Starting phenix.real_space_refine
on Mon Jul 28 14:38:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sun_25442/07_2025/7sun_25442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sun_25442/07_2025/7sun_25442.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sun_25442/07_2025/7sun_25442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sun_25442/07_2025/7sun_25442.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sun_25442/07_2025/7sun_25442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sun_25442/07_2025/7sun_25442.cif"
  }
  resolution = 3.6
  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=   0.000 sd=   0.005
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      52      5.16       5
     C    6852      2.51       5
     N    1692      2.21       5
     O    1858      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10454
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 675, 5227
          Classifications: {'peptide': 675}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 32, 'TRANS': 642}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Restraints were copied for chains:
    B
  Time building chain proxies: 10.30, per 1000 atoms: 0.99
  Number of scatterers: 10454
  At special positions: 0
  Unit cell: (101.46, 116.412, 115.344, 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      52     16.00
     O    1858      8.00
     N    1692      7.00
     C    6852      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: 3.10
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2504

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 5 sheets defined
      70.7% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 30
    Processing helix  chain 'A' and resid 41 through 48
      removed outlier: 3.640A  pdb=" N   LYS A  45 " --> pdb=" O   SER A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 66 through 71
      removed outlier: 3.695A  pdb=" N   TRP A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 66 through 71'
    Processing helix  chain 'A' and resid 75 through 105
      removed outlier: 4.053A  pdb=" N   VAL A  80 " --> pdb=" O   PHE A  76 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   LEU A  81 " --> pdb=" O   LYS A  77 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   GLY A  82 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 108 through 115
      removed outlier: 3.840A  pdb=" N   GLY A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 127
    Processing helix  chain 'A' and resid 137 through 152
    Processing helix  chain 'A' and resid 168 through 196
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 206 through 230
      removed outlier: 4.479A  pdb=" N   LYS A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   TYR A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 258 through 282
      removed outlier: 3.962A  pdb=" N   LEU A 262 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 308
      removed outlier: 3.821A  pdb=" N   PHE A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.636A  pdb=" N   SER A 312 " --> pdb=" O   ASN A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 338
      removed outlier: 4.045A  pdb=" N   HIS A 337 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 366
    Processing helix  chain 'A' and resid 370 through 387
      removed outlier: 3.896A  pdb=" N   LEU A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 407
    Processing helix  chain 'A' and resid 411 through 427
    Processing helix  chain 'A' and resid 428 through 433
      removed outlier: 3.786A  pdb=" N   GLU A 433 " --> pdb=" O   PHE A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
      removed outlier: 3.672A  pdb=" N   LEU A 440 " --> pdb=" O   PRO A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 455
      removed outlier: 3.826A  pdb=" N   MET A 453 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 463
      removed outlier: 3.630A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG A 463 " --> pdb=" O   PRO A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 481
    Processing helix  chain 'A' and resid 483 through 505
      removed outlier: 4.205A  pdb=" N   ILE A 489 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 560
      removed outlier: 4.819A  pdb=" N   ASP A 550 " --> pdb=" O   TYR A 546 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   LEU A 551 " --> pdb=" O   ALA A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'A' and resid 626 through 631
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 680 through 690
      removed outlier: 3.568A  pdb=" N   ASN A 690 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 694
      removed outlier: 3.545A  pdb=" N   GLU A 694 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 691 through 694'
    Processing helix  chain 'A' and resid 695 through 700
      removed outlier: 3.644A  pdb=" N   LYS A 699 " --> pdb=" O   PRO A 696 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   GLU A 700 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 726
    Processing helix  chain 'B' and resid 24 through 30
    Processing helix  chain 'B' and resid 41 through 48
      removed outlier: 3.639A  pdb=" N   LYS B  45 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 65
    Processing helix  chain 'B' and resid 66 through 71
      removed outlier: 3.696A  pdb=" N   TRP B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 66 through 71'
    Processing helix  chain 'B' and resid 75 through 105
      removed outlier: 4.052A  pdb=" N   VAL B  80 " --> pdb=" O   PHE B  76 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   LEU B  81 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   GLY B  82 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 108 through 115
      removed outlier: 3.841A  pdb=" N   GLY B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 127
    Processing helix  chain 'B' and resid 137 through 152
    Processing helix  chain 'B' and resid 168 through 196
    Processing helix  chain 'B' and resid 199 through 204
    Processing helix  chain 'B' and resid 206 through 230
      removed outlier: 4.479A  pdb=" N   LYS B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   TYR B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 258 through 282
      removed outlier: 3.962A  pdb=" N   LEU B 262 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 308
      removed outlier: 3.821A  pdb=" N   PHE B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.636A  pdb=" N   SER B 312 " --> pdb=" O   ASN B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 338
      removed outlier: 4.045A  pdb=" N   HIS B 337 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 366
    Processing helix  chain 'B' and resid 370 through 387
      removed outlier: 3.897A  pdb=" N   LEU B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 407
    Processing helix  chain 'B' and resid 411 through 427
    Processing helix  chain 'B' and resid 428 through 433
      removed outlier: 3.786A  pdb=" N   GLU B 433 " --> pdb=" O   PHE B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 449
      removed outlier: 3.673A  pdb=" N   LEU B 440 " --> pdb=" O   PRO B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 455
      removed outlier: 3.825A  pdb=" N   MET B 453 " --> pdb=" O   GLY B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 463
      removed outlier: 3.631A  pdb=" N   PHE B 460 " --> pdb=" O   SER B 456 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG B 463 " --> pdb=" O   PRO B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 481
    Processing helix  chain 'B' and resid 483 through 505
      removed outlier: 4.204A  pdb=" N   ILE B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   VAL B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 560
      removed outlier: 4.819A  pdb=" N   ASP B 550 " --> pdb=" O   TYR B 546 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   LEU B 551 " --> pdb=" O   ALA B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 579
    Processing helix  chain 'B' and resid 626 through 631
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 680 through 690
      removed outlier: 3.569A  pdb=" N   ASN B 690 " --> pdb=" O   ASP B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 691 through 694
      removed outlier: 3.545A  pdb=" N   GLU B 694 " --> pdb=" O   ARG B 691 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 691 through 694'
    Processing helix  chain 'B' and resid 695 through 700
      removed outlier: 3.643A  pdb=" N   LYS B 699 " --> pdb=" O   PRO B 696 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   GLU B 700 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 726
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20
      removed outlier: 3.870A  pdb=" N   VAL A  18 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL B  18 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 135
      removed outlier: 4.684A  pdb=" N   SER A 133 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522
      removed outlier: 4.190A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   GLN A 513 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 11.379A  pdb=" N   ILE A 535 " --> pdb=" O   GLN A 513 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA A 677 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   PHE A 703 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU A 676 " --> pdb=" O   PHE A 703 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 135
      removed outlier: 4.684A  pdb=" N   SER B 133 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522
      removed outlier: 4.190A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   GLN B 513 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 11.379A  pdb=" N   ILE B 535 " --> pdb=" O   GLN B 513 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   ASP B 645 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 645 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA B 677 " --> pdb=" O   LEU B 644 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   PHE B 703 " --> pdb=" O   VAL B 674 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU B 676 " --> pdb=" O   PHE B 703 " (cutoff:3.500A)

    658 hydrogen bonds defined for protein.
    1896 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: 3.25

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3240
        1.34 -     1.46: 2332
        1.46 -     1.58: 5028
        1.58 -     1.69: 0
        1.69 -     1.81: 86
  Bond restraints: 10686
  Sorted by residual:
  bond pdb=" CG  LEU B 401 "
       pdb=" CD1 LEU B 401 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.41e+00
  bond pdb=" CG  LEU A 401 "
       pdb=" CD1 LEU A 401 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.38e+00
  bond pdb=" CA  GLU B 527 "
       pdb=" C   GLU B 527 "
    ideal  model  delta    sigma   weight residual
    1.524  1.541 -0.016 1.50e-02 4.44e+03 1.19e+00
  bond pdb=" CA  THR B 623 "
       pdb=" CB  THR B 623 "
    ideal  model  delta    sigma   weight residual
    1.527  1.542 -0.015 1.44e-02 4.82e+03 1.14e+00
  bond pdb=" CA  GLU A 527 "
       pdb=" C   GLU A 527 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.015 1.50e-02 4.44e+03 1.06e+00
  ... (remaining 10681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 14149
        1.84 -     3.68: 286
        3.68 -     5.53: 49
        5.53 -     7.37: 26
        7.37 -     9.21: 6
  Bond angle restraints: 14516
  Sorted by residual:
  angle pdb=" CA  LEU B 514 "
        pdb=" CB  LEU B 514 "
        pdb=" CG  LEU B 514 "
      ideal   model   delta    sigma   weight residual
     116.30  125.51   -9.21 3.50e+00 8.16e-02 6.93e+00
  angle pdb=" CA  LEU A 514 "
        pdb=" CB  LEU A 514 "
        pdb=" CG  LEU A 514 "
      ideal   model   delta    sigma   weight residual
     116.30  125.49   -9.19 3.50e+00 8.16e-02 6.90e+00
  angle pdb=" C   PRO B 543 "
        pdb=" N   ILE B 544 "
        pdb=" CA  ILE B 544 "
      ideal   model   delta    sigma   weight residual
     121.97  126.39   -4.42 1.80e+00 3.09e-01 6.04e+00
  angle pdb=" C   PRO A 543 "
        pdb=" N   ILE A 544 "
        pdb=" CA  ILE A 544 "
      ideal   model   delta    sigma   weight residual
     121.97  126.35   -4.38 1.80e+00 3.09e-01 5.92e+00
  angle pdb=" CB  LEU B 401 "
        pdb=" CG  LEU B 401 "
        pdb=" CD1 LEU B 401 "
      ideal   model   delta    sigma   weight residual
     110.70  103.43    7.27 3.00e+00 1.11e-01 5.88e+00
  ... (remaining 14511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 5693
       17.46 -    34.93: 535
       34.93 -    52.39: 90
       52.39 -    69.86: 22
       69.86 -    87.32: 4
  Dihedral angle restraints: 6344
    sinusoidal: 2442
      harmonic: 3902
  Sorted by residual:
  dihedral pdb=" CA  LYS B  35 "
           pdb=" C   LYS B  35 "
           pdb=" N   ASP B  36 "
           pdb=" CA  ASP B  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  LYS A  35 "
           pdb=" C   LYS A  35 "
           pdb=" N   ASP A  36 "
           pdb=" CA  ASP A  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.67   21.33     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  ALA B 525 "
           pdb=" C   ALA B 525 "
           pdb=" N   TYR B 526 "
           pdb=" CA  TYR B 526 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.05  -18.95     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 6341 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1217
       0.045 -    0.091: 409
       0.091 -    0.136: 93
       0.136 -    0.182: 7
       0.182 -    0.227: 2
  Chirality restraints: 1728
  Sorted by residual:
  chirality pdb=" CB  ILE B 544 "
            pdb=" CA  ILE B 544 "
            pdb=" CG1 ILE B 544 "
            pdb=" CG2 ILE B 544 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  ILE A 544 "
            pdb=" CA  ILE A 544 "
            pdb=" CG1 ILE A 544 "
            pdb=" CG2 ILE A 544 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  GLU B 527 "
            pdb=" N   GLU B 527 "
            pdb=" C   GLU B 527 "
            pdb=" CB  GLU B 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.96e-01
  ... (remaining 1725 not shown)

  Planarity restraints: 1804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 542 "   -0.031 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO A 543 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 542 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO B 543 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 543 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 543 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 107 "   -0.024 5.00e-02 4.00e+02   3.69e-02 2.17e+00
        pdb=" N   PRO A 108 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 108 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 108 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1801 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2731
        2.80 -     3.33: 10639
        3.33 -     3.85: 17632
        3.85 -     4.38: 19419
        4.38 -     4.90: 33508
  Nonbonded interactions: 83929
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 556 "
            pdb=" OG1 THR B 560 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   LEU A 556 "
            pdb=" OG1 THR A 560 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   SER B  86 "
            pdb=" OG1 THR B  90 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   SER A  86 "
            pdb=" OG1 THR A  90 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" NH2 ARG B 150 "
            pdb=" OD2 ASP B 342 "
     model   vdw
     2.323 3.120
  ... (remaining 83924 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     31.070
  Find NCS groups from input model:        0.190
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
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      :  0.003   0.051  10686  Z= 0.144
  Angle     :  0.693   9.212  14516  Z= 0.343
  Chirality :  0.046   0.227   1728
  Planarity :  0.005   0.046   1804
  Dihedral  : 13.913  87.324   3840
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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:  0.67 (0.24), residues: 1338
  helix:  1.08 (0.18), residues: 884
  sheet:  3.81 (0.85), residues: 36
  loop : -1.19 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  70 
 HIS   0.002   0.001   HIS A  17 
 PHE   0.014   0.001   PHE B 432 
 TYR   0.024   0.001   TYR A 114 
 ARG   0.005   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14331 (  658)
  hydrogen bonds       : angle       5.35698 ( 1896)
  covalent geometry    : bond        0.00324 (10686)
  covalent geometry    : angle       0.69310 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  380 ILE cc_start: 0.6264 (tp) cc_final: 0.6054 (tp)
REVERT: A  428 THR cc_start: 0.7460 (m) cc_final: 0.7225 (p)
REVERT: A  458 LEU cc_start: 0.8777 (mm) cc_final: 0.8573 (mm)
REVERT: A  488 LEU cc_start: 0.8878 (tp) cc_final: 0.8582 (tp)
REVERT: B  428 THR cc_start: 0.7473 (m) cc_final: 0.7269 (p)
REVERT: B  458 LEU cc_start: 0.8775 (mm) cc_final: 0.8563 (mm)
REVERT: B  488 LEU cc_start: 0.8887 (tp) cc_final: 0.8597 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1997
  time to fit residues: 60.8543
Evaluate side-chains
  156 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    0.4980
   chunk 101 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 54 optimal weight:    0.6980
   chunk 105 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 121 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 389 GLN
A 447 ASN
B  48 GLN
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 389 GLN
B 447 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.124307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101688 restraints weight = 19912.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.103998 restraints weight = 10868.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.105397 restraints weight = 7601.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10686  Z= 0.116
  Angle     :  0.566   6.054  14516  Z= 0.286
  Chirality :  0.043   0.223   1728
  Planarity :  0.004   0.046   1804
  Dihedral  :  4.217  20.596   1442
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  8.43 %
    Favored  : 89.91 %
  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:  1.12 (0.24), residues: 1338
  helix:  1.44 (0.18), residues: 880
  sheet:  4.12 (0.88), residues: 36
  loop : -1.03 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  70 
 HIS   0.003   0.001   HIS B 640 
 PHE   0.010   0.001   PHE A 198 
 TYR   0.017   0.001   TYR A 545 
 ARG   0.002   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  658)
  hydrogen bonds       : angle       4.19745 ( 1896)
  covalent geometry    : bond        0.00252 (10686)
  covalent geometry    : angle       0.56635 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 1.099 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8815 (mm) cc_final: 0.8593 (mm)
REVERT: A  488 LEU cc_start: 0.8811 (tp) cc_final: 0.8584 (tp)
REVERT: B  354 THR cc_start: 0.8857 (m) cc_final: 0.8641 (t)
REVERT: B  458 LEU cc_start: 0.8792 (mm) cc_final: 0.8574 (mm)
REVERT: B  488 LEU cc_start: 0.8789 (tp) cc_final: 0.8572 (tp)
  outliers start: 19
  outliers final: 10
  residues processed: 176
  average time/residue: 0.1799
  time to fit residues: 48.1341
Evaluate side-chains
  159 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 96 optimal weight:    9.9990
   chunk 36 optimal weight:    0.8980
   chunk 123 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0980
   chunk 118 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 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 = 0.3566 r_free = 0.3566 target = 0.119020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.095806 restraints weight = 20529.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.098070 restraints weight = 11457.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.099443 restraints weight = 8050.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10686  Z= 0.147
  Angle     :  0.576   7.012  14516  Z= 0.286
  Chirality :  0.044   0.193   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  4.123  19.691   1442
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.17 %
    Favored  : 84.87 %
  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:  1.10 (0.24), residues: 1338
  helix:  1.44 (0.18), residues: 894
  sheet:  4.04 (0.84), residues: 36
  loop : -1.17 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 472 
 HIS   0.005   0.001   HIS B 640 
 PHE   0.008   0.001   PHE B 538 
 TYR   0.013   0.001   TYR A 237 
 ARG   0.002   0.000   ARG A 716 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03375 (  658)
  hydrogen bonds       : angle       4.08549 ( 1896)
  covalent geometry    : bond        0.00352 (10686)
  covalent geometry    : angle       0.57556 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 1.079 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8761 (mm) cc_final: 0.8508 (mm)
REVERT: A  578 TYR cc_start: 0.6733 (t80) cc_final: 0.6170 (t80)
REVERT: B   71 LEU cc_start: 0.8675 (mt) cc_final: 0.8468 (mt)
REVERT: B  458 LEU cc_start: 0.8754 (mm) cc_final: 0.8505 (mm)
REVERT: B  578 TYR cc_start: 0.6759 (t80) cc_final: 0.6185 (t80)
  outliers start: 34
  outliers final: 19
  residues processed: 178
  average time/residue: 0.1864
  time to fit residues: 50.4656
Evaluate side-chains
  163 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 126 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 35 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0070
   chunk 26 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 127 optimal weight:    0.7980
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 411 GLN
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.120302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.097311 restraints weight = 20265.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.099595 restraints weight = 11217.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.101047 restraints weight = 7884.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10686  Z= 0.112
  Angle     :  0.536   6.914  14516  Z= 0.267
  Chirality :  0.042   0.163   1728
  Planarity :  0.004   0.048   1804
  Dihedral  :  4.083  19.157   1442
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.52 %
    Favored  : 83.13 %
  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:  1.39 (0.24), residues: 1338
  helix:  1.61 (0.18), residues: 880
  sheet:  4.17 (0.84), residues: 36
  loop : -0.84 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 472 
 HIS   0.003   0.001   HIS B 640 
 PHE   0.007   0.001   PHE B 391 
 TYR   0.013   0.001   TYR A 114 
 ARG   0.002   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03017 (  658)
  hydrogen bonds       : angle       3.99121 ( 1896)
  covalent geometry    : bond        0.00252 (10686)
  covalent geometry    : angle       0.53596 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 1.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 LEU cc_start: 0.8777 (mm) cc_final: 0.8533 (mm)
REVERT: A  578 TYR cc_start: 0.6623 (t80) cc_final: 0.6098 (t80)
REVERT: B  458 LEU cc_start: 0.8768 (mm) cc_final: 0.8530 (mm)
REVERT: B  578 TYR cc_start: 0.6753 (t80) cc_final: 0.6149 (t80)
  outliers start: 27
  outliers final: 19
  residues processed: 171
  average time/residue: 0.1863
  time to fit residues: 48.9373
Evaluate side-chains
  167 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 115 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 119 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 124 optimal weight:    9.9990
   chunk 113 optimal weight:    4.9990
   chunk 130 optimal weight:    0.8980
   chunk 102 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.118193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.094836 restraints weight = 20392.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.097102 restraints weight = 11371.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.098495 restraints weight = 8041.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10686  Z= 0.139
  Angle     :  0.564   7.452  14516  Z= 0.278
  Chirality :  0.043   0.176   1728
  Planarity :  0.004   0.051   1804
  Dihedral  :  4.064  18.569   1442
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.83 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.19 (0.24), residues: 1338
  helix:  1.44 (0.18), residues: 912
  sheet:  4.14 (0.84), residues: 36
  loop : -1.09 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  70 
 HIS   0.004   0.001   HIS A 640 
 PHE   0.007   0.001   PHE B 538 
 TYR   0.013   0.001   TYR A 237 
 ARG   0.002   0.000   ARG B 502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03153 (  658)
  hydrogen bonds       : angle       4.01008 ( 1896)
  covalent geometry    : bond        0.00333 (10686)
  covalent geometry    : angle       0.56356 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 LEU cc_start: 0.8782 (mm) cc_final: 0.8482 (mm)
REVERT: A  578 TYR cc_start: 0.6657 (t80) cc_final: 0.6143 (t80)
REVERT: B  458 LEU cc_start: 0.8775 (mm) cc_final: 0.8510 (mm)
REVERT: B  578 TYR cc_start: 0.6758 (t80) cc_final: 0.6156 (t80)
  outliers start: 34
  outliers final: 24
  residues processed: 175
  average time/residue: 0.1767
  time to fit residues: 47.5216
Evaluate side-chains
  163 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 124 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 108 optimal weight:    0.8980
   chunk 109 optimal weight:    0.8980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 308 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.118690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095370 restraints weight = 20443.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.097632 restraints weight = 11345.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.099061 restraints weight = 8004.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10686  Z= 0.119
  Angle     :  0.541   7.279  14516  Z= 0.269
  Chirality :  0.042   0.166   1728
  Planarity :  0.004   0.048   1804
  Dihedral  :  4.048  18.356   1442
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.04 %
    Favored  : 79.91 %
  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:  1.25 (0.24), residues: 1338
  helix:  1.48 (0.18), residues: 912
  sheet:  4.18 (0.84), residues: 36
  loop : -1.05 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A 640 
 PHE   0.014   0.001   PHE A 198 
 TYR   0.013   0.001   TYR B 114 
 ARG   0.002   0.000   ARG B 502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03027 (  658)
  hydrogen bonds       : angle       3.94449 ( 1896)
  covalent geometry    : bond        0.00277 (10686)
  covalent geometry    : angle       0.54086 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 1.173 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8802 (mm) cc_final: 0.8509 (mm)
REVERT: A  578 TYR cc_start: 0.6814 (t80) cc_final: 0.6203 (t80)
REVERT: B  458 LEU cc_start: 0.8774 (mm) cc_final: 0.8517 (mm)
REVERT: B  578 TYR cc_start: 0.6756 (t80) cc_final: 0.6158 (t80)
  outliers start: 35
  outliers final: 26
  residues processed: 168
  average time/residue: 0.1875
  time to fit residues: 49.2529
Evaluate side-chains
  165 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 75 optimal weight:    0.6980
   chunk 103 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 102 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 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 = 0.3574 r_free = 0.3574 target = 0.119491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.096583 restraints weight = 20544.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.098891 restraints weight = 11204.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.100298 restraints weight = 7800.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10686  Z= 0.112
  Angle     :  0.538   7.166  14516  Z= 0.266
  Chirality :  0.042   0.168   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  4.030  17.803   1442
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.13 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.50 (0.24), residues: 1338
  helix:  1.69 (0.18), residues: 886
  sheet:  4.08 (0.83), residues: 36
  loop : -0.80 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  70 
 HIS   0.003   0.001   HIS B 640 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.009   0.001   TYR A 237 
 ARG   0.003   0.000   ARG B 502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02941 (  658)
  hydrogen bonds       : angle       3.90286 ( 1896)
  covalent geometry    : bond        0.00257 (10686)
  covalent geometry    : angle       0.53819 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 149
  time to evaluate  : 1.285 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8824 (mm) cc_final: 0.8549 (mm)
REVERT: A  578 TYR cc_start: 0.6803 (t80) cc_final: 0.6190 (t80)
REVERT: B  458 LEU cc_start: 0.8815 (mm) cc_final: 0.8544 (mm)
REVERT: B  578 TYR cc_start: 0.6745 (t80) cc_final: 0.6142 (t80)
  outliers start: 36
  outliers final: 28
  residues processed: 171
  average time/residue: 0.1767
  time to fit residues: 46.8247
Evaluate side-chains
  169 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    0.3980
   chunk 118 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 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 = 0.3565 r_free = 0.3565 target = 0.118861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.095987 restraints weight = 20289.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.098251 restraints weight = 11222.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.099645 restraints weight = 7856.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10686  Z= 0.120
  Angle     :  0.558   9.303  14516  Z= 0.273
  Chirality :  0.042   0.193   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  4.042  17.473   1442
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.57 %
    Favored  : 79.39 %
  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:  1.55 (0.24), residues: 1338
  helix:  1.71 (0.18), residues: 886
  sheet:  4.11 (0.82), residues: 36
  loop : -0.76 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  70 
 HIS   0.004   0.001   HIS A 640 
 PHE   0.009   0.001   PHE A 198 
 TYR   0.008   0.001   TYR B 237 
 ARG   0.001   0.000   ARG A 716 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02996 (  658)
  hydrogen bonds       : angle       3.91372 ( 1896)
  covalent geometry    : bond        0.00280 (10686)
  covalent geometry    : angle       0.55838 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 1.200 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8834 (mm) cc_final: 0.8529 (mm)
REVERT: A  578 TYR cc_start: 0.6806 (t80) cc_final: 0.6155 (t80)
REVERT: A  653 ASP cc_start: 0.8279 (m-30) cc_final: 0.8018 (m-30)
REVERT: B  253 ASN cc_start: 0.7319 (m110) cc_final: 0.7090 (m-40)
REVERT: B  458 LEU cc_start: 0.8790 (mm) cc_final: 0.8471 (mm)
REVERT: B  578 TYR cc_start: 0.6726 (t80) cc_final: 0.6136 (t80)
REVERT: B  653 ASP cc_start: 0.8345 (m-30) cc_final: 0.7899 (m-30)
  outliers start: 35
  outliers final: 29
  residues processed: 165
  average time/residue: 0.1825
  time to fit residues: 46.6446
Evaluate side-chains
  169 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 140
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  518 ASP
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 114 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0980
   chunk 94 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 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 = 0.3588 r_free = 0.3588 target = 0.120449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.097259 restraints weight = 20591.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099568 restraints weight = 11462.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.101021 restraints weight = 8044.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10686  Z= 0.107
  Angle     :  0.532   6.938  14516  Z= 0.263
  Chirality :  0.042   0.183   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  4.006  17.035   1442
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.09 %
    Favored  : 79.30 %
  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:  1.62 (0.24), residues: 1338
  helix:  1.75 (0.18), residues: 886
  sheet:  4.17 (0.83), residues: 36
  loop : -0.70 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  70 
 HIS   0.002   0.001   HIS B 640 
 PHE   0.008   0.001   PHE A 198 
 TYR   0.009   0.001   TYR B 237 
 ARG   0.001   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02884 (  658)
  hydrogen bonds       : angle       3.86870 ( 1896)
  covalent geometry    : bond        0.00242 (10686)
  covalent geometry    : angle       0.53225 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 1.101 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8889 (mm) cc_final: 0.8600 (mm)
REVERT: A  578 TYR cc_start: 0.6873 (t80) cc_final: 0.6168 (t80)
REVERT: B  458 LEU cc_start: 0.8855 (mm) cc_final: 0.8585 (mm)
REVERT: B  578 TYR cc_start: 0.6706 (t80) cc_final: 0.6104 (t80)
  outliers start: 30
  outliers final: 25
  residues processed: 168
  average time/residue: 0.1749
  time to fit residues: 45.3972
Evaluate side-chains
  168 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  518 ASP
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 84 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 87 optimal weight:    0.4980
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.120654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.097921 restraints weight = 20394.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.100231 restraints weight = 11235.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.101700 restraints weight = 7843.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3304
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3304
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10686  Z= 0.106
  Angle     :  0.547  10.289  14516  Z= 0.266
  Chirality :  0.042   0.184   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  3.970  16.737   1442
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.78 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.63 (0.24), residues: 1338
  helix:  1.76 (0.18), residues: 886
  sheet:  4.21 (0.82), residues: 36
  loop : -0.69 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  70 
 HIS   0.002   0.001   HIS A 640 
 PHE   0.007   0.001   PHE B 391 
 TYR   0.008   0.001   TYR B 237 
 ARG   0.001   0.000   ARG A 502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02871 (  658)
  hydrogen bonds       : angle       3.85671 ( 1896)
  covalent geometry    : bond        0.00239 (10686)
  covalent geometry    : angle       0.54713 (14516)

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 1.169 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8790 (mm) cc_final: 0.8498 (mm)
REVERT: A  578 TYR cc_start: 0.6726 (t80) cc_final: 0.6129 (t80)
REVERT: B  222 PHE cc_start: 0.7119 (t80) cc_final: 0.6515 (m-80)
REVERT: B  458 LEU cc_start: 0.8778 (mm) cc_final: 0.8505 (mm)
REVERT: B  578 TYR cc_start: 0.6765 (t80) cc_final: 0.6176 (t80)
  outliers start: 29
  outliers final: 24
  residues processed: 165
  average time/residue: 0.1776
  time to fit residues: 45.1475
Evaluate side-chains
  168 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 101 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 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 = 0.3578 r_free = 0.3578 target = 0.119810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.096819 restraints weight = 20261.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.099084 restraints weight = 11330.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.100510 restraints weight = 7986.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10686  Z= 0.123
  Angle     :  0.559  10.029  14516  Z= 0.273
  Chirality :  0.043   0.196   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  3.975  16.576   1442
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.22 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.59 (0.24), residues: 1338
  helix:  1.73 (0.18), residues: 886
  sheet:  4.12 (0.87), residues: 34
  loop : -0.65 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  70 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.007   0.001   PHE A 452 
 TYR   0.016   0.001   TYR B 545 
 ARG   0.002   0.000   ARG A 502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02954 (  658)
  hydrogen bonds       : angle       3.88889 ( 1896)
  covalent geometry    : bond        0.00291 (10686)
  covalent geometry    : angle       0.55917 (14516)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3383.23 seconds
wall clock time: 59 minutes 30.78 seconds (3570.78 seconds total)