Starting phenix.real_space_refine
on Fri Feb 14 17:01:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sun_25442/02_2025/7sun_25442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sun_25442/02_2025/7sun_25442.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sun_25442/02_2025/7sun_25442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sun_25442/02_2025/7sun_25442.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sun_25442/02_2025/7sun_25442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sun_25442/02_2025/7sun_25442.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    6852      2.51       5
     N    1692      2.21       5
     O    1858      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10454
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 675, 5227
          Classifications: {'peptide': 675}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 32, 'TRANS': 642}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.37, per 1000 atoms: 0.90
  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: 2.60
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 5 sheets defined
      70.7% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 30
    Processing helix  chain 'A' and resid 41 through 48
      removed outlier: 3.640A  pdb=" N   LYS A  45 " --> pdb=" O   SER A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 66 through 71
      removed outlier: 3.695A  pdb=" N   TRP A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 66 through 71'
    Processing helix  chain 'A' and resid 75 through 105
      removed outlier: 4.053A  pdb=" N   VAL A  80 " --> pdb=" O   PHE A  76 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   LEU A  81 " --> pdb=" O   LYS A  77 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   GLY A  82 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 108 through 115
      removed outlier: 3.840A  pdb=" N   GLY A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 127
    Processing helix  chain 'A' and resid 137 through 152
    Processing helix  chain 'A' and resid 168 through 196
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 206 through 230
      removed outlier: 4.479A  pdb=" N   LYS A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   TYR A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 258 through 282
      removed outlier: 3.962A  pdb=" N   LEU A 262 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 308
      removed outlier: 3.821A  pdb=" N   PHE A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.636A  pdb=" N   SER A 312 " --> pdb=" O   ASN A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 338
      removed outlier: 4.045A  pdb=" N   HIS A 337 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 366
    Processing helix  chain 'A' and resid 370 through 387
      removed outlier: 3.896A  pdb=" N   LEU A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 407
    Processing helix  chain 'A' and resid 411 through 427
    Processing helix  chain 'A' and resid 428 through 433
      removed outlier: 3.786A  pdb=" N   GLU A 433 " --> pdb=" O   PHE A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
      removed outlier: 3.672A  pdb=" N   LEU A 440 " --> pdb=" O   PRO A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 455
      removed outlier: 3.826A  pdb=" N   MET A 453 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 463
      removed outlier: 3.630A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG A 463 " --> pdb=" O   PRO A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 481
    Processing helix  chain 'A' and resid 483 through 505
      removed outlier: 4.205A  pdb=" N   ILE A 489 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 560
      removed outlier: 4.819A  pdb=" N   ASP A 550 " --> pdb=" O   TYR A 546 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   LEU A 551 " --> pdb=" O   ALA A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'A' and resid 626 through 631
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 680 through 690
      removed outlier: 3.568A  pdb=" N   ASN A 690 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 694
      removed outlier: 3.545A  pdb=" N   GLU A 694 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 691 through 694'
    Processing helix  chain 'A' and resid 695 through 700
      removed outlier: 3.644A  pdb=" N   LYS A 699 " --> pdb=" O   PRO A 696 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   GLU A 700 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 726
    Processing helix  chain 'B' and resid 24 through 30
    Processing helix  chain 'B' and resid 41 through 48
      removed outlier: 3.639A  pdb=" N   LYS B  45 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 65
    Processing helix  chain 'B' and resid 66 through 71
      removed outlier: 3.696A  pdb=" N   TRP B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 66 through 71'
    Processing helix  chain 'B' and resid 75 through 105
      removed outlier: 4.052A  pdb=" N   VAL B  80 " --> pdb=" O   PHE B  76 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   LEU B  81 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   GLY B  82 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 108 through 115
      removed outlier: 3.841A  pdb=" N   GLY B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 127
    Processing helix  chain 'B' and resid 137 through 152
    Processing helix  chain 'B' and resid 168 through 196
    Processing helix  chain 'B' and resid 199 through 204
    Processing helix  chain 'B' and resid 206 through 230
      removed outlier: 4.479A  pdb=" N   LYS B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   TYR B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 258 through 282
      removed outlier: 3.962A  pdb=" N   LEU B 262 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 308
      removed outlier: 3.821A  pdb=" N   PHE B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.636A  pdb=" N   SER B 312 " --> pdb=" O   ASN B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 338
      removed outlier: 4.045A  pdb=" N   HIS B 337 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 366
    Processing helix  chain 'B' and resid 370 through 387
      removed outlier: 3.897A  pdb=" N   LEU B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 407
    Processing helix  chain 'B' and resid 411 through 427
    Processing helix  chain 'B' and resid 428 through 433
      removed outlier: 3.786A  pdb=" N   GLU B 433 " --> pdb=" O   PHE B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 449
      removed outlier: 3.673A  pdb=" N   LEU B 440 " --> pdb=" O   PRO B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 455
      removed outlier: 3.825A  pdb=" N   MET B 453 " --> pdb=" O   GLY B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 463
      removed outlier: 3.631A  pdb=" N   PHE B 460 " --> pdb=" O   SER B 456 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG B 463 " --> pdb=" O   PRO B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 481
    Processing helix  chain 'B' and resid 483 through 505
      removed outlier: 4.204A  pdb=" N   ILE B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   VAL B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 560
      removed outlier: 4.819A  pdb=" N   ASP B 550 " --> pdb=" O   TYR B 546 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   LEU B 551 " --> pdb=" O   ALA B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 579
    Processing helix  chain 'B' and resid 626 through 631
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 680 through 690
      removed outlier: 3.569A  pdb=" N   ASN B 690 " --> pdb=" O   ASP B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 691 through 694
      removed outlier: 3.545A  pdb=" N   GLU B 694 " --> pdb=" O   ARG B 691 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 691 through 694'
    Processing helix  chain 'B' and resid 695 through 700
      removed outlier: 3.643A  pdb=" N   LYS B 699 " --> pdb=" O   PRO B 696 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   GLU B 700 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 726
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20
      removed outlier: 3.870A  pdb=" N   VAL A  18 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL B  18 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 135
      removed outlier: 4.684A  pdb=" N   SER A 133 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522
      removed outlier: 4.190A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   GLN A 513 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 11.379A  pdb=" N   ILE A 535 " --> pdb=" O   GLN A 513 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA A 677 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   PHE A 703 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU A 676 " --> pdb=" O   PHE A 703 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 135
      removed outlier: 4.684A  pdb=" N   SER B 133 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522
      removed outlier: 4.190A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   GLN B 513 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 11.379A  pdb=" N   ILE B 535 " --> pdb=" O   GLN B 513 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   ASP B 645 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 645 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA B 677 " --> pdb=" O   LEU B 644 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   PHE B 703 " --> pdb=" O   VAL B 674 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU B 676 " --> pdb=" O   PHE B 703 " (cutoff:3.500A)

    658 hydrogen bonds defined for protein.
    1896 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.37

  Time building geometry restraints manager: 2.99 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2731
        2.80 -     3.33: 10639
        3.33 -     3.85: 17632
        3.85 -     4.38: 19419
        4.38 -     4.90: 33508
  Nonbonded interactions: 83929
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 556 "
            pdb=" OG1 THR B 560 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   LEU A 556 "
            pdb=" OG1 THR A 560 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   SER B  86 "
            pdb=" OG1 THR B  90 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   SER A  86 "
            pdb=" OG1 THR A  90 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" NH2 ARG B 150 "
            pdb=" OD2 ASP B 342 "
     model   vdw
     2.323 3.120
  ... (remaining 83924 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.660
  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:             0.020
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.100
  Set scattering table:                    0.080
  Process input model:                     28.700
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.720
-------------------------------------------------------------------------------
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= 0.212
  Angle     :  0.693   9.212  14516  Z= 0.343
  Chirality :  0.046   0.227   1728
  Planarity :  0.005   0.046   1804
  Dihedral  : 13.913  87.324   3840
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.24), residues: 1338
  helix:  1.08 (0.18), residues: 884
  sheet:  3.81 (0.85), residues: 36
  loop : -1.19 (0.31), residues: 418

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

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

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.178 
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: 0.1837
  time to fit residues: 55.5315
Evaluate side-chains
  156 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    0.4980
   chunk 101 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 54 optimal weight:    0.6980
   chunk 105 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 121 optimal weight:    0.9980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.124307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101689 restraints weight = 19912.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.103982 restraints weight = 10867.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.105401 restraints weight = 7626.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10686  Z= 0.162
  Angle     :  0.566   6.054  14516  Z= 0.286
  Chirality :  0.043   0.223   1728
  Planarity :  0.004   0.046   1804
  Dihedral  :  4.217  20.596   1442
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  8.43 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.24), residues: 1338
  helix:  1.44 (0.18), residues: 880
  sheet:  4.12 (0.88), residues: 36
  loop : -1.03 (0.31), residues: 422

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

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

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 1.257 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8815 (mm) cc_final: 0.8594 (mm)
REVERT: A  488 LEU cc_start: 0.8812 (tp) cc_final: 0.8585 (tp)
REVERT: B  354 THR cc_start: 0.8857 (m) cc_final: 0.8641 (t)
REVERT: B  458 LEU cc_start: 0.8792 (mm) cc_final: 0.8574 (mm)
REVERT: B  488 LEU cc_start: 0.8788 (tp) cc_final: 0.8572 (tp)
  outliers start: 19
  outliers final: 10
  residues processed: 176
  average time/residue: 0.1876
  time to fit residues: 50.2467
Evaluate side-chains
  159 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 96 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 123 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 118 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.121312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.098314 restraints weight = 20523.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.100589 restraints weight = 11332.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.102017 restraints weight = 7984.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1395

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= 0.179
  Angle     :  0.546   6.305  14516  Z= 0.272
  Chirality :  0.043   0.182   1728
  Planarity :  0.004   0.046   1804
  Dihedral  :  4.066  19.470   1442
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.48 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.24), residues: 1338
  helix:  1.57 (0.18), residues: 880
  sheet:  4.04 (0.83), residues: 36
  loop : -0.89 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 472 
 HIS   0.005   0.001   HIS B 640 
 PHE   0.007   0.001   PHE B 391 
 TYR   0.014   0.001   TYR A 237 
 ARG   0.002   0.000   ARG B 716 

*********************** 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: 30
    poor density    : 159
  time to evaluate  : 1.269 
Fit side-chains
REVERT: A  380 ILE cc_start: 0.6595 (tp) cc_final: 0.6346 (tp)
REVERT: A  458 LEU cc_start: 0.8773 (mm) cc_final: 0.8570 (mm)
REVERT: A  578 TYR cc_start: 0.6708 (t80) cc_final: 0.6166 (t80)
REVERT: B  380 ILE cc_start: 0.6494 (tp) cc_final: 0.6197 (tp)
REVERT: B  458 LEU cc_start: 0.8731 (mm) cc_final: 0.8493 (mm)
  outliers start: 30
  outliers final: 17
  residues processed: 176
  average time/residue: 0.1878
  time to fit residues: 50.2083
Evaluate side-chains
  161 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain 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  642 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 126 optimal weight:    0.8980
   chunk 100 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 23 optimal weight:    0.2980
   chunk 26 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
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
A 650 ASN
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.094700 restraints weight = 20390.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.096923 restraints weight = 11380.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.098325 restraints weight = 8059.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3247
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1804

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= 0.244
  Angle     :  0.582   8.009  14516  Z= 0.291
  Chirality :  0.044   0.182   1728
  Planarity :  0.004   0.051   1804
  Dihedral  :  4.139  19.118   1442
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.35 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.24), residues: 1338
  helix:  1.39 (0.18), residues: 910
  sheet:  4.18 (0.84), residues: 36
  loop : -1.20 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  70 
 HIS   0.004   0.001   HIS A 640 
 PHE   0.009   0.001   PHE B 538 
 TYR   0.012   0.001   TYR B 578 
 ARG   0.002   0.000   ARG B 502 

*********************** 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
  186 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 1.278 
Fit side-chains
REVERT: A  458 LEU cc_start: 0.8790 (mm) cc_final: 0.8516 (mm)
REVERT: A  578 TYR cc_start: 0.6636 (t80) cc_final: 0.6114 (t80)
REVERT: B  458 LEU cc_start: 0.8781 (mm) cc_final: 0.8475 (mm)
REVERT: B  578 TYR cc_start: 0.6877 (t80) cc_final: 0.6523 (t80)
  outliers start: 28
  outliers final: 22
  residues processed: 174
  average time/residue: 0.1785
  time to fit residues: 47.9107
Evaluate side-chains
  162 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  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  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  642 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 124 optimal weight:    7.9990
   chunk 113 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 102 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 308 ASN
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 650 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.116885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.093507 restraints weight = 20386.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.095717 restraints weight = 11354.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.097082 restraints weight = 8031.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10686  Z= 0.232
  Angle     :  0.574   8.117  14516  Z= 0.286
  Chirality :  0.044   0.173   1728
  Planarity :  0.004   0.051   1804
  Dihedral  :  4.150  18.934   1442
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.52 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1338
  helix:  1.40 (0.18), residues: 908
  sheet:  4.07 (0.84), residues: 36
  loop : -1.18 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  70 
 HIS   0.003   0.001   HIS A 640 
 PHE   0.013   0.001   PHE A 198 
 TYR   0.016   0.001   TYR B 114 
 ARG   0.002   0.000   ARG A 502 

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

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 LEU cc_start: 0.8874 (mm) cc_final: 0.8587 (mm)
REVERT: A  578 TYR cc_start: 0.6668 (t80) cc_final: 0.6418 (t80)
REVERT: B  458 LEU cc_start: 0.8865 (mm) cc_final: 0.8584 (mm)
REVERT: B  578 TYR cc_start: 0.6815 (t80) cc_final: 0.6423 (t80)
  outliers start: 38
  outliers final: 26
  residues processed: 171
  average time/residue: 0.1810
  time to fit residues: 47.6884
Evaluate side-chains
  166 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 118 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 108 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   overall best weight:    1.7386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.116282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.093045 restraints weight = 20460.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.095273 restraints weight = 11283.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.096642 restraints weight = 7946.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2308

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= 0.229
  Angle     :  0.573   8.307  14516  Z= 0.284
  Chirality :  0.044   0.172   1728
  Planarity :  0.004   0.051   1804
  Dihedral  :  4.152  18.823   1442
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.96 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1338
  helix:  1.42 (0.18), residues: 910
  sheet:  4.00 (0.83), residues: 36
  loop : -1.21 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  70 
 HIS   0.003   0.001   HIS B 640 
 PHE   0.021   0.001   PHE A 294 
 TYR   0.010   0.001   TYR B 114 
 ARG   0.002   0.000   ARG B 502 

*********************** 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
  181 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 145
  time to evaluate  : 1.146 
Fit side-chains
REVERT: A  294 PHE cc_start: 0.8109 (t80) cc_final: 0.7470 (t80)
REVERT: A  458 LEU cc_start: 0.8873 (mm) cc_final: 0.8569 (mm)
REVERT: A  578 TYR cc_start: 0.6769 (t80) cc_final: 0.6445 (t80)
REVERT: A  653 ASP cc_start: 0.8453 (m-30) cc_final: 0.8086 (m-30)
REVERT: B  294 PHE cc_start: 0.8108 (t80) cc_final: 0.7459 (t80)
REVERT: B  458 LEU cc_start: 0.8859 (mm) cc_final: 0.8554 (mm)
REVERT: B  578 TYR cc_start: 0.6657 (t80) cc_final: 0.6357 (t80)
REVERT: B  653 ASP cc_start: 0.8454 (m-30) cc_final: 0.8117 (m-30)
  outliers start: 36
  outliers final: 28
  residues processed: 164
  average time/residue: 0.1837
  time to fit residues: 46.5653
Evaluate side-chains
  163 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
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  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 126 optimal weight:    0.1980
   chunk 85 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   chunk 102 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 220 HIS
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.118190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.095393 restraints weight = 20504.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.097655 restraints weight = 11178.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.099079 restraints weight = 7785.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3252
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3252
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2347

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= 0.170
  Angle     :  0.556   8.517  14516  Z= 0.274
  Chirality :  0.043   0.155   1728
  Planarity :  0.004   0.050   1804
  Dihedral  :  4.120  17.844   1442
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.91 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.24), residues: 1338
  helix:  1.47 (0.18), residues: 910
  sheet:  4.04 (0.83), residues: 36
  loop : -1.17 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A 640 
 PHE   0.016   0.001   PHE B 294 
 TYR   0.009   0.001   TYR B 237 
 ARG   0.002   0.000   ARG A 716 

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

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

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

  2676 Ramachandran restraints generated.
    1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 150
  time to evaluate  : 1.125 
Fit side-chains
REVERT: A  294 PHE cc_start: 0.8134 (t80) cc_final: 0.7503 (t80)
REVERT: A  458 LEU cc_start: 0.8874 (mm) cc_final: 0.8591 (mm)
REVERT: A  578 TYR cc_start: 0.6794 (t80) cc_final: 0.6454 (t80)
REVERT: A  653 ASP cc_start: 0.8358 (m-30) cc_final: 0.7970 (m-30)
REVERT: B  294 PHE cc_start: 0.8120 (t80) cc_final: 0.7488 (t80)
REVERT: B  458 LEU cc_start: 0.8846 (mm) cc_final: 0.8561 (mm)
REVERT: B  578 TYR cc_start: 0.6664 (t80) cc_final: 0.6379 (t80)
REVERT: B  653 ASP cc_start: 0.8414 (m-30) cc_final: 0.8075 (m-30)
  outliers start: 35
  outliers final: 24
  residues processed: 171
  average time/residue: 0.1799
  time to fit residues: 47.0297
Evaluate side-chains
  162 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 118 optimal weight:    0.0980
   chunk 9 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 253 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.118031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.095004 restraints weight = 20257.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.097258 restraints weight = 11224.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.098660 restraints weight = 7898.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10686  Z= 0.182
  Angle     :  0.556   7.781  14516  Z= 0.274
  Chirality :  0.043   0.202   1728
  Planarity :  0.004   0.051   1804
  Dihedral  :  4.082  17.576   1442
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.09 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.24), residues: 1338
  helix:  1.63 (0.18), residues: 894
  sheet:  4.14 (0.84), residues: 36
  loop : -0.90 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  70 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.014   0.001   PHE B 294 
 TYR   0.021   0.001   TYR A 114 
 ARG   0.001   0.000   ARG A 130 

*********************** 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
  173 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 1.116 
Fit side-chains
REVERT: A  222 PHE cc_start: 0.7147 (t80) cc_final: 0.6566 (m-80)
REVERT: A  294 PHE cc_start: 0.8141 (t80) cc_final: 0.7522 (t80)
REVERT: A  458 LEU cc_start: 0.8858 (mm) cc_final: 0.8591 (mm)
REVERT: A  578 TYR cc_start: 0.6807 (t80) cc_final: 0.6459 (t80)
REVERT: A  653 ASP cc_start: 0.8357 (m-30) cc_final: 0.7961 (m-30)
REVERT: B  294 PHE cc_start: 0.8142 (t80) cc_final: 0.7517 (t80)
REVERT: B  458 LEU cc_start: 0.8842 (mm) cc_final: 0.8560 (mm)
REVERT: B  578 TYR cc_start: 0.6665 (t80) cc_final: 0.6377 (t80)
REVERT: B  653 ASP cc_start: 0.8506 (m-30) cc_final: 0.8181 (m-30)
  outliers start: 31
  outliers final: 26
  residues processed: 161
  average time/residue: 0.1805
  time to fit residues: 44.7608
Evaluate side-chains
  161 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 TYR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain B residue   74 TYR
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Chi-restraints excluded: chain B residue  643 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 105 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   overall best weight:    1.3384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.117445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094077 restraints weight = 20640.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096345 restraints weight = 11448.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.097776 restraints weight = 8044.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2497

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= 0.198
  Angle     :  0.572   9.349  14516  Z= 0.281
  Chirality :  0.043   0.177   1728
  Planarity :  0.004   0.051   1804
  Dihedral  :  4.097  17.084   1442
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.17 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.24), residues: 1338
  helix:  1.63 (0.18), residues: 894
  sheet:  4.13 (0.83), residues: 36
  loop : -0.90 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A 640 
 PHE   0.014   0.001   PHE B 294 
 TYR   0.019   0.001   TYR A 114 
 ARG   0.002   0.000   ARG B 150 

*********************** 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
  169 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 137
  time to evaluate  : 1.133 
Fit side-chains
REVERT: A  222 PHE cc_start: 0.7118 (t80) cc_final: 0.6544 (m-80)
REVERT: A  294 PHE cc_start: 0.8188 (t80) cc_final: 0.7563 (t80)
REVERT: A  458 LEU cc_start: 0.8872 (mm) cc_final: 0.8583 (mm)
REVERT: A  578 TYR cc_start: 0.6809 (t80) cc_final: 0.6464 (t80)
REVERT: A  653 ASP cc_start: 0.8421 (m-30) cc_final: 0.8113 (m-30)
REVERT: B  294 PHE cc_start: 0.8191 (t80) cc_final: 0.7561 (t80)
REVERT: B  458 LEU cc_start: 0.8864 (mm) cc_final: 0.8570 (mm)
REVERT: B  578 TYR cc_start: 0.6647 (t80) cc_final: 0.6367 (t80)
REVERT: B  653 ASP cc_start: 0.8534 (m-30) cc_final: 0.8129 (m-30)
  outliers start: 32
  outliers final: 22
  residues processed: 157
  average time/residue: 0.1737
  time to fit residues: 42.0334
Evaluate side-chains
  158 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  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  376 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  428 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Chi-restraints excluded: chain B residue  643 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   chunk 50 optimal weight:    0.0570
   chunk 84 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.5700

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.119974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.096686 restraints weight = 20353.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.098968 restraints weight = 11382.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.100412 restraints weight = 8011.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10686  Z= 0.150
  Angle     :  0.543   7.337  14516  Z= 0.268
  Chirality :  0.042   0.189   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  4.023  16.082   1442
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.13 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.24), residues: 1338
  helix:  1.75 (0.18), residues: 884
  sheet:  4.18 (0.84), residues: 36
  loop : -0.80 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  70 
 HIS   0.002   0.001   HIS B  17 
 PHE   0.012   0.001   PHE B 294 
 TYR   0.024   0.001   TYR B 114 
 ARG   0.001   0.000   ARG A 281 

********************** 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
  179 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 1.170 
Fit side-chains
REVERT: A  222 PHE cc_start: 0.7081 (t80) cc_final: 0.6535 (m-80)
REVERT: A  294 PHE cc_start: 0.8173 (t80) cc_final: 0.7524 (t80)
REVERT: A  458 LEU cc_start: 0.8805 (mm) cc_final: 0.8542 (mm)
REVERT: A  518 ASP cc_start: 0.7514 (t0) cc_final: 0.7305 (t0)
REVERT: A  578 TYR cc_start: 0.6796 (t80) cc_final: 0.6441 (t80)
REVERT: A  653 ASP cc_start: 0.8408 (m-30) cc_final: 0.8042 (m-30)
REVERT: B  294 PHE cc_start: 0.8182 (t80) cc_final: 0.7539 (t80)
REVERT: B  458 LEU cc_start: 0.8774 (mm) cc_final: 0.8509 (mm)
REVERT: B  578 TYR cc_start: 0.6659 (t80) cc_final: 0.6371 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 171
  average time/residue: 0.1796
  time to fit residues: 47.4554
Evaluate side-chains
  158 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
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  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  510 VAL
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  623 THR
Chi-restraints excluded: chain B residue  641 THR
Chi-restraints excluded: chain B residue  642 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 18 optimal weight:    0.0370
   chunk 57 optimal weight:   20.0000
   chunk 101 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.9462

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.119277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096086 restraints weight = 20167.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098353 restraints weight = 11328.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.099761 restraints weight = 8006.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3258
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3258
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10686  Z= 0.170
  Angle     :  0.572  10.800  14516  Z= 0.276
  Chirality :  0.043   0.195   1728
  Planarity :  0.004   0.049   1804
  Dihedral  :  4.023  16.915   1442
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 19.30 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.24), residues: 1338
  helix:  1.74 (0.18), residues: 886
  sheet:  4.19 (0.83), residues: 36
  loop : -0.81 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  70 
 HIS   0.002   0.001   HIS A 640 
 PHE   0.012   0.001   PHE B 294 
 TYR   0.024   0.001   TYR B 114 
 ARG   0.001   0.000   ARG A 130 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3166.80 seconds
wall clock time: 57 minutes 51.71 seconds (3471.71 seconds total)