Starting phenix.real_space_refine
on Wed Mar  4 03:20:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sun_25442/03_2026/7sun_25442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sun_25442/03_2026/7sun_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sun_25442/03_2026/7sun_25442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sun_25442/03_2026/7sun_25442.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sun_25442/03_2026/7sun_25442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sun_25442/03_2026/7sun_25442.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 3.96, per 1000 atoms: 0.38
  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: 0.80
  Conformation dependent library (CDL) restraints added in 466.7 milliseconds
  

  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: 0.34
  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: 1.64

  Time building geometry restraints manager: 1.03 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: 0.02
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:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.850
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.220
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  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
 ARG   0.005   0.001   ARG A 281 
 TYR   0.024   0.001   TYR A 114 
 PHE   0.014   0.001   PHE B 432 
 TRP   0.008   0.001   TRP A  70 
 HIS   0.002   0.001   HIS A  17 

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

*********************** 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  : 0.315 
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: 0.0775
  time to fit residues: 23.8213
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  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.123456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.100873 restraints weight = 20139.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.103164 restraints weight = 10962.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.104627 restraints weight = 7631.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.105412 restraints weight = 6180.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.105922 restraints weight = 5553.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    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 = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10686  Z= 0.124
  Angle     :  0.576   6.383  14516  Z= 0.291
  Chirality :  0.043   0.230   1728
  Planarity :  0.004   0.046   1804
  Dihedral  :  4.216  20.744   1442
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.24), residues: 1338
  helix:  1.45 (0.18), residues: 878
  sheet:  4.16 (0.89), residues: 36
  loop : -1.08 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 197 
 TYR   0.015   0.001   TYR B 545 
 PHE   0.010   0.001   PHE A 198 
 TRP   0.005   0.001   TRP B 472 
 HIS   0.003   0.001   HIS B 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10686)
  covalent geometry    : angle       0.57588 (14516)
  hydrogen bonds       : bond        0.03358 (  658)
  hydrogen bonds       : angle       4.22965 ( 1896)

*********************** 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
  186 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  488 LEU cc_start: 0.8821 (tp) cc_final: 0.8592 (tp)
REVERT: A  578 TYR cc_start: 0.6574 (t80) cc_final: 0.6101 (t80)
REVERT: B  458 LEU cc_start: 0.8811 (mm) cc_final: 0.8589 (mm)
REVERT: B  482 LEU cc_start: 0.7994 (tt) cc_final: 0.7767 (mp)
REVERT: B  488 LEU cc_start: 0.8811 (tp) cc_final: 0.8586 (tp)
  outliers start: 20
  outliers final: 11
  residues processed: 173
  average time/residue: 0.0786
  time to fit residues: 20.9886
Evaluate side-chains
  161 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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 A residue  633 MET
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 34 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3609 r_free = 0.3609 target = 0.121917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.099321 restraints weight = 20528.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.101626 restraints weight = 11211.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.103060 restraints weight = 7811.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.103851 restraints weight = 6355.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.104403 restraints weight = 5685.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10686  Z= 0.110
  Angle     :  0.536   6.020  14516  Z= 0.267
  Chirality :  0.042   0.191   1728
  Planarity :  0.004   0.045   1804
  Dihedral  :  4.080  19.380   1442
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.65 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.24), residues: 1338
  helix:  1.57 (0.18), residues: 880
  sheet:  4.01 (0.83), residues: 36
  loop : -0.89 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 716 
 TYR   0.014   0.001   TYR A 237 
 PHE   0.008   0.001   PHE A 391 
 TRP   0.004   0.001   TRP A 472 
 HIS   0.003   0.001   HIS B 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10686)
  covalent geometry    : angle       0.53622 (14516)
  hydrogen bonds       : bond        0.03101 (  658)
  hydrogen bonds       : angle       4.01455 ( 1896)

*********************** 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
  189 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 162
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  380 ILE cc_start: 0.6605 (tp) cc_final: 0.6343 (tp)
REVERT: A  578 TYR cc_start: 0.6653 (t80) cc_final: 0.6180 (t80)
REVERT: B  380 ILE cc_start: 0.6405 (tp) cc_final: 0.6127 (tp)
REVERT: B  482 LEU cc_start: 0.7993 (tt) cc_final: 0.7790 (mp)
  outliers start: 27
  outliers final: 15
  residues processed: 176
  average time/residue: 0.0760
  time to fit residues: 20.5336
Evaluate side-chains
  160 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  244 VAL
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 56 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 58 optimal weight:    0.0060
   chunk 71 optimal weight:    5.9990
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.122640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.099919 restraints weight = 20477.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.102224 restraints weight = 11198.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.103691 restraints weight = 7825.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.104538 restraints weight = 6361.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.104910 restraints weight = 5677.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10686  Z= 0.103
  Angle     :  0.524   6.228  14516  Z= 0.262
  Chirality :  0.042   0.163   1728
  Planarity :  0.004   0.044   1804
  Dihedral  :  4.008  18.760   1442
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.70 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.24), residues: 1338
  helix:  1.67 (0.18), residues: 872
  sheet:  4.20 (0.84), residues: 36
  loop : -0.78 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 281 
 TYR   0.017   0.001   TYR A 114 
 PHE   0.007   0.001   PHE B 391 
 TRP   0.004   0.001   TRP B 472 
 HIS   0.003   0.001   HIS A 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10686)
  covalent geometry    : angle       0.52445 (14516)
  hydrogen bonds       : bond        0.02885 (  658)
  hydrogen bonds       : angle       3.93973 ( 1896)

*********************** 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
  185 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A  380 ILE cc_start: 0.6544 (tp) cc_final: 0.6291 (tp)
REVERT: A  578 TYR cc_start: 0.6698 (t80) cc_final: 0.6197 (t80)
REVERT: B  380 ILE cc_start: 0.6460 (tp) cc_final: 0.6207 (tp)
REVERT: B  578 TYR cc_start: 0.6653 (t80) cc_final: 0.6180 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 173
  average time/residue: 0.0743
  time to fit residues: 19.9276
Evaluate side-chains
  158 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 131 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 132 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 650 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.114582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.091126 restraints weight = 20574.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.093294 restraints weight = 11565.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.094641 restraints weight = 8200.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.095425 restraints weight = 6752.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095743 restraints weight = 6067.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  10686  Z= 0.222
  Angle     :  0.656   9.084  14516  Z= 0.327
  Chirality :  0.047   0.216   1728
  Planarity :  0.005   0.055   1804
  Dihedral  :  4.301  18.970   1442
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.24), residues: 1338
  helix:  1.31 (0.18), residues: 906
  sheet:  4.04 (0.85), residues: 36
  loop : -1.28 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 502 
 TYR   0.014   0.002   TYR B 340 
 PHE   0.010   0.001   PHE B 538 
 TRP   0.006   0.001   TRP B  70 
 HIS   0.005   0.001   HIS A 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (10686)
  covalent geometry    : angle       0.65587 (14516)
  hydrogen bonds       : bond        0.03829 (  658)
  hydrogen bonds       : angle       4.26246 ( 1896)

*********************** 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
  190 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 153
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  294 PHE cc_start: 0.7537 (t80) cc_final: 0.7334 (t80)
REVERT: A  458 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8580 (mm)
REVERT: A  578 TYR cc_start: 0.6766 (t80) cc_final: 0.6544 (t80)
REVERT: B  458 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8606 (mm)
REVERT: B  578 TYR cc_start: 0.6779 (t80) cc_final: 0.6422 (t80)
  outliers start: 37
  outliers final: 24
  residues processed: 174
  average time/residue: 0.0738
  time to fit residues: 20.0653
Evaluate side-chains
  158 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  342 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  458 LEU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
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  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  458 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  494 ILE
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  643 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   chunk 96 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 308 ASN
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.115405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.091788 restraints weight = 20704.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.093988 restraints weight = 11493.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.095362 restraints weight = 8148.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.096146 restraints weight = 6703.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096500 restraints weight = 6032.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10686  Z= 0.161
  Angle     :  0.595   9.149  14516  Z= 0.296
  Chirality :  0.044   0.172   1728
  Planarity :  0.004   0.054   1804
  Dihedral  :  4.259  18.809   1442
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.87 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.24), residues: 1338
  helix:  1.32 (0.18), residues: 908
  sheet:  4.05 (0.86), residues: 36
  loop : -1.23 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 502 
 TYR   0.017   0.001   TYR A 114 
 PHE   0.014   0.001   PHE A 198 
 TRP   0.005   0.001   TRP B 462 
 HIS   0.003   0.001   HIS A 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (10686)
  covalent geometry    : angle       0.59457 (14516)
  hydrogen bonds       : bond        0.03438 (  658)
  hydrogen bonds       : angle       4.12370 ( 1896)

*********************** 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
  176 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 135
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  294 PHE cc_start: 0.7524 (t80) cc_final: 0.7317 (t80)
REVERT: A  458 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8612 (mm)
REVERT: A  578 TYR cc_start: 0.6767 (t80) cc_final: 0.6546 (t80)
REVERT: B  458 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8607 (mm)
REVERT: B  578 TYR cc_start: 0.6758 (t80) cc_final: 0.6407 (t80)
  outliers start: 41
  outliers final: 29
  residues processed: 160
  average time/residue: 0.0750
  time to fit residues: 18.7185
Evaluate side-chains
  159 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  395 CYS
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  458 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 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  448 LEU
Chi-restraints excluded: chain B residue  458 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 83 optimal weight:    0.7980
   chunk 67 optimal weight:    0.1980
   chunk 80 optimal weight:    0.7980
   chunk 131 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   chunk 125 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:    0.7980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3539 r_free = 0.3539 target = 0.117162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.093834 restraints weight = 20350.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.096081 restraints weight = 11276.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.097480 restraints weight = 7921.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.098166 restraints weight = 6498.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.098706 restraints weight = 5880.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3251
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3251
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10686  Z= 0.124
  Angle     :  0.558   8.438  14516  Z= 0.277
  Chirality :  0.043   0.157   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  4.150  17.715   1442
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.83 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.24), residues: 1338
  helix:  1.46 (0.18), residues: 910
  sheet:  4.07 (0.87), residues: 36
  loop : -1.24 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 502 
 TYR   0.013   0.001   TYR B 237 
 PHE   0.012   0.001   PHE A 198 
 TRP   0.004   0.001   TRP B 462 
 HIS   0.002   0.001   HIS B 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10686)
  covalent geometry    : angle       0.55827 (14516)
  hydrogen bonds       : bond        0.03137 (  658)
  hydrogen bonds       : angle       4.03142 ( 1896)

*********************** 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
  179 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  294 PHE cc_start: 0.7526 (t80) cc_final: 0.7313 (t80)
REVERT: A  458 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8638 (mm)
REVERT: A  578 TYR cc_start: 0.6757 (t80) cc_final: 0.6224 (t80)
REVERT: A  653 ASP cc_start: 0.8372 (m-30) cc_final: 0.7980 (m-30)
REVERT: B  273 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8081 (mp)
REVERT: B  294 PHE cc_start: 0.8090 (t80) cc_final: 0.7556 (t80)
REVERT: B  458 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8572 (mm)
REVERT: B  578 TYR cc_start: 0.6625 (t80) cc_final: 0.6363 (t80)
REVERT: B  653 ASP cc_start: 0.8400 (m-30) cc_final: 0.7988 (m-30)
  outliers start: 34
  outliers final: 29
  residues processed: 167
  average time/residue: 0.0796
  time to fit residues: 20.3714
Evaluate side-chains
  167 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 135
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  357 MET
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  458 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 B residue   81 LEU
Chi-restraints excluded: chain B residue  273 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  448 LEU
Chi-restraints excluded: chain B residue  458 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 110 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.116480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.093314 restraints weight = 20443.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.095549 restraints weight = 11314.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.096934 restraints weight = 7951.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.097754 restraints weight = 6522.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.098112 restraints weight = 5842.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10686  Z= 0.140
  Angle     :  0.583   8.692  14516  Z= 0.286
  Chirality :  0.043   0.160   1728
  Planarity :  0.004   0.052   1804
  Dihedral  :  4.154  17.056   1442
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.17 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.24), residues: 1338
  helix:  1.57 (0.18), residues: 894
  sheet:  3.79 (0.84), residues: 36
  loop : -1.06 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 130 
 TYR   0.020   0.001   TYR A 114 
 PHE   0.008   0.001   PHE A 198 
 TRP   0.005   0.001   TRP B 462 
 HIS   0.004   0.001   HIS B 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10686)
  covalent geometry    : angle       0.58270 (14516)
  hydrogen bonds       : bond        0.03222 (  658)
  hydrogen bonds       : angle       4.04651 ( 1896)

*********************** 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
  174 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 135
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A  294 PHE cc_start: 0.7531 (t80) cc_final: 0.7316 (t80)
REVERT: A  458 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8603 (mm)
REVERT: A  578 TYR cc_start: 0.6757 (t80) cc_final: 0.6527 (t80)
REVERT: A  653 ASP cc_start: 0.8387 (m-30) cc_final: 0.8081 (m-30)
REVERT: B  294 PHE cc_start: 0.8084 (t80) cc_final: 0.7564 (t80)
REVERT: B  458 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8548 (mm)
REVERT: B  578 TYR cc_start: 0.6600 (t80) cc_final: 0.6346 (t80)
REVERT: B  653 ASP cc_start: 0.8408 (m-30) cc_final: 0.8104 (m-30)
  outliers start: 39
  outliers final: 30
  residues processed: 160
  average time/residue: 0.0738
  time to fit residues: 18.4620
Evaluate side-chains
  160 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  395 CYS
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  458 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 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  448 LEU
Chi-restraints excluded: chain B residue  458 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  518 ASP
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 26 optimal weight:    0.3980
   chunk 6 optimal weight:    9.9990
   chunk 90 optimal weight:    0.0030
   chunk 17 optimal weight:    8.9990
   chunk 18 optimal weight:    0.0870
   chunk 100 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 112 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.3568

-------------------------------------------------------------------------------
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 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 = 0.120509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.097464 restraints weight = 20215.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.099742 restraints weight = 11182.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.101185 restraints weight = 7870.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.101869 restraints weight = 6396.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.102454 restraints weight = 5775.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3294
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3294
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10686  Z= 0.102
  Angle     :  0.533   7.049  14516  Z= 0.265
  Chirality :  0.042   0.169   1728
  Planarity :  0.004   0.052   1804
  Dihedral  :  4.036  16.185   1442
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.78 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.24), residues: 1338
  helix:  1.75 (0.18), residues: 884
  sheet:  3.96 (0.84), residues: 36
  loop : -0.92 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 399 
 TYR   0.016   0.001   TYR A 114 
 PHE   0.009   0.001   PHE A 198 
 TRP   0.004   0.001   TRP B 472 
 HIS   0.002   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (10686)
  covalent geometry    : angle       0.53255 (14516)
  hydrogen bonds       : bond        0.02843 (  658)
  hydrogen bonds       : angle       3.92343 ( 1896)

*********************** 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
  184 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  578 TYR cc_start: 0.6816 (t80) cc_final: 0.6232 (t80)
REVERT: B  294 PHE cc_start: 0.8173 (t80) cc_final: 0.7636 (t80)
REVERT: B  578 TYR cc_start: 0.6631 (t80) cc_final: 0.6354 (t80)
  outliers start: 31
  outliers final: 20
  residues processed: 173
  average time/residue: 0.0708
  time to fit residues: 19.4106
Evaluate side-chains
  151 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  395 CYS
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  623 THR
Chi-restraints excluded: chain A residue  641 THR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 125 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0070
   chunk 48 optimal weight:    0.0010
   chunk 79 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.5206

-------------------------------------------------------------------------------
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 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 = 0.3588 r_free = 0.3588 target = 0.120526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.097618 restraints weight = 20019.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.099902 restraints weight = 11140.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.101299 restraints weight = 7843.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.102189 restraints weight = 6416.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.102558 restraints weight = 5696.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2517

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     :  0.589  11.024  14516  Z= 0.278
  Chirality :  0.043   0.210   1728
  Planarity :  0.004   0.052   1804
  Dihedral  :  4.039  17.904   1442
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.91 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.24), residues: 1338
  helix:  1.77 (0.18), residues: 886
  sheet:  4.07 (0.84), residues: 36
  loop : -0.90 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 281 
 TYR   0.011   0.001   TYR B 237 
 PHE   0.007   0.001   PHE B 391 
 TRP   0.004   0.001   TRP B  70 
 HIS   0.002   0.001   HIS A  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (10686)
  covalent geometry    : angle       0.58860 (14516)
  hydrogen bonds       : bond        0.02910 (  658)
  hydrogen bonds       : angle       3.92111 ( 1896)

********************** 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
  168 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A  578 TYR cc_start: 0.6819 (t80) cc_final: 0.6229 (t80)
REVERT: B  294 PHE cc_start: 0.8188 (t80) cc_final: 0.7633 (t80)
REVERT: B  578 TYR cc_start: 0.6631 (t80) cc_final: 0.6361 (t80)
  outliers start: 24
  outliers final: 21
  residues processed: 159
  average time/residue: 0.0733
  time to fit residues: 18.3279
Evaluate side-chains
  157 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
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  623 THR
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  259 VAL
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   chunk 91 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 130 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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  94 GLN
** 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 = 0.3541 r_free = 0.3541 target = 0.117304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.093982 restraints weight = 20377.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.096229 restraints weight = 11361.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.097594 restraints weight = 7996.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.098224 restraints weight = 6582.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.098844 restraints weight = 5964.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2640

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= 0.165
  Angle     :  0.620  11.108  14516  Z= 0.302
  Chirality :  0.045   0.234   1728
  Planarity :  0.004   0.052   1804
  Dihedral  :  4.106  17.982   1442
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.65 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.24), residues: 1338
  helix:  1.63 (0.18), residues: 896
  sheet:  4.06 (0.85), residues: 36
  loop : -0.98 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 502 
 TYR   0.013   0.001   TYR A 545 
 PHE   0.009   0.001   PHE B 198 
 TRP   0.007   0.001   TRP B  70 
 HIS   0.021   0.002   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (10686)
  covalent geometry    : angle       0.61960 (14516)
  hydrogen bonds       : bond        0.03271 (  658)
  hydrogen bonds       : angle       4.03569 ( 1896)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1712.62 seconds
wall clock time: 30 minutes 20.27 seconds (1820.27 seconds total)