A  670 ILE cc_start: 0.9836 (tp) cc_final: 0.9532 (pt)
REVERT: A  766 MET cc_start: 0.9301 (mtm) cc_final: 0.8895 (mpp)
REVERT: B  163 MET cc_start: 0.9252 (tpt) cc_final: 0.9047 (tpp)
REVERT: B  297 GLU cc_start: 0.9008 (mp0) cc_final: 0.8650 (mp0)
REVERT: B  370 TRP cc_start: 0.9362 (m-90) cc_final: 0.9096 (m100)
REVERT: B  476 PHE cc_start: 0.9123 (p90) cc_final: 0.8766 (p90)
REVERT: B  512 MET cc_start: 0.9129 (ptp) cc_final: 0.8814 (ptm)
REVERT: B  693 TRP cc_start: 0.9757 (t60) cc_final: 0.9533 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0793
  time to fit residues: 21.1136
Evaluate side-chains
  134 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 123 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 77 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 78 optimal weight:    6.9990
   chunk 92 optimal weight:    0.7980
   chunk 121 optimal weight:    0.9980
   chunk 132 optimal weight:   30.0000
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.075293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.048186 restraints weight = 67502.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.049698 restraints weight = 51929.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.050886 restraints weight = 42685.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.051687 restraints weight = 36625.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.052428 restraints weight = 32812.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  12527  Z= 0.103
  Angle     :  0.578   9.532  16975  Z= 0.283
  Chirality :  0.040   0.240   1905
  Planarity :  0.004   0.049   2206
  Dihedral  :  3.848  21.473   1659
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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:  0.65 (0.22), residues: 1529
  helix:  0.64 (0.17), residues: 985
  sheet:  0.79 (0.61), residues: 79
  loop :  0.20 (0.31), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 451 
 TYR   0.013   0.001   TYR B 288 
 PHE   0.034   0.001   PHE B 760 
 TRP   0.012   0.001   TRP B 370 
 HIS   0.014   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (12527)
  covalent geometry    : angle       0.57797 (16975)
  hydrogen bonds       : bond        0.03108 (  641)
  hydrogen bonds       : angle       4.25065 ( 1887)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6549 (tmm) cc_final: 0.5948 (tmm)
REVERT: A  169 HIS cc_start: 0.9229 (m90) cc_final: 0.8992 (m170)
REVERT: A  272 MET cc_start: 0.8883 (ttt) cc_final: 0.8508 (ttt)
REVERT: A  317 MET cc_start: 0.9198 (mtt) cc_final: 0.8989 (mmt)
REVERT: A  364 TRP cc_start: 0.7875 (m100) cc_final: 0.7314 (m100)
REVERT: A  467 MET cc_start: 0.7905 (ptp) cc_final: 0.7643 (ptt)
REVERT: A  515 PHE cc_start: 0.9575 (m-80) cc_final: 0.9294 (m-80)
REVERT: A  516 MET cc_start: 0.9483 (tpp) cc_final: 0.9173 (tpp)
REVERT: A  670 ILE cc_start: 0.9822 (tp) cc_final: 0.9512 (pt)
REVERT: A  766 MET cc_start: 0.9304 (mtm) cc_final: 0.8898 (mpp)
REVERT: B  163 MET cc_start: 0.9266 (tpt) cc_final: 0.9065 (tpp)
REVERT: B  370 TRP cc_start: 0.9362 (m-90) cc_final: 0.9096 (m100)
REVERT: B  476 PHE cc_start: 0.9129 (p90) cc_final: 0.8752 (p90)
REVERT: B  512 MET cc_start: 0.9091 (ptp) cc_final: 0.8773 (ptm)
REVERT: B  632 TYR cc_start: 0.8915 (t80) cc_final: 0.8704 (t80)
REVERT: B  693 TRP cc_start: 0.9752 (t60) cc_final: 0.9527 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0772
  time to fit residues: 20.6776
Evaluate side-chains
  135 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 140 optimal weight:    9.9990
   chunk 133 optimal weight:    7.9990
   chunk 116 optimal weight:    0.0070
   chunk 20 optimal weight:    6.9990
   chunk 100 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 102 optimal weight:    9.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    2.1404

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 483 HIS
B 539 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.074356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.047436 restraints weight = 68211.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.048914 restraints weight = 52329.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.050021 restraints weight = 42973.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.050916 restraints weight = 36964.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.051409 restraints weight = 32906.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12527  Z= 0.128
  Angle     :  0.580   8.682  16975  Z= 0.290
  Chirality :  0.040   0.180   1905
  Planarity :  0.004   0.048   2206
  Dihedral  :  3.903  21.990   1659
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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:  0.65 (0.22), residues: 1529
  helix:  0.66 (0.17), residues: 986
  sheet:  0.67 (0.61), residues: 79
  loop :  0.17 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.013   0.001   TYR B 288 
 PHE   0.033   0.002   PHE B 760 
 TRP   0.011   0.001   TRP B 364 
 HIS   0.015   0.001   HIS B 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (12527)
  covalent geometry    : angle       0.58041 (16975)
  hydrogen bonds       : bond        0.03133 (  641)
  hydrogen bonds       : angle       4.27906 ( 1887)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2100.04 seconds
wall clock time: 37 minutes 3.42 seconds (2223.42 seconds total)