Starting phenix.real_space_refine
on Tue Mar  3 23:32:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n59_24183/03_2026/7n59_24183.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n59_24183/03_2026/7n59_24183.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n59_24183/03_2026/7n59_24183.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n59_24183/03_2026/7n59_24183.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n59_24183/03_2026/7n59_24183.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n59_24183/03_2026/7n59_24183.map"
  }
  resolution = 3.6
  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=   0.001 sd=   0.021
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      36      5.16       5
     C    5892      2.51       5
     N    1584      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9238
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4599
          Classifications: {'peptide': 590}
          Link IDs: {'PTRANS': 13, 'TRANS': 576}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4599
          Classifications: {'peptide': 590}
          Link IDs: {'PTRANS': 13, 'TRANS': 576}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'GDS': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" CB1 GDS A 801 " occ=0.50
      ... (38 atoms not shown)
      pdb=" SG5 GDS A 801 " occ=0.50
  Time building chain proxies: 2.12, per 1000 atoms: 0.23
  Number of scatterers: 9238
  At special positions: 0
  Unit cell: (81.225, 98.325, 142.785, 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      36     16.00
     O    1726      8.00
     N    1584      7.00
     C    5892      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: 0.74
  Conformation dependent library (CDL) restraints added in 371.1 milliseconds
  

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 6 sheets defined
      69.2% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 117 through 133
    Processing helix  chain 'A' and resid 136 through 175
      removed outlier: 4.217A  pdb=" N   ARG A 140 " --> pdb=" O   ASN A 136 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ARG A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
      removed outlier: 3.602A  pdb=" N   PHE A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 243
      removed outlier: 3.703A  pdb=" N   VAL A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLY A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   VAL A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 253
      removed outlier: 3.542A  pdb=" N   HIS A 250 " --> pdb=" O   ASP A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 279
    Processing helix  chain 'A' and resid 279 through 294
    Processing helix  chain 'A' and resid 300 through 348
      removed outlier: 3.761A  pdb=" N   TRP A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   VAL A 310 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LYS A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ALA A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP A 335 " --> pdb=" O   MET A 331 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN A 348 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 355
      removed outlier: 3.649A  pdb=" N   VAL A 352 " --> pdb=" O   ASN A 348 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   PHE A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 412
      removed outlier: 3.598A  pdb=" N   GLU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLY A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 431
      removed outlier: 3.592A  pdb=" N   LEU A 431 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 434
      No H-bonds generated for 'chain 'A' and resid 432 through 434'
    Processing helix  chain 'A' and resid 435 through 457
    Processing helix  chain 'A' and resid 513 through 517
      removed outlier: 3.811A  pdb=" N   GLY A 517 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 526
    Processing helix  chain 'A' and resid 547 through 554
      removed outlier: 3.913A  pdb=" N   LEU A 551 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 575
    Processing helix  chain 'A' and resid 581 through 592
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 617 through 633
    Processing helix  chain 'A' and resid 647 through 662
    Processing helix  chain 'A' and resid 673 through 677
    Processing helix  chain 'A' and resid 696 through 704
    Processing helix  chain 'A' and resid 705 through 713
      removed outlier: 3.678A  pdb=" N   GLN A 709 " --> pdb=" O   GLY A 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 133
      removed outlier: 3.685A  pdb=" N   MET B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 175
      removed outlier: 4.432A  pdb=" N   ARG B 140 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
      Proline residue:  B 161  - end of helix
    Processing helix  chain 'B' and resid 197 through 245
      removed outlier: 3.563A  pdb=" N   VAL B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASP B 244 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 245 " --> pdb=" O   HIS B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 253
      removed outlier: 3.975A  pdb=" N   HIS B 250 " --> pdb=" O   ASP B 246 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ARG B 253 " --> pdb=" O   TYR B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 279
      removed outlier: 4.104A  pdb=" N   ARG B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 296
    Processing helix  chain 'B' and resid 300 through 348
      removed outlier: 3.654A  pdb=" N   TRP B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   LYS B 326 " --> pdb=" O   GLN B 322 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   PHE B 327 " --> pdb=" O   TRP B 323 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN B 348 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 355
      removed outlier: 3.519A  pdb=" N   VAL B 352 " --> pdb=" O   ASN B 348 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 412
      removed outlier: 3.515A  pdb=" N   LYS B 364 " --> pdb=" O   TYR B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 431
      removed outlier: 3.631A  pdb=" N   LEU B 431 " --> pdb=" O   PHE B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 434
      No H-bonds generated for 'chain 'B' and resid 432 through 434'
    Processing helix  chain 'B' and resid 435 through 457
      removed outlier: 3.705A  pdb=" N   LEU B 457 " --> pdb=" O   MET B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 517
      removed outlier: 3.865A  pdb=" N   GLY B 517 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 526
    Processing helix  chain 'B' and resid 547 through 554
      removed outlier: 3.890A  pdb=" N   LEU B 551 " --> pdb=" O   ARG B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 575
    Processing helix  chain 'B' and resid 581 through 592
    Processing helix  chain 'B' and resid 594 through 600
      removed outlier: 3.675A  pdb=" N   ASN B 600 " --> pdb=" O   GLU B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 633
    Processing helix  chain 'B' and resid 647 through 662
    Processing helix  chain 'B' and resid 673 through 680
      removed outlier: 4.204A  pdb=" N   MET B 678 " --> pdb=" O   THR B 675 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN B 679 " --> pdb=" O   THR B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 704
    Processing helix  chain 'B' and resid 705 through 713
      removed outlier: 3.586A  pdb=" N   GLN B 709 " --> pdb=" O   GLY B 705 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498
      removed outlier: 4.878A  pdb=" N   VAL A 484 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 498
      removed outlier: 4.878A  pdb=" N   VAL A 484 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   VAL A 484 " --> pdb=" O   SER A 533 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   SER A 533 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 557
      removed outlier: 3.554A  pdb=" N   ILE A 670 " --> pdb=" O   CYS A 639 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   VAL A 508 " --> pdb=" O   PHE A 669 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   SER A 507 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   VAL A 684 " --> pdb=" O   SER A 507 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   ALA A 509 " --> pdb=" O   VAL A 684 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   LEU A 686 " --> pdb=" O   ALA A 509 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   VAL A 511 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLU A 693 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 495 through 498
      removed outlier: 3.657A  pdb=" N   LEU B 495 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE B 486 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
      removed outlier: 4.997A  pdb=" N   VAL B 484 " --> pdb=" O   GLY B 497 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 495 through 498
      removed outlier: 3.657A  pdb=" N   LEU B 495 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE B 486 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
      removed outlier: 4.997A  pdb=" N   VAL B 484 " --> pdb=" O   GLY B 497 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASN B 535 " --> pdb=" O   GLU B 482 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   VAL B 484 " --> pdb=" O   SER B 533 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   SER B 533 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 557
      removed outlier: 6.609A  pdb=" N   LEU B 637 " --> pdb=" O   ILE B 668 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE B 670 " --> pdb=" O   LEU B 637 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   CYS B 639 " --> pdb=" O   ILE B 670 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   VAL B 508 " --> pdb=" O   PHE B 669 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   SER B 507 " --> pdb=" O   GLU B 682 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   VAL B 684 " --> pdb=" O   SER B 507 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   ALA B 509 " --> pdb=" O   VAL B 684 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   LEU B 686 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   VAL B 511 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ILE B 683 " --> pdb=" O   GLN B 694 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLN B 694 " --> pdb=" O   ILE B 683 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   VAL B 685 " --> pdb=" O   VAL B 692 " (cutoff:3.500A)

    619 hydrogen bonds defined for protein.
    1821 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.18 -     1.37: 3059
        1.37 -     1.55: 6273
        1.55 -     1.73: 0
        1.73 -     1.92: 64
        1.92 -     2.10: 1
  Bond restraints: 9397
  Sorted by residual:
  bond pdb=" C5  GDS A 801 "
       pdb=" N4  GDS A 801 "
    ideal  model  delta    sigma   weight residual
    1.333  1.451 -0.118 2.00e-02 2.50e+03 3.47e+01
  bond pdb=" C2  GDS A 801 "
       pdb=" N3  GDS A 801 "
    ideal  model  delta    sigma   weight residual
    1.334  1.450 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" CD1 GDS A 801 "
       pdb=" N2  GDS A 801 "
    ideal  model  delta    sigma   weight residual
    1.339  1.451 -0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" CD6 GDS A 801 "
       pdb=" N5  GDS A 801 "
    ideal  model  delta    sigma   weight residual
    1.349  1.451 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" CD1 GDS A 801 "
       pdb=" O1  GDS A 801 "
    ideal  model  delta    sigma   weight residual
    1.242  1.184  0.058 2.00e-02 2.50e+03 8.48e+00
  ... (remaining 9392 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 12400
        1.64 -     3.28: 239
        3.28 -     4.91: 43
        4.91 -     6.55: 16
        6.55 -     8.19: 10
  Bond angle restraints: 12708
  Sorted by residual:
  angle pdb=" CB1 GDS A 801 "
        pdb=" CG1 GDS A 801 "
        pdb=" CD1 GDS A 801 "
      ideal   model   delta    sigma   weight residual
     117.94  109.75    8.19 3.00e+00 1.11e-01 7.45e+00
  angle pdb=" C   LEU B 242 "
        pdb=" N   HIS B 243 "
        pdb=" CA  HIS B 243 "
      ideal   model   delta    sigma   weight residual
     120.72  116.57    4.15 1.67e+00 3.59e-01 6.18e+00
  angle pdb=" OE5 GDS A 801 "
        pdb=" C4  GDS A 801 "
        pdb=" OE6 GDS A 801 "
      ideal   model   delta    sigma   weight residual
     127.28  120.08    7.20 3.00e+00 1.11e-01 5.76e+00
  angle pdb=" CB  MET A 121 "
        pdb=" CG  MET A 121 "
        pdb=" SD  MET A 121 "
      ideal   model   delta    sigma   weight residual
     112.70  119.79   -7.09 3.00e+00 1.11e-01 5.58e+00
  angle pdb=" OE3 GDS A 801 "
        pdb=" C3  GDS A 801 "
        pdb=" OE4 GDS A 801 "
      ideal   model   delta    sigma   weight residual
     127.19  120.15    7.04 3.00e+00 1.11e-01 5.50e+00
  ... (remaining 12703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.66: 5368
       26.66 -    53.32: 255
       53.32 -    79.98: 20
       79.98 -   106.64: 4
      106.64 -   133.30: 2
  Dihedral angle restraints: 5649
    sinusoidal: 2233
      harmonic: 3416
  Sorted by residual:
  dihedral pdb=" N4  GDS A 801 "
           pdb=" C5  GDS A 801 "
           pdb=" CA5 GDS A 801 "
           pdb=" N5  GDS A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     133.37    0.07  133.30     1      3.00e+01 1.11e-03 1.80e+01
  dihedral pdb=" CB5 GDS A 801 "
           pdb=" C5  GDS A 801 "
           pdb=" CA5 GDS A 801 "
           pdb=" N4  GDS A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     106.65 -121.23 -132.12     1      3.00e+01 1.11e-03 1.78e+01
  dihedral pdb=" CB2 GDS A 801 "
           pdb=" C2  GDS A 801 "
           pdb=" CA2 GDS A 801 "
           pdb=" O2  GDS A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      95.13    1.49   93.64     1      3.00e+01 1.11e-03 1.13e+01
  ... (remaining 5646 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1369
       0.075 -    0.151: 113
       0.151 -    0.226: 3
       0.226 -    0.301: 0
       0.301 -    0.377: 1
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" CA2 GDS A 801 "
            pdb=" CB2 GDS A 801 "
            pdb=" C2  GDS A 801 "
            pdb=" N2  GDS A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.24   -2.62    0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" CA1 GDS A 801 "
            pdb=" CB1 GDS A 801 "
            pdb=" C1  GDS A 801 "
            pdb=" N1  GDS A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.43   -2.61    0.18 2.00e-01 2.50e+01 8.35e-01
  chirality pdb=" CB  ILE B 538 "
            pdb=" CA  ILE B 538 "
            pdb=" CG1 ILE B 538 "
            pdb=" CG2 ILE B 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.30e-01
  ... (remaining 1483 not shown)

  Planarity restraints: 1614
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 711 "    0.021 2.00e-02 2.50e+03   1.76e-02 7.75e+00
        pdb=" CG  TRP B 711 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 711 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 711 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 711 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 711 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 711 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 711 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 711 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 711 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 323 "    0.019 2.00e-02 2.50e+03   1.55e-02 6.03e+00
        pdb=" CG  TRP A 323 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 323 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 323 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 323 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 323 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 323 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 323 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 323 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 323 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 711 "   -0.010 2.00e-02 2.50e+03   9.38e-03 2.20e+00
        pdb=" CG  TRP A 711 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 711 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 711 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 711 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 711 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 711 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 711 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 711 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 711 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1611 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1394
        2.76 -     3.29: 9460
        3.29 -     3.83: 15148
        3.83 -     4.36: 15671
        4.36 -     4.90: 27867
  Nonbonded interactions: 69540
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 358 "
            pdb=" OG  SER B 240 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" ND1 HIS A 243 "
            pdb=" OE2 GLU B 358 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   GLN B 709 "
            pdb=" OG1 THR B 712 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OD2 ASP A 366 "
            pdb=" NH1 ARG B 236 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   LEU B 661 "
            pdb=" NH2 ARG B 665 "
     model   vdw
     2.333 3.120
  ... (remaining 69535 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 117 through 716)
  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=0.50 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:             2.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.080
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.118   9397  Z= 0.196
  Angle     :  0.616   8.191  12708  Z= 0.309
  Chirality :  0.041   0.377   1486
  Planarity :  0.003   0.028   1614
  Dihedral  : 14.741 133.305   3441
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.20 %
    Favored  : 99.70 %
  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 are not related in a simple way.
  whole:  1.69 (0.25), residues: 1172
  helix:  2.28 (0.18), residues: 780
  sheet:  0.15 (0.66), residues: 72
  loop : -1.70 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 341 
 TYR   0.020   0.001   TYR B 707 
 PHE   0.018   0.001   PHE A 394 
 TRP   0.047   0.003   TRP B 711 
 HIS   0.005   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9397)
  covalent geometry    : angle       0.61573 (12708)
  hydrogen bonds       : bond        0.12953 (  615)
  hydrogen bonds       : angle       4.78874 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  121 MET cc_start: 0.7833 (tmm) cc_final: 0.7621 (tpt)
REVERT: A  286 GLU cc_start: 0.8134 (tp30) cc_final: 0.7613 (tt0)
REVERT: A  396 THR cc_start: 0.8851 (t) cc_final: 0.8596 (m)
REVERT: B  506 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7620 (mmtm)
REVERT: B  541 GLN cc_start: 0.7750 (tp40) cc_final: 0.7379 (tp40)
REVERT: B  688 ASN cc_start: 0.8256 (m-40) cc_final: 0.7899 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0863
  time to fit residues: 16.1898
Evaluate side-chains
  97 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0010
   chunk 65 optimal weight:    0.0010
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
A 688 ASN
B 390 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.185534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.139328 restraints weight = 12801.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.143627 restraints weight = 6687.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.146293 restraints weight = 4406.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.148017 restraints weight = 3436.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.148925 restraints weight = 2947.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3949 r_free = 0.3949    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9397  Z= 0.131
  Angle     :  0.525   7.158  12708  Z= 0.278
  Chirality :  0.039   0.140   1486
  Planarity :  0.004   0.049   1614
  Dihedral  :  8.977 114.072   1319
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.33 %
    Favored  : 90.46 %
  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 are not related in a simple way.
  whole:  2.04 (0.25), residues: 1172
  helix:  2.55 (0.18), residues: 780
  sheet:  0.19 (0.66), residues: 74
  loop : -1.58 (0.29), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 253 
 TYR   0.018   0.001   TYR B 205 
 PHE   0.017   0.001   PHE B 394 
 TRP   0.022   0.001   TRP A 323 
 HIS   0.003   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9397)
  covalent geometry    : angle       0.52505 (12708)
  hydrogen bonds       : bond        0.06354 (  615)
  hydrogen bonds       : angle       3.74840 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  286 GLU cc_start: 0.8100 (tp30) cc_final: 0.7624 (tt0)
REVERT: A  697 HIS cc_start: 0.7523 (p-80) cc_final: 0.7233 (p-80)
REVERT: B  506 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7592 (mmtm)
REVERT: B  541 GLN cc_start: 0.7928 (tp40) cc_final: 0.7706 (tp40)
REVERT: B  688 ASN cc_start: 0.8142 (m-40) cc_final: 0.7930 (p0)
  outliers start: 12
  outliers final: 6
  residues processed: 113
  average time/residue: 0.0848
  time to fit residues: 14.3204
Evaluate side-chains
  104 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  691 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0010
   chunk 99 optimal weight:    6.9990
   chunk 116 optimal weight:   20.0000
   chunk 61 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.8992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.183197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.137254 restraints weight = 12800.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.141170 restraints weight = 6962.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.143723 restraints weight = 4706.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.145049 restraints weight = 3706.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146033 restraints weight = 3234.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3870 r_free = 0.3870    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3869 r_free = 0.3869    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9397  Z= 0.137
  Angle     :  0.501   5.755  12708  Z= 0.268
  Chirality :  0.039   0.153   1486
  Planarity :  0.003   0.055   1614
  Dihedral  :  8.077  92.124   1319
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.05 %
    Favored  : 86.55 %
  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 are not related in a simple way.
  whole:  2.19 (0.24), residues: 1172
  helix:  2.64 (0.18), residues: 780
  sheet:  1.70 (0.77), residues: 48
  loop : -1.55 (0.28), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 236 
 TYR   0.017   0.001   TYR B 205 
 PHE   0.017   0.001   PHE A 394 
 TRP   0.012   0.001   TRP A 323 
 HIS   0.005   0.001   HIS B 697 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9397)
  covalent geometry    : angle       0.50091 (12708)
  hydrogen bonds       : bond        0.06453 (  615)
  hydrogen bonds       : angle       3.55848 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  286 GLU cc_start: 0.8149 (tp30) cc_final: 0.7715 (tt0)
REVERT: A  697 HIS cc_start: 0.7568 (p-80) cc_final: 0.7255 (p-80)
REVERT: B  506 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7608 (mmtm)
  outliers start: 14
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0812
  time to fit residues: 13.1628
Evaluate side-chains
  109 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  691 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 688 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.183598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.137601 restraints weight = 12947.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.141545 restraints weight = 7051.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.144100 restraints weight = 4746.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.145338 restraints weight = 3729.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.146548 restraints weight = 3266.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9397  Z= 0.129
  Angle     :  0.482   6.796  12708  Z= 0.257
  Chirality :  0.038   0.150   1486
  Planarity :  0.003   0.055   1614
  Dihedral  :  7.754  84.535   1319
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.15 %
    Favored  : 85.04 %
  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 are not related in a simple way.
  whole:  2.30 (0.24), residues: 1172
  helix:  2.73 (0.18), residues: 780
  sheet:  1.88 (0.77), residues: 48
  loop : -1.55 (0.27), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 236 
 TYR   0.017   0.001   TYR B 205 
 PHE   0.016   0.001   PHE A 394 
 TRP   0.009   0.001   TRP A 323 
 HIS   0.004   0.001   HIS B 697 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9397)
  covalent geometry    : angle       0.48186 (12708)
  hydrogen bonds       : bond        0.06258 (  615)
  hydrogen bonds       : angle       3.44594 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  286 GLU cc_start: 0.8160 (tp30) cc_final: 0.7709 (tt0)
REVERT: A  541 GLN cc_start: 0.8023 (tp40) cc_final: 0.7749 (tp40)
REVERT: A  697 HIS cc_start: 0.7604 (p-80) cc_final: 0.7283 (p-80)
REVERT: B  506 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7831 (mmtm)
  outliers start: 18
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0815
  time to fit residues: 13.3931
Evaluate side-chains
  113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  691 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0980
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    0.2980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.194396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.146660 restraints weight = 12474.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.150454 restraints weight = 6548.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.152918 restraints weight = 4313.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.154368 restraints weight = 3338.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.155137 restraints weight = 2884.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9397  Z= 0.141
  Angle     :  0.493   6.987  12708  Z= 0.265
  Chirality :  0.039   0.173   1486
  Planarity :  0.003   0.054   1614
  Dihedral  :  7.612  82.843   1319
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.96 %
    Favored  : 83.73 %
  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 are not related in a simple way.
  whole:  2.27 (0.24), residues: 1172
  helix:  2.70 (0.18), residues: 780
  sheet:  1.90 (0.77), residues: 48
  loop : -1.56 (0.28), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.017   0.001   TYR B 205 
 PHE   0.016   0.001   PHE A 394 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.004   0.001   HIS B 697 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9397)
  covalent geometry    : angle       0.49272 (12708)
  hydrogen bonds       : bond        0.06542 (  615)
  hydrogen bonds       : angle       3.47035 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  243 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8581 (t-90)
REVERT: A  541 GLN cc_start: 0.8181 (tp40) cc_final: 0.7906 (tp40)
REVERT: A  601 PHE cc_start: 0.6971 (m-80) cc_final: 0.6629 (m-80)
REVERT: A  697 HIS cc_start: 0.7615 (p-80) cc_final: 0.7378 (p-80)
REVERT: B  506 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7753 (mmtm)
  outliers start: 23
  outliers final: 17
  residues processed: 115
  average time/residue: 0.0843
  time to fit residues: 14.4183
Evaluate side-chains
  118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  691 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 105 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 115 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.186833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.145081 restraints weight = 12177.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.146014 restraints weight = 6812.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.146431 restraints weight = 5136.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.146999 restraints weight = 4396.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.147133 restraints weight = 4327.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3872
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3872 r_free = 0.3872    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3872 r_free = 0.3872    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3872
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9397  Z= 0.130
  Angle     :  0.479   7.696  12708  Z= 0.258
  Chirality :  0.038   0.166   1486
  Planarity :  0.003   0.053   1614
  Dihedral  :  7.488  82.661   1319
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.37 %
    Favored  : 81.83 %
  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 are not related in a simple way.
  whole:  2.37 (0.25), residues: 1172
  helix:  2.78 (0.18), residues: 780
  sheet:  1.93 (0.77), residues: 48
  loop : -1.53 (0.28), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.017   0.001   TYR B 205 
 PHE   0.016   0.001   PHE A 394 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.011   0.001   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9397)
  covalent geometry    : angle       0.47853 (12708)
  hydrogen bonds       : bond        0.06322 (  615)
  hydrogen bonds       : angle       3.39078 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  253 ARG cc_start: 0.6999 (mmm-85) cc_final: 0.6725 (mmm-85)
REVERT: A  601 PHE cc_start: 0.7048 (m-80) cc_final: 0.6736 (m-80)
REVERT: A  697 HIS cc_start: 0.7485 (p-80) cc_final: 0.7246 (p-80)
REVERT: B  506 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7887 (mmtm)
REVERT: B  541 GLN cc_start: 0.7865 (tp40) cc_final: 0.7603 (tp40)
  outliers start: 18
  outliers final: 16
  residues processed: 109
  average time/residue: 0.0804
  time to fit residues: 13.1238
Evaluate side-chains
  119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 117 optimal weight:    4.9990
   chunk 89 optimal weight:    0.5980
   chunk 51 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9990
   chunk 113 optimal weight:    6.9990
   chunk 46 optimal weight:    0.3980
   chunk 105 optimal weight:    7.9990
   overall best weight:    1.3584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.178764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.131678 restraints weight = 12953.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.135467 restraints weight = 7140.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.137893 restraints weight = 4892.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.139437 restraints weight = 3883.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139870 restraints weight = 3381.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3815
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3815 r_free = 0.3815    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3815 r_free = 0.3815    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3815
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9397  Z= 0.163
  Angle     :  0.525   7.621  12708  Z= 0.283
  Chirality :  0.039   0.159   1486
  Planarity :  0.003   0.052   1614
  Dihedral  :  7.175  82.574   1319
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.67 %
    Favored  : 80.72 %
  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 are not related in a simple way.
  whole:  2.18 (0.24), residues: 1172
  helix:  2.63 (0.18), residues: 780
  sheet:  1.88 (0.77), residues: 48
  loop : -1.61 (0.28), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 341 
 TYR   0.017   0.001   TYR B 205 
 PHE   0.016   0.001   PHE A 394 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9397)
  covalent geometry    : angle       0.52498 (12708)
  hydrogen bonds       : bond        0.07055 (  615)
  hydrogen bonds       : angle       3.57266 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  243 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.8162 (t-90)
REVERT: A  601 PHE cc_start: 0.7089 (m-80) cc_final: 0.6699 (m-80)
REVERT: A  697 HIS cc_start: 0.7597 (p-80) cc_final: 0.7394 (p-80)
REVERT: B  358 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6388 (mm-30)
REVERT: B  506 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7829 (mmtm)
REVERT: B  541 GLN cc_start: 0.7994 (tp40) cc_final: 0.7642 (tp40)
REVERT: B  697 HIS cc_start: 0.7382 (p90) cc_final: 0.6980 (p-80)
  outliers start: 26
  outliers final: 21
  residues processed: 116
  average time/residue: 0.0853
  time to fit residues: 14.6810
Evaluate side-chains
  121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  680 CYS
Chi-restraints excluded: chain B residue  691 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0870
   chunk 42 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 117 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.6158

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.185922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.140447 restraints weight = 12235.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.144132 restraints weight = 6568.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.146495 restraints weight = 4417.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.147841 restraints weight = 3461.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.148657 restraints weight = 2999.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3880 r_free = 0.3880    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3880 r_free = 0.3880    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9397  Z= 0.129
  Angle     :  0.487   7.783  12708  Z= 0.262
  Chirality :  0.038   0.186   1486
  Planarity :  0.003   0.050   1614
  Dihedral  :  6.879  83.417   1319
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.77 %
    Favored  : 80.52 %
  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 are not related in a simple way.
  whole:  2.38 (0.25), residues: 1172
  helix:  2.82 (0.18), residues: 780
  sheet:  0.51 (0.66), residues: 74
  loop : -1.51 (0.29), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.019   0.001   TYR A 605 
 PHE   0.017   0.001   PHE A 394 
 TRP   0.009   0.001   TRP A 711 
 HIS   0.007   0.001   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9397)
  covalent geometry    : angle       0.48747 (12708)
  hydrogen bonds       : bond        0.06322 (  615)
  hydrogen bonds       : angle       3.38171 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  243 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8380 (t-90)
REVERT: A  253 ARG cc_start: 0.7025 (mmm-85) cc_final: 0.6756 (mmm-85)
REVERT: A  601 PHE cc_start: 0.7145 (m-80) cc_final: 0.6861 (m-80)
REVERT: A  697 HIS cc_start: 0.7511 (p-80) cc_final: 0.7225 (p-80)
REVERT: B  506 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7874 (mmtm)
REVERT: B  541 GLN cc_start: 0.7843 (tp40) cc_final: 0.7643 (tp40)
REVERT: B  601 PHE cc_start: 0.6681 (m-80) cc_final: 0.6268 (m-80)
REVERT: B  697 HIS cc_start: 0.7228 (p90) cc_final: 0.6900 (p-80)
  outliers start: 17
  outliers final: 11
  residues processed: 113
  average time/residue: 0.0779
  time to fit residues: 13.2154
Evaluate side-chains
  114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 35 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
B 243 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.186549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.144033 restraints weight = 12154.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.145040 restraints weight = 6639.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.145460 restraints weight = 5494.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.146031 restraints weight = 4405.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.146275 restraints weight = 4068.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9397  Z= 0.133
  Angle     :  0.500   7.493  12708  Z= 0.266
  Chirality :  0.038   0.178   1486
  Planarity :  0.003   0.049   1614
  Dihedral  :  6.663  84.849   1319
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.37 %
    Favored  : 80.02 %
  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 are not related in a simple way.
  whole:  2.41 (0.25), residues: 1172
  helix:  2.86 (0.18), residues: 778
  sheet:  0.50 (0.66), residues: 74
  loop : -1.52 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.017   0.001   TYR B 205 
 PHE   0.017   0.001   PHE A 394 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.003   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9397)
  covalent geometry    : angle       0.49981 (12708)
  hydrogen bonds       : bond        0.06269 (  615)
  hydrogen bonds       : angle       3.36009 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7072 (mmm-85) cc_final: 0.6816 (mmm-85)
REVERT: A  601 PHE cc_start: 0.7214 (m-80) cc_final: 0.6857 (m-80)
REVERT: A  697 HIS cc_start: 0.7472 (p-80) cc_final: 0.7205 (p-80)
REVERT: B  506 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7910 (mmtm)
REVERT: B  601 PHE cc_start: 0.6599 (m-80) cc_final: 0.6103 (m-80)
REVERT: B  697 HIS cc_start: 0.7138 (p90) cc_final: 0.6896 (p-80)
  outliers start: 16
  outliers final: 13
  residues processed: 106
  average time/residue: 0.0850
  time to fit residues: 13.2640
Evaluate side-chains
  113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  568 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0470
   chunk 5 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.186981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.141404 restraints weight = 12165.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.145211 restraints weight = 6453.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.147672 restraints weight = 4292.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.148902 restraints weight = 3349.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.149945 restraints weight = 2911.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9397  Z= 0.127
  Angle     :  0.509  10.542  12708  Z= 0.267
  Chirality :  0.038   0.174   1486
  Planarity :  0.003   0.048   1614
  Dihedral  :  6.566  86.222   1319
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.47 %
    Favored  : 80.02 %
  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 are not related in a simple way.
  whole:  2.47 (0.25), residues: 1172
  helix:  2.91 (0.18), residues: 778
  sheet:  0.57 (0.66), residues: 74
  loop : -1.51 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.017   0.001   TYR B 205 
 PHE   0.018   0.001   PHE A 394 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.009   0.001   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9397)
  covalent geometry    : angle       0.50872 (12708)
  hydrogen bonds       : bond        0.06062 (  615)
  hydrogen bonds       : angle       3.30368 ( 1821)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7085 (mmm-85) cc_final: 0.6852 (mmm-85)
REVERT: A  286 GLU cc_start: 0.8205 (tp30) cc_final: 0.7766 (tt0)
REVERT: A  601 PHE cc_start: 0.7168 (m-80) cc_final: 0.6937 (m-80)
REVERT: A  697 HIS cc_start: 0.7508 (p-80) cc_final: 0.7255 (p-80)
REVERT: B  506 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7879 (mmtm)
REVERT: B  601 PHE cc_start: 0.6576 (m-80) cc_final: 0.6068 (m-80)
REVERT: B  697 HIS cc_start: 0.7228 (p90) cc_final: 0.6962 (p-80)
  outliers start: 15
  outliers final: 14
  residues processed: 112
  average time/residue: 0.0858
  time to fit residues: 14.1570
Evaluate side-chains
  116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  568 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 113 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 82 optimal weight:    0.4980
   chunk 116 optimal weight:    0.0870
   chunk 38 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.188754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.143581 restraints weight = 12034.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.147303 restraints weight = 6440.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.149773 restraints weight = 4298.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.151096 restraints weight = 3338.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.152123 restraints weight = 2888.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3922 r_free = 0.3922    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3922 r_free = 0.3922    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9397  Z= 0.126
  Angle     :  0.506   9.953  12708  Z= 0.266
  Chirality :  0.038   0.173   1486
  Planarity :  0.003   0.047   1614
  Dihedral  :  6.442  88.493   1319
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.38 %
    Favored  : 79.22 %
  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 are not related in a simple way.
  whole:  2.51 (0.25), residues: 1172
  helix:  2.93 (0.18), residues: 778
  sheet:  0.59 (0.66), residues: 74
  loop : -1.49 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 341 
 TYR   0.017   0.001   TYR B 205 
 PHE   0.017   0.001   PHE A 394 
 TRP   0.008   0.001   TRP A 711 
 HIS   0.006   0.001   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9397)
  covalent geometry    : angle       0.50593 (12708)
  hydrogen bonds       : bond        0.05885 (  615)
  hydrogen bonds       : angle       3.26430 ( 1821)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1726.25 seconds
wall clock time: 30 minutes 25.22 seconds (1825.22 seconds total)