Starting phenix.real_space_refine
on Sun Jun  8 12:10:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fwk_29511/06_2025/8fwk_29511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fwk_29511/06_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_29511/06_2025/8fwk_29511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fwk_29511/06_2025/8fwk_29511.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fwk_29511/06_2025/8fwk_29511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fwk_29511/06_2025/8fwk_29511.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.89, per 1000 atoms: 0.62
  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: 2.28
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.89
  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: 2.46

  Time building geometry restraints manager: 2.70 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: 0.05
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:             1.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.210
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.570
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.023   0.002   TRP B 360 
 HIS   0.009   0.001   HIS B 352 
 PHE   0.017   0.002   PHE A 611 
 TYR   0.024   0.002   TYR B 536 
 ARG   0.004   0.000   ARG A 807 

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

*********************** 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  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  599 TYR cc_start: 0.5351 (m-10) cc_final: 0.4387 (m-10)
REVERT: B  614 MET cc_start: 0.7748 (ptp) cc_final: 0.7409 (tmm)
REVERT: B  710 MET cc_start: 0.5602 (mmp) cc_final: 0.5383 (mmp)
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: 0.7470 (ptt)
REVERT: A  775 ASN cc_start: 0.8139 (m-40) cc_final: 0.7824 (t0)
  outliers start: 13
  outliers final: 4
  residues processed: 217
  average time/residue: 0.2527
  time to fit residues: 74.1272
Evaluate side-chains
  111 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
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 99 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0970
   chunk 92 optimal weight:    0.0370
   chunk 35 optimal weight:    0.0970
   chunk 56 optimal weight:    7.9990
   chunk 68 optimal weight:    0.4980
   chunk 107 optimal weight:    8.9990
   overall best weight:    0.2654

-------------------------------------------------------------------------------
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 484 GLN
B 617 GLN
B 693 ASN
** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 808 HIS
** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 GLN
A 410 ASN
A 617 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.108752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.088400 restraints weight = 30885.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.091406 restraints weight = 15420.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.093491 restraints weight = 9732.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9648  Z= 0.136
  Angle     :  0.697   9.828  13082  Z= 0.365
  Chirality :  0.042   0.153   1502
  Planarity :  0.004   0.031   1658
  Dihedral  :  5.849  48.190   1330
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  9.75 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.17 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.22), residues: 1190
  helix: -0.53 (0.19), residues: 684
  sheet: -1.93 (0.72), residues: 44
  loop : -4.06 (0.22), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 822 
 HIS   0.005   0.001   HIS A 352 
 PHE   0.023   0.001   PHE A 597 
 TYR   0.028   0.001   TYR B 716 
 ARG   0.004   0.000   ARG B 814 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04438 (  485)
  hydrogen bonds       : angle       4.29048 ( 1431)
  covalent geometry    : bond        0.00259 ( 9648)
  covalent geometry    : angle       0.69745 (13082)

*********************** 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
  142 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  614 MET cc_start: 0.7743 (ptp) cc_final: 0.7520 (tmm)
REVERT: A  239 TRP cc_start: 0.3737 (p90) cc_final: 0.3398 (p90)
REVERT: A  530 TYR cc_start: 0.8504 (t80) cc_final: 0.8297 (t80)
REVERT: A  561 MET cc_start: 0.8189 (tmm) cc_final: 0.7865 (tmm)
REVERT: A  608 ASP cc_start: 0.8570 (m-30) cc_final: 0.7772 (p0)
REVERT: A  614 MET cc_start: 0.7456 (ptp) cc_final: 0.7061 (mmp)
REVERT: A  775 ASN cc_start: 0.8021 (m-40) cc_final: 0.7768 (t0)
  outliers start: 28
  outliers final: 16
  residues processed: 131
  average time/residue: 0.2030
  time to fit residues: 38.2117
Evaluate side-chains
  104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
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  349 ILE
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  592 PHE
Chi-restraints excluded: chain B residue  612 THR
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  585 PHE
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 9 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0000
   chunk 26 optimal weight:    0.7980
   chunk 59 optimal weight:   30.0000
   chunk 23 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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**
A 445 GLN
A 793 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.102468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.081096 restraints weight = 30671.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.083864 restraints weight = 15334.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.085772 restraints weight = 9834.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3849

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= 0.131
  Angle     :  0.663   9.642  13082  Z= 0.345
  Chirality :  0.043   0.171   1502
  Planarity :  0.004   0.027   1658
  Dihedral  :  5.057  32.670   1322
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.84 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 13.96 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.24), residues: 1190
  helix:  0.29 (0.20), residues: 688
  sheet: -1.59 (0.75), residues: 44
  loop : -3.90 (0.24), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 360 
 HIS   0.006   0.001   HIS B 361 
 PHE   0.023   0.001   PHE A 460 
 TYR   0.020   0.001   TYR A 466 
 ARG   0.003   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04670 (  485)
  hydrogen bonds       : angle       3.92260 ( 1431)
  covalent geometry    : bond        0.00273 ( 9648)
  covalent geometry    : angle       0.66307 (13082)

*********************** 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
  128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 91
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 MET cc_start: 0.8453 (tmm) cc_final: 0.7951 (tmm)
REVERT: B  346 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: B  614 MET cc_start: 0.7834 (ptp) cc_final: 0.7480 (ppp)
REVERT: A  561 MET cc_start: 0.8367 (tmm) cc_final: 0.7978 (tmm)
REVERT: A  608 ASP cc_start: 0.8686 (m-30) cc_final: 0.7996 (p0)
REVERT: A  614 MET cc_start: 0.7607 (ptp) cc_final: 0.6959 (mmp)
REVERT: A  775 ASN cc_start: 0.8101 (m-40) cc_final: 0.7783 (t0)
  outliers start: 37
  outliers final: 19
  residues processed: 120
  average time/residue: 0.2384
  time to fit residues: 40.7680
Evaluate side-chains
  97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
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  495 VAL
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  542 MET
Chi-restraints excluded: chain B residue  592 PHE
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 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  541 TYR
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  636 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 86 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    0.2980
   chunk 49 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0040
   chunk 113 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0050
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.4006

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.103054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.081609 restraints weight = 30187.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.084388 restraints weight = 15161.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.086294 restraints weight = 9771.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9648  Z= 0.117
  Angle     :  0.630   9.527  13082  Z= 0.325
  Chirality :  0.041   0.151   1502
  Planarity :  0.003   0.051   1658
  Dihedral  :  4.859  32.154   1322
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 10.25 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.24), residues: 1190
  helix:  0.65 (0.20), residues: 690
  sheet: -1.11 (0.79), residues: 44
  loop : -3.82 (0.24), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 239 
 HIS   0.005   0.001   HIS B 352 
 PHE   0.010   0.001   PHE A 460 
 TYR   0.017   0.001   TYR B 530 
 ARG   0.002   0.000   ARG B 450 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  485)
  hydrogen bonds       : angle       3.74541 ( 1431)
  covalent geometry    : bond        0.00228 ( 9648)
  covalent geometry    : angle       0.63011 (13082)

*********************** 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
  121 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 88
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 MET cc_start: 0.8472 (tmm) cc_final: 0.7983 (tmm)
REVERT: B  346 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: B  487 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8111 (pp20)
REVERT: B  614 MET cc_start: 0.8100 (ptp) cc_final: 0.7739 (ppp)
REVERT: A  322 SER cc_start: 0.8523 (p) cc_final: 0.8295 (p)
REVERT: A  561 MET cc_start: 0.8436 (tmm) cc_final: 0.7990 (tmm)
REVERT: A  775 ASN cc_start: 0.8018 (m-40) cc_final: 0.7697 (t0)
  outliers start: 33
  outliers final: 22
  residues processed: 111
  average time/residue: 0.2380
  time to fit residues: 38.0999
Evaluate side-chains
  105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  360 TRP
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  592 PHE
Chi-restraints excluded: chain B residue  595 VAL
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  823 GLN
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  541 TYR
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  636 LEU
Chi-restraints excluded: chain A residue  684 ILE
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 31 optimal weight:    0.1980
   chunk 69 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 112 optimal weight:    6.9990
   chunk 47 optimal weight:    0.3980
   chunk 80 optimal weight:    8.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 361 HIS
** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 484 GLN
A 656 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.096714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.075102 restraints weight = 30739.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.077741 restraints weight = 15462.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.079540 restraints weight = 10038.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9648  Z= 0.150
  Angle     :  0.675  10.054  13082  Z= 0.350
  Chirality :  0.043   0.156   1502
  Planarity :  0.004   0.063   1658
  Dihedral  :  4.997  33.312   1322
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 11.26 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 15.74 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.24), residues: 1190
  helix:  0.83 (0.20), residues: 694
  sheet: -1.21 (0.89), residues: 34
  loop : -3.78 (0.24), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 488 
 HIS   0.004   0.001   HIS B 361 
 PHE   0.015   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A 716 
 ARG   0.006   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05125 (  485)
  hydrogen bonds       : angle       3.85126 ( 1431)
  covalent geometry    : bond        0.00327 ( 9648)
  covalent geometry    : angle       0.67489 (13082)

*********************** 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
  122 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 78
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4161 (p90) cc_final: 0.3897 (p90)
REVERT: B  272 MET cc_start: 0.8465 (tmm) cc_final: 0.7990 (tmm)
REVERT: B  311 PHE cc_start: 0.8705 (t80) cc_final: 0.8465 (t80)
REVERT: B  346 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: B  487 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8197 (pp20)
REVERT: B  751 ASP cc_start: 0.7079 (t0) cc_final: 0.6820 (t0)
REVERT: A  302 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8737 (tp)
REVERT: A  322 SER cc_start: 0.8691 (p) cc_final: 0.8418 (p)
REVERT: A  561 MET cc_start: 0.8457 (tmm) cc_final: 0.7982 (tmm)
REVERT: A  585 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.5986 (m-10)
REVERT: A  589 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5932 (tpp-160)
REVERT: A  592 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.5593 (t80)
REVERT: A  771 LYS cc_start: 0.8225 (tppt) cc_final: 0.7596 (tmtt)
REVERT: A  775 ASN cc_start: 0.8207 (m-40) cc_final: 0.7663 (t0)
REVERT: A  823 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8745 (mm110)
  outliers start: 44
  outliers final: 19
  residues processed: 110
  average time/residue: 0.1930
  time to fit residues: 30.9053
Evaluate side-chains
  95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  360 TRP
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  542 MET
Chi-restraints excluded: chain B residue  592 PHE
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 A residue  282 VAL
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  585 PHE
Chi-restraints excluded: chain A residue  589 ARG
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  614 MET
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  636 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 116 optimal weight:    0.3980
   chunk 71 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   chunk 113 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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**
** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 823 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.097542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.076053 restraints weight = 30322.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.078732 restraints weight = 15150.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.080564 restraints weight = 9833.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9648  Z= 0.124
  Angle     :  0.641  10.216  13082  Z= 0.331
  Chirality :  0.041   0.157   1502
  Planarity :  0.003   0.034   1658
  Dihedral  :  4.901  33.019   1322
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 10.92 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.13 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.25), residues: 1190
  helix:  1.00 (0.20), residues: 696
  sheet: -1.18 (0.87), residues: 34
  loop : -3.78 (0.24), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 488 
 HIS   0.003   0.001   HIS B 352 
 PHE   0.013   0.001   PHE B 460 
 TYR   0.017   0.001   TYR B 530 
 ARG   0.008   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04654 (  485)
  hydrogen bonds       : angle       3.77145 ( 1431)
  covalent geometry    : bond        0.00254 ( 9648)
  covalent geometry    : angle       0.64137 (13082)

*********************** 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
  120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 81
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4206 (p90) cc_final: 0.3952 (p90)
REVERT: B  272 MET cc_start: 0.8477 (tmm) cc_final: 0.7885 (tmm)
REVERT: B  275 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: B  346 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8039 (tm-30)
REVERT: B  487 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8166 (pp20)
REVERT: B  584 ARG cc_start: 0.7519 (tpt90) cc_final: 0.7086 (mtm-85)
REVERT: B  614 MET cc_start: 0.8035 (ptp) cc_final: 0.7271 (ppp)
REVERT: B  751 ASP cc_start: 0.6900 (t0) cc_final: 0.6576 (t70)
REVERT: A  322 SER cc_start: 0.8661 (p) cc_final: 0.8393 (p)
REVERT: A  359 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6641 (mtp-110)
REVERT: A  487 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8306 (pp20)
REVERT: A  561 MET cc_start: 0.8468 (tmm) cc_final: 0.8003 (tmm)
REVERT: A  567 LEU cc_start: 0.8769 (mp) cc_final: 0.8402 (pp)
REVERT: A  585 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.5915 (m-10)
REVERT: A  592 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5154 (t80)
REVERT: A  775 ASN cc_start: 0.8208 (m-40) cc_final: 0.7634 (t0)
  outliers start: 39
  outliers final: 19
  residues processed: 112
  average time/residue: 0.2490
  time to fit residues: 39.0831
Evaluate side-chains
  94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
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  392 ILE
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  592 PHE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  359 ARG
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  558 PHE
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  636 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 93 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0030
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 100 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 823 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.097854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.076157 restraints weight = 30600.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.078906 restraints weight = 15347.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.080788 restraints weight = 9966.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9648  Z= 0.124
  Angle     :  0.650  10.483  13082  Z= 0.335
  Chirality :  0.041   0.161   1502
  Planarity :  0.004   0.053   1658
  Dihedral  :  4.831  32.882   1322
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 11.01 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.25), residues: 1190
  helix:  1.20 (0.21), residues: 682
  sheet: -1.10 (0.88), residues: 34
  loop : -3.65 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.013   0.001   PHE B 460 
 TYR   0.016   0.001   TYR A 716 
 ARG   0.006   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04473 (  485)
  hydrogen bonds       : angle       3.73425 ( 1431)
  covalent geometry    : bond        0.00255 ( 9648)
  covalent geometry    : angle       0.65026 (13082)

*********************** 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: 30
    poor density    : 75
  time to evaluate  : 1.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4189 (p90) cc_final: 0.3941 (p90)
REVERT: B  272 MET cc_start: 0.8486 (tmm) cc_final: 0.7894 (tmm)
REVERT: B  275 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8270 (tm-30)
REVERT: B  311 PHE cc_start: 0.8743 (t80) cc_final: 0.8472 (t80)
REVERT: B  346 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: B  421 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6886 (tmm)
REVERT: B  487 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8138 (pp20)
REVERT: B  584 ARG cc_start: 0.7656 (tpt90) cc_final: 0.7202 (mtm-85)
REVERT: A  322 SER cc_start: 0.8642 (p) cc_final: 0.8364 (p)
REVERT: A  359 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6665 (mtp180)
REVERT: A  541 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7157 (t80)
REVERT: A  561 MET cc_start: 0.8491 (tmm) cc_final: 0.8011 (tmm)
REVERT: A  567 LEU cc_start: 0.8749 (mp) cc_final: 0.8432 (pp)
REVERT: A  585 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.6006 (m-10)
REVERT: A  775 ASN cc_start: 0.8126 (m-40) cc_final: 0.7548 (t0)
  outliers start: 30
  outliers final: 17
  residues processed: 96
  average time/residue: 0.2250
  time to fit residues: 31.5758
Evaluate side-chains
  96 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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  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  592 PHE
Chi-restraints excluded: chain B residue  595 VAL
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  359 ARG
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  495 VAL
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  633 LEU
Chi-restraints excluded: chain A residue  636 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 90 optimal weight:    0.0870
   chunk 22 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 112 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    0.7962

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.096955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.075205 restraints weight = 31126.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.077932 restraints weight = 15588.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.079832 restraints weight = 10118.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.5805

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= 0.130
  Angle     :  0.649  10.573  13082  Z= 0.336
  Chirality :  0.041   0.150   1502
  Planarity :  0.003   0.028   1658
  Dihedral  :  4.841  32.861   1322
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.85 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.92 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.25), residues: 1190
  helix:  1.23 (0.20), residues: 682
  sheet: -1.11 (0.86), residues: 34
  loop : -3.50 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.012   0.001   PHE B 460 
 TYR   0.016   0.001   TYR B 530 
 ARG   0.005   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04550 (  485)
  hydrogen bonds       : angle       3.73116 ( 1431)
  covalent geometry    : bond        0.00276 ( 9648)
  covalent geometry    : angle       0.64934 (13082)

*********************** 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
  109 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 78
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4279 (p90) cc_final: 0.4012 (p90)
REVERT: B  272 MET cc_start: 0.8494 (tmm) cc_final: 0.7901 (tmm)
REVERT: B  275 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: B  346 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8016 (tm-30)
REVERT: B  421 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7072 (tmm)
REVERT: B  487 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8155 (pp20)
REVERT: B  584 ARG cc_start: 0.7679 (tpt90) cc_final: 0.7326 (mtm-85)
REVERT: A  239 TRP cc_start: 0.3855 (p90) cc_final: 0.3563 (p90)
REVERT: A  272 MET cc_start: 0.8372 (tmm) cc_final: 0.7822 (tmm)
REVERT: A  322 SER cc_start: 0.8678 (p) cc_final: 0.8398 (p)
REVERT: A  359 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6800 (mtp180)
REVERT: A  487 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8189 (pp20)
REVERT: A  561 MET cc_start: 0.8500 (tmm) cc_final: 0.8012 (tmm)
REVERT: A  567 LEU cc_start: 0.8760 (mp) cc_final: 0.8477 (pp)
REVERT: A  775 ASN cc_start: 0.8086 (m-40) cc_final: 0.7469 (t0)
  outliers start: 31
  outliers final: 19
  residues processed: 101
  average time/residue: 0.2269
  time to fit residues: 33.2094
Evaluate side-chains
  97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
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  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  592 PHE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  640 TYR
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  359 ARG
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  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  636 LEU
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  686 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0970
   chunk 8 optimal weight:    0.4980
   chunk 64 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 103 optimal weight:    0.0670
   overall best weight:    0.4316

-------------------------------------------------------------------------------
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 596 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.098629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.077048 restraints weight = 30528.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.079841 restraints weight = 15335.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.081758 restraints weight = 9926.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.5919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9648  Z= 0.120
  Angle     :  0.639  10.985  13082  Z= 0.329
  Chirality :  0.041   0.148   1502
  Planarity :  0.003   0.029   1658
  Dihedral  :  4.735  32.209   1322
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.84 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.22 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.25), residues: 1190
  helix:  1.16 (0.20), residues: 694
  sheet: -0.98 (0.89), residues: 34
  loop : -3.50 (0.25), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 822 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.012   0.001   PHE B 460 
 TYR   0.015   0.001   TYR A 716 
 ARG   0.006   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04161 (  485)
  hydrogen bonds       : angle       3.66580 ( 1431)
  covalent geometry    : bond        0.00244 ( 9648)
  covalent geometry    : angle       0.63946 (13082)

*********************** 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
  116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4293 (p90) cc_final: 0.4015 (p90)
REVERT: B  272 MET cc_start: 0.8464 (tmm) cc_final: 0.7900 (tmm)
REVERT: B  275 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8169 (tm-30)
REVERT: B  346 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8034 (tm-30)
REVERT: B  421 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7019 (tmm)
REVERT: B  487 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8034 (pp20)
REVERT: B  584 ARG cc_start: 0.7655 (tpt90) cc_final: 0.7424 (mtm-85)
REVERT: A  239 TRP cc_start: 0.4055 (p90) cc_final: 0.3763 (p90)
REVERT: A  487 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8088 (pp20)
REVERT: A  561 MET cc_start: 0.8483 (tmm) cc_final: 0.8001 (tmm)
REVERT: A  567 LEU cc_start: 0.8700 (mp) cc_final: 0.8474 (pp)
REVERT: A  771 LYS cc_start: 0.8218 (tppt) cc_final: 0.7492 (mmtp)
REVERT: A  775 ASN cc_start: 0.7941 (m-40) cc_final: 0.7312 (t0)
  outliers start: 28
  outliers final: 17
  residues processed: 108
  average time/residue: 0.2349
  time to fit residues: 35.7505
Evaluate side-chains
  98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
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  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  592 PHE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  640 TYR
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  457 LEU
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  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 88 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.6784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.093029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.071504 restraints weight = 30830.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.074077 restraints weight = 15316.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.075812 restraints weight = 9947.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.6493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9648  Z= 0.185
  Angle     :  0.729  11.195  13082  Z= 0.376
  Chirality :  0.045   0.156   1502
  Planarity :  0.004   0.031   1658
  Dihedral  :  5.138  34.602   1322
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 12.44 %
    Favored  : 87.31 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.25), residues: 1190
  helix:  1.14 (0.20), residues: 684
  sheet: -1.25 (0.84), residues: 34
  loop : -3.60 (0.24), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 488 
 HIS   0.005   0.001   HIS A 352 
 PHE   0.016   0.002   PHE B 325 
 TYR   0.013   0.002   TYR A 541 
 ARG   0.008   0.000   ARG A 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05556 (  485)
  hydrogen bonds       : angle       3.98094 ( 1431)
  covalent geometry    : bond        0.00425 ( 9648)
  covalent geometry    : angle       0.72933 (13082)

********************** 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: 24
    poor density    : 76
  time to evaluate  : 1.275 
Fit side-chains
   revert: symmetry clash
REVERT: B  239 TRP cc_start: 0.4383 (p90) cc_final: 0.4046 (p90)
REVERT: B  272 MET cc_start: 0.8478 (tmm) cc_final: 0.7915 (tmm)
REVERT: B  275 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: B  346 GLU cc_start: 0.8626 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: B  421 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7449 (tmm)
REVERT: B  487 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8320 (pp20)
REVERT: A  239 TRP cc_start: 0.4044 (p90) cc_final: 0.3776 (p90)
REVERT: A  322 SER cc_start: 0.8812 (p) cc_final: 0.8543 (p)
REVERT: A  487 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8254 (pp20)
REVERT: A  561 MET cc_start: 0.8553 (tmm) cc_final: 0.8048 (tmm)
REVERT: A  567 LEU cc_start: 0.8835 (mp) cc_final: 0.8560 (pp)
REVERT: A  587 LYS cc_start: 0.5908 (tmtt) cc_final: 0.5617 (tmtt)
REVERT: A  771 LYS cc_start: 0.8268 (tppt) cc_final: 0.7539 (mmtp)
REVERT: A  775 ASN cc_start: 0.8058 (m-40) cc_final: 0.7463 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 92
  average time/residue: 0.2780
  time to fit residues: 36.4399
Evaluate side-chains
  89 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
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  392 ILE
Chi-restraints excluded: chain B residue  421 MET
Chi-restraints excluded: chain B residue  487 GLU
Chi-restraints excluded: chain B residue  592 PHE
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  640 TYR
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  487 GLU
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  679 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 2 optimal weight:    0.0000
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.1980
   chunk 116 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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 = 0.3864 r_free = 0.3864 target = 0.096262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.074394 restraints weight = 30319.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.077042 restraints weight = 15288.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.078870 restraints weight = 9939.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.6481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9648  Z= 0.130
  Angle     :  0.684  11.496  13082  Z= 0.351
  Chirality :  0.042   0.179   1502
  Planarity :  0.004   0.050   1658
  Dihedral  :  4.894  33.503   1322
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.34 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.21 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.25), residues: 1190
  helix:  1.24 (0.20), residues: 686
  sheet: -1.11 (0.85), residues: 34
  loop : -3.53 (0.24), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 488 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.027   0.001   PHE B 325 
 TYR   0.017   0.001   TYR B 530 
 ARG   0.005   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04561 (  485)
  hydrogen bonds       : angle       3.76398 ( 1431)
  covalent geometry    : bond        0.00270 ( 9648)
  covalent geometry    : angle       0.68424 (13082)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3646.14 seconds
wall clock time: 66 minutes 32.16 seconds (3992.16 seconds total)