Starting phenix.real_space_refine
on Sat Aug 23 03:57:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fwk_29511/08_2025/8fwk_29511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fwk_29511/08_2025/8fwk_29511.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fwk_29511/08_2025/8fwk_29511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fwk_29511/08_2025/8fwk_29511.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fwk_29511/08_2025/8fwk_29511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fwk_29511/08_2025/8fwk_29511.cif"
  }
  resolution = 3.5
  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=   0.005 sd=   0.078
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      34      5.16       5
     C    6072      2.51       5
     N    1640      2.21       5
     O    1716      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9462
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4731
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 13, 'TRANS': 583}
    Chain: "A"
      Number of atoms: 4731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4731
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 13, 'TRANS': 583}
  Time building chain proxies: 2.73, per 1000 atoms: 0.29
  Number of scatterers: 9462
  At special positions: 0
  Unit cell: (104.76, 87.48, 137.16, 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      34     16.00
     O    1716      8.00
     N    1640      7.00
     C    6072      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: 0.71
  Conformation dependent library (CDL) restraints added in 321.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2196

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 4 sheets defined
      59.2% alpha, 2.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 239 through 245
    Processing helix  chain 'B' and resid 261 through 294
      removed outlier: 3.500A  pdb=" N   VAL B 265 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL B 280 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 298 through 301
    Processing helix  chain 'B' and resid 302 through 315
    Processing helix  chain 'B' and resid 326 through 353
      removed outlier: 4.770A  pdb=" N   ARG B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   VAL B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 390
    Processing helix  chain 'B' and resid 391 through 408
    Processing helix  chain 'B' and resid 412 through 458
      removed outlier: 3.969A  pdb=" N   ILE B 416 " --> pdb=" O   TRP B 412 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LYS B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   PHE B 438 " --> pdb=" O   TRP B 434 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA B 453 " --> pdb=" O   THR B 449 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ASP B 455 " --> pdb=" O   ALA B 451 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER B 456 " --> pdb=" O   ARG B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 465
    Processing helix  chain 'B' and resid 468 through 510
      removed outlier: 3.645A  pdb=" N   GLU B 472 " --> pdb=" O   ALA B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 511 through 516
      removed outlier: 3.844A  pdb=" N   CYS B 516 " --> pdb=" O   SER B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 541
      removed outlier: 4.081A  pdb=" N   VAL B 531 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE B 533 " --> pdb=" O   ASP B 529 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ILE B 538 " --> pdb=" O   GLY B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 548
      removed outlier: 3.765A  pdb=" N   PHE B 547 " --> pdb=" O   LEU B 544 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLY B 548 " --> pdb=" O   ASN B 545 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 544 through 548'
    Processing helix  chain 'B' and resid 550 through 567
      removed outlier: 3.504A  pdb=" N   LEU B 567 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 634
      removed outlier: 3.660A  pdb=" N   ILE B 632 " --> pdb=" O   GLY B 628 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU B 633 " --> pdb=" O   LYS B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 659 through 665
    Processing helix  chain 'B' and resid 680 through 685
      removed outlier: 3.546A  pdb=" N   ARG B 685 " --> pdb=" O   ALA B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 688
      No H-bonds generated for 'chain 'B' and resid 686 through 688'
    Processing helix  chain 'B' and resid 698 through 703
    Processing helix  chain 'B' and resid 705 through 710
    Processing helix  chain 'B' and resid 729 through 742
      removed outlier: 4.086A  pdb=" N   GLN B 733 " --> pdb=" O   GLY B 729 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 770
      removed outlier: 4.121A  pdb=" N   GLU B 762 " --> pdb=" O   ASP B 758 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA B 764 " --> pdb=" O   SER B 760 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ALA B 767 " --> pdb=" O   ARG B 763 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   SER B 768 " --> pdb=" O   ALA B 764 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 807 through 814
    Processing helix  chain 'B' and resid 817 through 829
    Processing helix  chain 'A' and resid 239 through 245
    Processing helix  chain 'A' and resid 261 through 294
      removed outlier: 3.876A  pdb=" N   VAL A 280 " --> pdb=" O   ARG A 276 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
    Processing helix  chain 'A' and resid 298 through 301
    Processing helix  chain 'A' and resid 302 through 315
    Processing helix  chain 'A' and resid 326 through 353
      removed outlier: 4.770A  pdb=" N   ARG A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   VAL A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 390
    Processing helix  chain 'A' and resid 391 through 408
    Processing helix  chain 'A' and resid 412 through 458
      removed outlier: 3.970A  pdb=" N   ILE A 416 " --> pdb=" O   TRP A 412 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   LYS A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE A 438 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA A 453 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ASP A 455 " --> pdb=" O   ALA A 451 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 465
    Processing helix  chain 'A' and resid 468 through 510
      removed outlier: 3.645A  pdb=" N   GLU A 472 " --> pdb=" O   ALA A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 516
      removed outlier: 3.845A  pdb=" N   CYS A 516 " --> pdb=" O   SER A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 541
      removed outlier: 4.080A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ILE A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 548
      removed outlier: 3.764A  pdb=" N   PHE A 547 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLY A 548 " --> pdb=" O   ASN A 545 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 544 through 548'
    Processing helix  chain 'A' and resid 550 through 567
      removed outlier: 3.504A  pdb=" N   LEU A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 637
      removed outlier: 4.335A  pdb=" N   ARG A 634 " --> pdb=" O   SER A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 665
    Processing helix  chain 'A' and resid 680 through 685
    Processing helix  chain 'A' and resid 698 through 703
    Processing helix  chain 'A' and resid 705 through 710
    Processing helix  chain 'A' and resid 729 through 742
      removed outlier: 4.086A  pdb=" N   GLN A 733 " --> pdb=" O   GLY A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 770
      removed outlier: 4.120A  pdb=" N   GLU A 762 " --> pdb=" O   ASP A 758 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A 764 " --> pdb=" O   SER A 760 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ALA A 767 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   SER A 768 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 814
    Processing helix  chain 'A' and resid 817 through 829
    Processing sheet with id=AA1, first strand: chain 'B' and resid 590 through 591
    Processing sheet with id=AA2, first strand: chain 'B' and resid 617 through 620
      removed outlier: 5.516A  pdb=" N   GLN B 617 " --> pdb=" O   THR B 778 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   VAL B 780 " --> pdb=" O   GLN B 617 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   LEU B 619 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 591
    Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 620
      removed outlier: 5.517A  pdb=" N   GLN A 617 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   VAL A 780 " --> pdb=" O   GLN A 617 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   LEU A 619 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ILE A 748 " --> pdb=" O   ILE A 779 " (cutoff:3.500A)
      removed outlier: 8.658A  pdb=" N   VAL A 781 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   LEU A 750 " --> pdb=" O   VAL A 781 " (cutoff:3.500A)

    485 hydrogen bonds defined for protein.
    1431 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: 1.18

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1520
        1.30 -     1.43: 2556
        1.43 -     1.55: 5510
        1.55 -     1.68: 6
        1.68 -     1.81: 56
  Bond restraints: 9648
  Sorted by residual:
  bond pdb=" C   TRP B 360 "
       pdb=" O   TRP B 360 "
    ideal  model  delta    sigma   weight residual
    1.235  1.170  0.065 1.33e-02 5.65e+03 2.42e+01
  bond pdb=" CA  TRP B 360 "
       pdb=" C   TRP B 360 "
    ideal  model  delta    sigma   weight residual
    1.523  1.455  0.068 1.56e-02 4.11e+03 1.90e+01
  bond pdb=" N   ARG B 364 "
       pdb=" CA  ARG B 364 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.046 1.29e-02 6.01e+03 1.30e+01
  bond pdb=" C   HIS B 361 "
       pdb=" O   HIS B 361 "
    ideal  model  delta    sigma   weight residual
    1.236  1.191  0.045 1.47e-02 4.63e+03 9.40e+00
  bond pdb=" CA  HIS B 361 "
       pdb=" CB  HIS B 361 "
    ideal  model  delta    sigma   weight residual
    1.531  1.486  0.045 1.62e-02 3.81e+03 7.62e+00
  ... (remaining 9643 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 12538
        2.32 -     4.64: 427
        4.64 -     6.95: 80
        6.95 -     9.27: 28
        9.27 -    11.59: 9
  Bond angle restraints: 13082
  Sorted by residual:
  angle pdb=" N   ARG B 359 "
        pdb=" CA  ARG B 359 "
        pdb=" C   ARG B 359 "
      ideal   model   delta    sigma   weight residual
     111.28  100.04   11.24 1.09e+00 8.42e-01 1.06e+02
  angle pdb=" N   ILE A 632 "
        pdb=" CA  ILE A 632 "
        pdb=" C   ILE A 632 "
      ideal   model   delta    sigma   weight residual
     110.62  119.69   -9.07 1.02e+00 9.61e-01 7.90e+01
  angle pdb=" N   GLY A 687 "
        pdb=" CA  GLY A 687 "
        pdb=" C   GLY A 687 "
      ideal   model   delta    sigma   weight residual
     112.73  120.21   -7.48 1.20e+00 6.94e-01 3.88e+01
  angle pdb=" N   LEU B 750 "
        pdb=" CA  LEU B 750 "
        pdb=" C   LEU B 750 "
      ideal   model   delta    sigma   weight residual
     110.23  101.25    8.98 1.45e+00 4.76e-01 3.84e+01
  angle pdb=" N   ARG B 688 "
        pdb=" CA  ARG B 688 "
        pdb=" C   ARG B 688 "
      ideal   model   delta    sigma   weight residual
     111.14  117.73   -6.59 1.08e+00 8.57e-01 3.72e+01
  ... (remaining 13077 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.16: 5245
       15.16 -    30.32: 312
       30.32 -    45.48: 95
       45.48 -    60.64: 16
       60.64 -    75.81: 20
  Dihedral angle restraints: 5688
    sinusoidal: 2256
      harmonic: 3432
  Sorted by residual:
  dihedral pdb=" C   HIS B 361 "
           pdb=" N   HIS B 361 "
           pdb=" CA  HIS B 361 "
           pdb=" CB  HIS B 361 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.34   15.74     0      2.50e+00 1.60e-01 3.96e+01
  dihedral pdb=" N   HIS B 361 "
           pdb=" C   HIS B 361 "
           pdb=" CA  HIS B 361 "
           pdb=" CB  HIS B 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.44  -15.64     0      2.50e+00 1.60e-01 3.91e+01
  dihedral pdb=" CA  ARG B 685 "
           pdb=" C   ARG B 685 "
           pdb=" N   TYR B 686 "
           pdb=" CA  TYR B 686 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.58  -24.42     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 5685 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.159: 1468
       0.159 -    0.319: 30
       0.319 -    0.478: 3
       0.478 -    0.637: 0
       0.637 -    0.797: 1
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" CA  HIS B 361 "
            pdb=" N   HIS B 361 "
            pdb=" C   HIS B 361 "
            pdb=" CB  HIS B 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.71    0.80 2.00e-01 2.50e+01 1.59e+01
  chirality pdb=" CA  LEU A 356 "
            pdb=" N   LEU A 356 "
            pdb=" C   LEU A 356 "
            pdb=" CB  LEU A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.11e+00
  chirality pdb=" CA  SER B 357 "
            pdb=" N   SER B 357 "
            pdb=" C   SER B 357 "
            pdb=" CB  SER B 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.04e+00
  ... (remaining 1499 not shown)

  Planarity restraints: 1658
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 687 "    0.028 2.00e-02 2.50e+03   5.56e-02 3.09e+01
        pdb=" C   GLY B 687 "   -0.096 2.00e-02 2.50e+03
        pdb=" O   GLY B 687 "    0.036 2.00e-02 2.50e+03
        pdb=" N   ARG B 688 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 356 "    0.022 2.00e-02 2.50e+03   4.55e-02 2.07e+01
        pdb=" C   LEU B 356 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   LEU B 356 "    0.030 2.00e-02 2.50e+03
        pdb=" N   SER B 357 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 360 "    0.022 2.00e-02 2.50e+03   4.24e-02 1.80e+01
        pdb=" C   TRP B 360 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   TRP B 360 "    0.027 2.00e-02 2.50e+03
        pdb=" N   HIS B 361 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1655 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2620
        2.81 -     3.33: 9011
        3.33 -     3.86: 15034
        3.86 -     4.38: 16342
        4.38 -     4.90: 27933
  Nonbonded interactions: 70940
  Sorted by model distance:
  nonbonded pdb=" O   THR B 323 "
            pdb=" OG  SER B 327 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   THR A 323 "
            pdb=" OG  SER A 327 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   GLY B 588 "
            pdb=" OG1 THR B 777 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   GLY A 588 "
            pdb=" OG1 THR A 777 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   GLY A 692 "
            pdb=" CB  ASN A 693 "
     model   vdw
     2.305 3.440
  ... (remaining 70935 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.530
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
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      :  0.005   0.068   9648  Z= 0.266
  Angle     :  1.070  11.590  13082  Z= 0.619
  Chirality :  0.065   0.797   1502
  Planarity :  0.007   0.056   1658
  Dihedral  : 12.403  75.806   3492
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 11.60 %
    Favored  : 87.23 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  2.38 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.60 (0.18), residues: 1190
  helix: -2.26 (0.15), residues: 696
  sheet: -1.84 (1.02), residues: 24
  loop : -4.34 (0.20), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 807 
 TYR   0.024   0.002   TYR B 536 
 PHE   0.017   0.002   PHE A 611 
 TRP   0.023   0.002   TRP B 360 
 HIS   0.009   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 9648)
  covalent geometry    : angle       1.07015 (13082)
  hydrogen bonds       : bond        0.12591 (  485)
  hydrogen bonds       : angle       5.76626 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 209
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 ILE cc_start: 0.8661 (mm) cc_final: 0.8443 (mp)
REVERT: B  599 TYR cc_start: 0.5351 (m-10) cc_final: 0.4388 (m-10)
REVERT: B  614 MET cc_start: 0.7748 (ptp) cc_final: 0.7410 (tmm)
REVERT: B  775 ASN cc_start: 0.7737 (m-40) cc_final: 0.7513 (t0)
REVERT: A  274 LEU cc_start: 0.8346 (tp) cc_final: 0.8122 (tp)
REVERT: A  530 TYR cc_start: 0.8701 (t80) cc_final: 0.8059 (t80)
REVERT: A  553 MET cc_start: 0.8271 (mmp) cc_final: 0.8037 (ttm)
REVERT: A  561 MET cc_start: 0.7879 (tmm) cc_final: 0.7626 (tmm)
REVERT: A  614 MET cc_start: 0.7702 (ptp) cc_final: 0.7497 (ptt)
REVERT: A  775 ASN cc_start: 0.8139 (m-40) cc_final: 0.7823 (t0)
  outliers start: 13
  outliers final: 4
  residues processed: 217
  average time/residue: 0.1054
  time to fit residues: 30.7493
Evaluate side-chains
  110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain A residue  633 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0770
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 117 optimal weight:    5.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B 354 HIS
B 410 ASN
B 445 GLN
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 484 GLN
B 617 GLN
B 693 ASN
B 706 HIS
** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 808 HIS
B 826 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 ASN
A 445 GLN
A 617 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.105466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.084695 restraints weight = 30760.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.087562 restraints weight = 15405.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.089569 restraints weight = 9825.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.090903 restraints weight = 7194.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.091879 restraints weight = 5806.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9648  Z= 0.137
  Angle     :  0.701  10.459  13082  Z= 0.367
  Chirality :  0.043   0.159   1502
  Planarity :  0.004   0.037   1658
  Dihedral  :  5.809  48.211   1330
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  : 10.17 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 12.77 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.22), residues: 1190
  helix: -0.49 (0.19), residues: 690
  sheet: -2.03 (0.71), residues: 44
  loop : -4.07 (0.22), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 359 
 TYR   0.027   0.002   TYR B 716 
 PHE   0.018   0.001   PHE A 597 
 TRP   0.013   0.001   TRP B 822 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9648)
  covalent geometry    : angle       0.70072 (13082)
  hydrogen bonds       : bond        0.04666 (  485)
  hydrogen bonds       : angle       4.21412 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: B  464 LYS cc_start: 0.6668 (mmtt) cc_final: 0.6419 (mttp)
REVERT: B  595 VAL cc_start: 0.8405 (t) cc_final: 0.8186 (t)
REVERT: A  239 TRP cc_start: 0.3816 (p90) cc_final: 0.3470 (p90)
REVERT: A  561 MET cc_start: 0.8256 (tmm) cc_final: 0.7885 (tmm)
REVERT: A  775 ASN cc_start: 0.8085 (m-40) cc_final: 0.7786 (t0)
  outliers start: 30
  outliers final: 19
  residues processed: 128
  average time/residue: 0.0949
  time to fit residues: 17.7203
Evaluate side-chains
  103 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  612 THR
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain B residue  783 HIS
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  542 MET
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  684 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B 484 GLN
** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 826 GLN
A 339 GLN
A 793 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.098882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.077321 restraints weight = 30055.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.080011 restraints weight = 15103.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.081847 restraints weight = 9739.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.083115 restraints weight = 7247.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.083966 restraints weight = 5942.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9648  Z= 0.144
  Angle     :  0.679  10.102  13082  Z= 0.355
  Chirality :  0.043   0.158   1502
  Planarity :  0.004   0.035   1658
  Dihedral  :  5.262  45.779   1324
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.76 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 14.26 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.24), residues: 1190
  helix:  0.36 (0.20), residues: 690
  sheet: -1.43 (0.76), residues: 44
  loop : -3.94 (0.24), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 589 
 TYR   0.018   0.002   TYR A 466 
 PHE   0.014   0.001   PHE A 409 
 TRP   0.018   0.001   TRP B 360 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9648)
  covalent geometry    : angle       0.67902 (13082)
  hydrogen bonds       : bond        0.05134 (  485)
  hydrogen bonds       : angle       3.95992 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 89
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 MET cc_start: 0.8513 (tmm) cc_final: 0.8000 (tmm)
REVERT: B  346 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8030 (tm-30)
REVERT: B  355 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8113 (mp0)
REVERT: B  406 SER cc_start: 0.7834 (t) cc_final: 0.7560 (p)
REVERT: B  474 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7781 (tm-30)
REVERT: A  239 TRP cc_start: 0.4118 (p90) cc_final: 0.3641 (p90)
REVERT: A  561 MET cc_start: 0.8453 (tmm) cc_final: 0.8036 (tmm)
REVERT: A  592 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.6032 (t80)
REVERT: A  751 ASP cc_start: 0.7815 (p0) cc_final: 0.7481 (p0)
REVERT: A  775 ASN cc_start: 0.8129 (m-40) cc_final: 0.7832 (t0)
  outliers start: 38
  outliers final: 16
  residues processed: 118
  average time/residue: 0.1038
  time to fit residues: 17.3345
Evaluate side-chains
  89 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  612 THR
Chi-restraints excluded: chain B residue  631 THR
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain B residue  783 HIS
Chi-restraints excluded: chain B residue  823 GLN
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  823 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 92 optimal weight:    0.1980
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    0.2980
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 484 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.097737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.075972 restraints weight = 30794.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.078644 restraints weight = 15385.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.080496 restraints weight = 9977.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.081761 restraints weight = 7452.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.082551 restraints weight = 6122.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.4783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9648  Z= 0.132
  Angle     :  0.639   9.443  13082  Z= 0.335
  Chirality :  0.042   0.149   1502
  Planarity :  0.004   0.059   1658
  Dihedral  :  4.997  29.602   1322
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 10.67 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.44 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.24), residues: 1190
  helix:  0.83 (0.20), residues: 682
  sheet: -1.25 (0.89), residues: 34
  loop : -3.74 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 552 
 TYR   0.018   0.001   TYR A 716 
 PHE   0.013   0.001   PHE B 460 
 TRP   0.016   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9648)
  covalent geometry    : angle       0.63950 (13082)
  hydrogen bonds       : bond        0.04729 (  485)
  hydrogen bonds       : angle       3.84528 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 78
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 MET cc_start: 0.8497 (tmm) cc_final: 0.7826 (tmm)
REVERT: B  275 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: B  311 PHE cc_start: 0.8587 (t80) cc_final: 0.8349 (t80)
REVERT: B  346 GLU cc_start: 0.8609 (tm-30) cc_final: 0.7949 (tm-30)
REVERT: B  406 SER cc_start: 0.8129 (t) cc_final: 0.7908 (p)
REVERT: B  487 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8171 (pp20)
REVERT: B  751 ASP cc_start: 0.7103 (t0) cc_final: 0.6835 (t0)
REVERT: A  322 SER cc_start: 0.8632 (p) cc_final: 0.8362 (p)
REVERT: A  561 MET cc_start: 0.8461 (tmm) cc_final: 0.8055 (tmm)
REVERT: A  775 ASN cc_start: 0.8198 (m-40) cc_final: 0.7713 (t0)
  outliers start: 36
  outliers final: 20
  residues processed: 103
  average time/residue: 0.0973
  time to fit residues: 14.4612
Evaluate side-chains
  95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  541 TYR
Chi-restraints excluded: chain B residue  612 THR
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain B residue  777 THR
Chi-restraints excluded: chain B residue  783 HIS
Chi-restraints excluded: chain B residue  823 GLN
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  823 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 115 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 339 GLN
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.096382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.074503 restraints weight = 30582.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.077188 restraints weight = 15350.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.079017 restraints weight = 9988.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.080196 restraints weight = 7537.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.081051 restraints weight = 6275.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9648  Z= 0.135
  Angle     :  0.645   9.691  13082  Z= 0.336
  Chirality :  0.042   0.147   1502
  Planarity :  0.004   0.066   1658
  Dihedral  :  4.961  32.866   1322
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 11.43 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 15.84 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.25), residues: 1190
  helix:  0.97 (0.20), residues: 682
  sheet: -1.15 (0.88), residues: 34
  loop : -3.64 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 371 
 TYR   0.014   0.001   TYR A 716 
 PHE   0.011   0.001   PHE B 460 
 TRP   0.017   0.001   TRP B 488 
 HIS   0.003   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9648)
  covalent geometry    : angle       0.64460 (13082)
  hydrogen bonds       : bond        0.04845 (  485)
  hydrogen bonds       : angle       3.82049 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 81
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 MET cc_start: 0.8499 (tmm) cc_final: 0.7844 (tmm)
REVERT: B  275 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8271 (tm-30)
REVERT: B  311 PHE cc_start: 0.8662 (t80) cc_final: 0.8433 (t80)
REVERT: B  346 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8050 (tm-30)
REVERT: B  361 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (t-90)
REVERT: B  487 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8164 (pp20)
REVERT: B  553 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7278 (ppp)
REVERT: B  584 ARG cc_start: 0.7641 (tpt90) cc_final: 0.7085 (mtm-85)
REVERT: B  751 ASP cc_start: 0.7279 (t0) cc_final: 0.7063 (t0)
REVERT: A  322 SER cc_start: 0.8660 (p) cc_final: 0.8407 (p)
REVERT: A  561 MET cc_start: 0.8517 (tmm) cc_final: 0.8056 (tmm)
REVERT: A  751 ASP cc_start: 0.7529 (p0) cc_final: 0.7248 (p0)
REVERT: A  775 ASN cc_start: 0.8184 (m-40) cc_final: 0.7635 (t0)
REVERT: A  823 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8761 (mm110)
  outliers start: 36
  outliers final: 19
  residues processed: 106
  average time/residue: 0.0963
  time to fit residues: 14.8038
Evaluate side-chains
  98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  541 TYR
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain B residue  783 HIS
Chi-restraints excluded: chain B residue  823 GLN
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  564 MET
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  823 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 56 optimal weight:    0.3980
   chunk 100 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0040
   chunk 61 optimal weight:    0.0170
   chunk 108 optimal weight:    0.0870
   chunk 68 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.3010

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.098946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.076959 restraints weight = 30540.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.079711 restraints weight = 15188.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.081599 restraints weight = 9822.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.082925 restraints weight = 7355.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.083780 restraints weight = 6034.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.5355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9648  Z= 0.117
  Angle     :  0.622  10.348  13082  Z= 0.322
  Chirality :  0.041   0.143   1502
  Planarity :  0.003   0.041   1658
  Dihedral  :  4.758  31.798   1322
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 10.67 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.82 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.25), residues: 1190
  helix:  1.10 (0.21), residues: 682
  sheet: -0.92 (0.92), residues: 34
  loop : -3.51 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 371 
 TYR   0.019   0.001   TYR B 530 
 PHE   0.010   0.001   PHE B 460 
 TRP   0.010   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9648)
  covalent geometry    : angle       0.62205 (13082)
  hydrogen bonds       : bond        0.04169 (  485)
  hydrogen bonds       : angle       3.70644 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 MET cc_start: 0.8485 (tmm) cc_final: 0.7829 (tmm)
REVERT: B  275 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: B  346 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: B  487 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7998 (pp20)
REVERT: B  584 ARG cc_start: 0.7663 (tpt90) cc_final: 0.7207 (mtm-85)
REVERT: A  322 SER cc_start: 0.8626 (p) cc_final: 0.8375 (p)
REVERT: A  487 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8082 (pp20)
REVERT: A  561 MET cc_start: 0.8491 (tmm) cc_final: 0.8019 (tmm)
REVERT: A  585 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.6115 (m-80)
REVERT: A  775 ASN cc_start: 0.8069 (m-40) cc_final: 0.7521 (t0)
REVERT: A  823 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8741 (mm110)
  outliers start: 29
  outliers final: 14
  residues processed: 100
  average time/residue: 0.0990
  time to fit residues: 14.3639
Evaluate side-chains
  91 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  564 MET
Chi-restraints excluded: chain A residue  585 PHE
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  823 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 115 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0470
   chunk 68 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.8880

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

Flipped N/Q/H residues before XYZ refinement:
B 467 ASN
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.096495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.074860 restraints weight = 30766.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.077491 restraints weight = 15483.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.079335 restraints weight = 10095.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.080569 restraints weight = 7592.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.081361 restraints weight = 6278.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.5674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9648  Z= 0.132
  Angle     :  0.638  10.187  13082  Z= 0.332
  Chirality :  0.042   0.160   1502
  Planarity :  0.003   0.032   1658
  Dihedral  :  4.758  32.043   1322
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 11.43 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.42 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.25), residues: 1190
  helix:  1.16 (0.20), residues: 682
  sheet: -0.93 (0.90), residues: 34
  loop : -3.44 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 371 
 TYR   0.012   0.001   TYR B 716 
 PHE   0.010   0.001   PHE B 460 
 TRP   0.014   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9648)
  covalent geometry    : angle       0.63809 (13082)
  hydrogen bonds       : bond        0.04534 (  485)
  hydrogen bonds       : angle       3.78363 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4308 (p90) cc_final: 0.3985 (p90)
REVERT: B  272 MET cc_start: 0.8513 (tmm) cc_final: 0.7855 (tmm)
REVERT: B  275 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: B  346 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: B  487 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8074 (pp20)
REVERT: B  584 ARG cc_start: 0.7578 (tpt90) cc_final: 0.7359 (mtm-85)
REVERT: A  239 TRP cc_start: 0.3931 (p90) cc_final: 0.3629 (p90)
REVERT: A  272 MET cc_start: 0.8407 (tmm) cc_final: 0.7873 (tmm)
REVERT: A  322 SER cc_start: 0.8639 (p) cc_final: 0.8406 (p)
REVERT: A  487 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8132 (pp20)
REVERT: A  561 MET cc_start: 0.8504 (tmm) cc_final: 0.8031 (tmm)
REVERT: A  567 LEU cc_start: 0.8702 (mp) cc_final: 0.8411 (pp)
REVERT: A  585 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.6159 (m-80)
REVERT: A  592 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5936 (t80)
REVERT: A  751 ASP cc_start: 0.7534 (p0) cc_final: 0.7226 (p0)
REVERT: A  775 ASN cc_start: 0.8094 (m-40) cc_final: 0.7489 (t0)
  outliers start: 29
  outliers final: 16
  residues processed: 93
  average time/residue: 0.1009
  time to fit residues: 13.4406
Evaluate side-chains
  94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  542 MET
Chi-restraints excluded: chain B residue  564 MET
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  564 MET
Chi-restraints excluded: chain A residue  585 PHE
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  633 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0980
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 59 optimal weight:   20.0000
   chunk 70 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.095550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.073949 restraints weight = 30875.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.076592 restraints weight = 15479.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.078397 restraints weight = 10072.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.079644 restraints weight = 7594.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.080436 restraints weight = 6263.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.5966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9648  Z= 0.137
  Angle     :  0.655  10.625  13082  Z= 0.339
  Chirality :  0.042   0.162   1502
  Planarity :  0.003   0.028   1658
  Dihedral  :  4.835  33.841   1322
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.76 %
    Favored  : 87.98 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.02 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.25), residues: 1190
  helix:  1.20 (0.20), residues: 682
  sheet: -1.07 (0.87), residues: 34
  loop : -3.41 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 371 
 TYR   0.016   0.001   TYR B 530 
 PHE   0.010   0.001   PHE B 460 
 TRP   0.014   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9648)
  covalent geometry    : angle       0.65513 (13082)
  hydrogen bonds       : bond        0.04687 (  485)
  hydrogen bonds       : angle       3.81691 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4336 (p90) cc_final: 0.4015 (p90)
REVERT: B  272 MET cc_start: 0.8557 (tmm) cc_final: 0.7891 (tmm)
REVERT: B  275 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: B  346 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: B  487 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8116 (pp20)
REVERT: B  821 MET cc_start: 0.8516 (mtm) cc_final: 0.8291 (mtp)
REVERT: A  239 TRP cc_start: 0.4012 (p90) cc_final: 0.3721 (p90)
REVERT: A  322 SER cc_start: 0.8676 (p) cc_final: 0.8444 (p)
REVERT: A  487 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8100 (pp20)
REVERT: A  561 MET cc_start: 0.8512 (tmm) cc_final: 0.8042 (tmm)
REVERT: A  567 LEU cc_start: 0.8714 (mp) cc_final: 0.8445 (pp)
REVERT: A  585 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.6026 (m-80)
REVERT: A  592 PHE cc_start: 0.6134 (OUTLIER) cc_final: 0.5830 (t80)
REVERT: A  775 ASN cc_start: 0.8159 (m-40) cc_final: 0.7591 (t0)
  outliers start: 32
  outliers final: 20
  residues processed: 96
  average time/residue: 0.0973
  time to fit residues: 13.4178
Evaluate side-chains
  96 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  542 MET
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain B residue  783 HIS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  564 MET
Chi-restraints excluded: chain A residue  585 PHE
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  633 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 85 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 GLN
A 823 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.093082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071236 restraints weight = 30942.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.073841 restraints weight = 15305.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.075593 restraints weight = 9915.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.076794 restraints weight = 7482.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.077502 restraints weight = 6202.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.6389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9648  Z= 0.159
  Angle     :  0.686  10.566  13082  Z= 0.356
  Chirality :  0.043   0.196   1502
  Planarity :  0.004   0.030   1658
  Dihedral  :  4.971  35.224   1322
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.93 %
    Favored  : 87.82 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.51 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.25), residues: 1190
  helix:  1.20 (0.20), residues: 682
  sheet: -0.21 (1.11), residues: 20
  loop : -3.50 (0.24), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 365 
 TYR   0.012   0.001   TYR B 716 
 PHE   0.010   0.001   PHE B 519 
 TRP   0.016   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9648)
  covalent geometry    : angle       0.68628 (13082)
  hydrogen bonds       : bond        0.05215 (  485)
  hydrogen bonds       : angle       3.96729 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4376 (p90) cc_final: 0.4060 (p90)
REVERT: B  272 MET cc_start: 0.8505 (tmm) cc_final: 0.7915 (tmm)
REVERT: B  275 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8223 (tm-30)
REVERT: B  322 SER cc_start: 0.8826 (m) cc_final: 0.8113 (p)
REVERT: B  346 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: B  371 ARG cc_start: 0.8806 (tmm-80) cc_final: 0.8601 (tmm-80)
REVERT: B  487 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8213 (pp20)
REVERT: B  614 MET cc_start: 0.8119 (ptp) cc_final: 0.7346 (ppp)
REVERT: A  239 TRP cc_start: 0.4105 (p90) cc_final: 0.3842 (p90)
REVERT: A  322 SER cc_start: 0.8741 (p) cc_final: 0.8513 (p)
REVERT: A  487 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8171 (pp20)
REVERT: A  561 MET cc_start: 0.8574 (tmm) cc_final: 0.8094 (tmm)
REVERT: A  567 LEU cc_start: 0.8848 (mp) cc_final: 0.8561 (pp)
REVERT: A  585 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.6018 (m-80)
REVERT: A  614 MET cc_start: 0.8112 (ptp) cc_final: 0.7388 (ppp)
REVERT: A  751 ASP cc_start: 0.7476 (p0) cc_final: 0.7203 (p0)
REVERT: A  775 ASN cc_start: 0.8299 (m-40) cc_final: 0.7668 (t0)
  outliers start: 28
  outliers final: 20
  residues processed: 98
  average time/residue: 0.1022
  time to fit residues: 14.2826
Evaluate side-chains
  94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  542 MET
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain B residue  783 HIS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  564 MET
Chi-restraints excluded: chain A residue  585 PHE
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  679 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 117 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.094493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.072692 restraints weight = 30723.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.075329 restraints weight = 15149.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.077102 restraints weight = 9815.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.078332 restraints weight = 7417.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.079110 restraints weight = 6142.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.6447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9648  Z= 0.139
  Angle     :  0.683  11.266  13082  Z= 0.353
  Chirality :  0.043   0.223   1502
  Planarity :  0.003   0.029   1658
  Dihedral  :  4.922  34.293   1322
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 11.76 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.41 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.25), residues: 1190
  helix:  1.12 (0.20), residues: 692
  sheet: -1.22 (0.85), residues: 34
  loop : -3.52 (0.25), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 371 
 TYR   0.020   0.001   TYR B 541 
 PHE   0.009   0.001   PHE B 460 
 TRP   0.011   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9648)
  covalent geometry    : angle       0.68309 (13082)
  hydrogen bonds       : bond        0.04915 (  485)
  hydrogen bonds       : angle       3.92214 ( 1431)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4399 (p90) cc_final: 0.4095 (p90)
REVERT: B  272 MET cc_start: 0.8509 (tmm) cc_final: 0.7924 (tmm)
REVERT: B  275 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: B  322 SER cc_start: 0.8840 (m) cc_final: 0.8158 (p)
REVERT: B  346 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8259 (tm-30)
REVERT: B  371 ARG cc_start: 0.8801 (tmm-80) cc_final: 0.8595 (tmm-80)
REVERT: B  487 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8189 (pp20)
REVERT: A  239 TRP cc_start: 0.4121 (p90) cc_final: 0.3849 (p90)
REVERT: A  487 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8096 (pp20)
REVERT: A  561 MET cc_start: 0.8582 (tmm) cc_final: 0.8103 (tmm)
REVERT: A  567 LEU cc_start: 0.8769 (mp) cc_final: 0.8505 (pp)
REVERT: A  585 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5864 (m-80)
REVERT: A  587 LYS cc_start: 0.5443 (tttt) cc_final: 0.5155 (tmtt)
REVERT: A  614 MET cc_start: 0.7999 (ptp) cc_final: 0.7361 (ppp)
REVERT: A  775 ASN cc_start: 0.8235 (m-40) cc_final: 0.7577 (t0)
  outliers start: 25
  outliers final: 19
  residues processed: 91
  average time/residue: 0.0963
  time to fit residues: 12.6427
Evaluate side-chains
  95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  360 TRP
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain B residue  783 HIS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  564 MET
Chi-restraints excluded: chain A residue  585 PHE
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  679 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 115 optimal weight:    0.1980
   chunk 68 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 114 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   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 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.097120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.075739 restraints weight = 30236.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.078290 restraints weight = 15962.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.079992 restraints weight = 10685.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.081128 restraints weight = 8192.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.081847 restraints weight = 6887.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.6613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9648  Z= 0.144
  Angle     :  0.679  10.952  13082  Z= 0.351
  Chirality :  0.043   0.210   1502
  Planarity :  0.003   0.029   1658
  Dihedral  :  4.913  35.047   1322
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 11.68 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.41 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.25), residues: 1190
  helix:  1.18 (0.20), residues: 692
  sheet: -0.21 (1.13), residues: 20
  loop : -3.58 (0.24), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 371 
 TYR   0.018   0.001   TYR B 541 
 PHE   0.011   0.001   PHE B 597 
 TRP   0.013   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9648)
  covalent geometry    : angle       0.67868 (13082)
  hydrogen bonds       : bond        0.04956 (  485)
  hydrogen bonds       : angle       3.92970 ( 1431)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1794.60 seconds
wall clock time: 31 minutes 42.18 seconds (1902.18 seconds total)