Starting phenix.real_space_refine
on Wed Mar  4 04:16:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pqe_13591/03_2026/7pqe_13591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pqe_13591/03_2026/7pqe_13591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pqe_13591/03_2026/7pqe_13591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pqe_13591/03_2026/7pqe_13591.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pqe_13591/03_2026/7pqe_13591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pqe_13591/03_2026/7pqe_13591.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     Mg      1      5.21       5
     S      35      5.16       5
     C    6833      2.51       5
     N    1828      2.21       5
     O    2048      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10746
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3870
          Classifications: {'peptide': 492}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 22, 'TRANS': 469}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 5995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 739, 5995
          Classifications: {'peptide': 739}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 31, 'TRANS': 707}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 879
          Classifications: {'peptide': 134}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 2, 'TRANS': 131}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 191
          Unresolved non-hydrogen angles: 239
          Unresolved non-hydrogen dihedrals: 154
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 4, 'ARG:plan': 5, 'PHE:plan': 2, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 144
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.50, per 1000 atoms: 0.23
  Number of scatterers: 10746
  At special positions: 0
  Unit cell: (140.209, 102.569, 94.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      35     16.00
     Mg      1     11.99
     O    2048      8.00
     N    1828      7.00
     C    6833      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 552.1 milliseconds
  

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2584

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 12 sheets defined
      55.5% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 239 through 251
    Processing helix  chain 'A' and resid 278 through 303
    Processing helix  chain 'A' and resid 314 through 318
    Processing helix  chain 'A' and resid 319 through 332
      removed outlier: 4.428A  pdb=" N   PHE A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 365
    Processing helix  chain 'A' and resid 366 through 369
    Processing helix  chain 'A' and resid 376 through 389
    Processing helix  chain 'A' and resid 397 through 410
      removed outlier: 4.066A  pdb=" N   ILE A 403 " --> pdb=" O   ALA A 399 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLY A 406 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP A 410 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 431
      removed outlier: 3.827A  pdb=" N   PHE A 421 " --> pdb=" O   PRO A 417 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 452
    Processing helix  chain 'A' and resid 515 through 521
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 554 through 561
      removed outlier: 4.006A  pdb=" N   ALA A 558 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 587
      Proline residue:  A 582  - end of helix
    Processing helix  chain 'A' and resid 771 through 787
      removed outlier: 3.663A  pdb=" N   GLN A 781 " --> pdb=" O   GLY A 777 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   MET A 785 " --> pdb=" O   GLN A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 808
      removed outlier: 3.660A  pdb=" N   ALA A 801 " --> pdb=" O   HIS A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 830
    Processing helix  chain 'C' and resid 135 through 158
      removed outlier: 3.747A  pdb=" N   ASN C 141 " --> pdb=" O   GLU C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 163
      removed outlier: 3.671A  pdb=" N   ILE C 163 " --> pdb=" O   LEU C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 182
    Processing helix  chain 'C' and resid 184 through 206
      Proline residue:  C 197  - end of helix
    Processing helix  chain 'C' and resid 206 through 218
    Processing helix  chain 'C' and resid 222 through 226
    Processing helix  chain 'C' and resid 236 through 245
    Processing helix  chain 'C' and resid 251 through 261
    Processing helix  chain 'C' and resid 270 through 281
    Processing helix  chain 'C' and resid 301 through 311
      removed outlier: 4.013A  pdb=" N   THR C 306 " --> pdb=" O   HIS C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 342 through 344
      No H-bonds generated for 'chain 'C' and resid 342 through 344'
    Processing helix  chain 'C' and resid 374 through 391
      removed outlier: 4.205A  pdb=" N   LEU C 378 " --> pdb=" O   PRO C 374 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 396
    Processing helix  chain 'C' and resid 412 through 419
    Processing helix  chain 'C' and resid 424 through 432
    Processing helix  chain 'C' and resid 446 through 450
    Processing helix  chain 'C' and resid 459 through 481
    Processing helix  chain 'C' and resid 525 through 530
      removed outlier: 3.679A  pdb=" N   VAL C 530 " --> pdb=" O   TRP C 526 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 542 through 546
      removed outlier: 4.155A  pdb=" N   ASP C 545 " --> pdb=" O   ASP C 542 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER C 546 " --> pdb=" O   LEU C 543 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 542 through 546'
    Processing helix  chain 'C' and resid 549 through 554
      removed outlier: 3.811A  pdb=" N   PHE C 553 " --> pdb=" O   ILE C 549 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 556 through 563
    Processing helix  chain 'C' and resid 563 through 568
    Processing helix  chain 'C' and resid 589 through 622
      removed outlier: 3.881A  pdb=" N   LEU C 593 " --> pdb=" O   GLY C 589 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   GLY C 595 " --> pdb=" O   ARG C 591 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASN C 596 " --> pdb=" O   ARG C 592 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TYR C 597 " --> pdb=" O   LEU C 593 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 623 through 625
      No H-bonds generated for 'chain 'C' and resid 623 through 625'
    Processing helix  chain 'C' and resid 627 through 655
    Processing helix  chain 'C' and resid 657 through 667
    Processing helix  chain 'C' and resid 670 through 682
    Processing helix  chain 'C' and resid 683 through 688
      removed outlier: 3.801A  pdb=" N   TYR C 686 " --> pdb=" O   THR C 683 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS C 688 " --> pdb=" O   ASP C 685 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 690 through 703
    Processing helix  chain 'C' and resid 738 through 774
      removed outlier: 3.741A  pdb=" N   GLU C 742 " --> pdb=" O   LEU C 738 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLN C 768 " --> pdb=" O   LYS C 764 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE C 772 " --> pdb=" O   GLN C 768 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 780 through 794
      removed outlier: 3.790A  pdb=" N   CYS C 784 " --> pdb=" O   ASP C 780 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 799 through 817
      removed outlier: 3.842A  pdb=" N   LYS C 803 " --> pdb=" O   CYS C 799 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 822 through 824
      No H-bonds generated for 'chain 'C' and resid 822 through 824'
    Processing helix  chain 'C' and resid 825 through 848
      removed outlier: 3.785A  pdb=" N   PHE C 829 " --> pdb=" O   TYR C 825 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   THR C 848 " --> pdb=" O   PHE C 844 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 20
    Processing helix  chain 'B' and resid 32 through 39
    Processing helix  chain 'B' and resid 45 through 55
      removed outlier: 4.141A  pdb=" N   MET B  52 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 77
    Processing helix  chain 'B' and resid 82 through 91
      removed outlier: 3.767A  pdb=" N   ILE B  86 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 110
    Processing helix  chain 'B' and resid 118 through 129
    Processing helix  chain 'B' and resid 139 through 144
    Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267
    Processing sheet with id=AA2, first strand: chain 'A' and resid 468 through 469
      removed outlier: 3.674A  pdb=" N   GLY A 474 " --> pdb=" O   VAL A 469 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 767 through 768
      removed outlier: 3.587A  pdb=" N   GLU A 839 " --> pdb=" O   PHE A 893 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 767 through 768
      removed outlier: 3.587A  pdb=" N   GLU A 839 " --> pdb=" O   PHE A 893 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ARG A 890 " --> pdb=" O   ASP A 881 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 850 through 852
      removed outlier: 4.534A  pdb=" N   GLU A 862 " --> pdb=" O   VAL A 852 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 105 through 109
    Processing sheet with id=AA7, first strand: chain 'C' and resid 121 through 124
      removed outlier: 8.366A  pdb=" N   ALA C 583 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   SER C 585 " --> pdb=" O   PRO C 130 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   LYS C 132 " --> pdb=" O   SER C 585 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR C 582 " --> pdb=" O   ASP C 577 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 291 through 292
      removed outlier: 3.516A  pdb=" N   ASN C 299 " --> pdb=" O   PHE C 292 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 346 through 350
      removed outlier: 4.654A  pdb=" N   ARG C 348 " --> pdb=" O   LEU C 355 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   LYS C 444 " --> pdb=" O   PRO C 404 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 482 through 483
    Processing sheet with id=AB2, first strand: chain 'C' and resid 535 through 536
    Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 29

    557 hydrogen bonds defined for protein.
    1608 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.83

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3528
        1.34 -     1.46: 2247
        1.46 -     1.58: 5128
        1.58 -     1.70: 0
        1.70 -     1.81: 65
  Bond restraints: 10968
  Sorted by residual:
  bond pdb=" CG1 ILE B  53 "
       pdb=" CD1 ILE B  53 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.76e+00
  bond pdb=" CG1 ILE C 610 "
       pdb=" CD1 ILE C 610 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 1.95e+00
  bond pdb=" CG  LEU C 535 "
       pdb=" CD2 LEU C 535 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.45e+00
  bond pdb=" C   THR C 313 "
       pdb=" N   GLU C 314 "
    ideal  model  delta    sigma   weight residual
    1.331  1.306  0.025 2.07e-02 2.33e+03 1.42e+00
  bond pdb=" CB  TRP C 681 "
       pdb=" CG  TRP C 681 "
    ideal  model  delta    sigma   weight residual
    1.498  1.461  0.037 3.10e-02 1.04e+03 1.42e+00
  ... (remaining 10963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 14374
        1.68 -     3.35: 404
        3.35 -     5.03: 47
        5.03 -     6.71: 8
        6.71 -     8.39: 3
  Bond angle restraints: 14836
  Sorted by residual:
  angle pdb=" N   ILE A 525 "
        pdb=" CA  ILE A 525 "
        pdb=" C   ILE A 525 "
      ideal   model   delta    sigma   weight residual
     113.53  110.53    3.00 9.80e-01 1.04e+00 9.40e+00
  angle pdb=" CB  MET B  73 "
        pdb=" CG  MET B  73 "
        pdb=" SD  MET B  73 "
      ideal   model   delta    sigma   weight residual
     112.70  121.09   -8.39 3.00e+00 1.11e-01 7.81e+00
  angle pdb=" C   GLY A 542 "
        pdb=" N   MET A 543 "
        pdb=" CA  MET A 543 "
      ideal   model   delta    sigma   weight residual
     121.31  125.34   -4.03 1.49e+00 4.50e-01 7.30e+00
  angle pdb=" C   ASP C 627 "
        pdb=" N   LYS C 628 "
        pdb=" CA  LYS C 628 "
      ideal   model   delta    sigma   weight residual
     120.58  124.01   -3.43 1.32e+00 5.74e-01 6.73e+00
  angle pdb=" CA  GLY C 569 "
        pdb=" C   GLY C 569 "
        pdb=" O   GLY C 569 "
      ideal   model   delta    sigma   weight residual
     122.59  120.04    2.55 1.04e+00 9.25e-01 6.00e+00
  ... (remaining 14831 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 6043
       17.38 -    34.77: 482
       34.77 -    52.15: 66
       52.15 -    69.53: 17
       69.53 -    86.91: 11
  Dihedral angle restraints: 6619
    sinusoidal: 2624
      harmonic: 3995
  Sorted by residual:
  dihedral pdb=" CA  TYR C 702 "
           pdb=" C   TYR C 702 "
           pdb=" N   SER C 703 "
           pdb=" CA  SER C 703 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.96   20.04     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  ALA A 787 "
           pdb=" C   ALA A 787 "
           pdb=" N   ASN A 788 "
           pdb=" CA  ASN A 788 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.32   19.68     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  LYS C 316 "
           pdb=" C   LYS C 316 "
           pdb=" N   GLU C 317 "
           pdb=" CA  GLU C 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.68   19.32     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 6616 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1308
       0.053 -    0.105: 309
       0.105 -    0.158: 30
       0.158 -    0.211: 2
       0.211 -    0.263: 1
  Chirality restraints: 1650
  Sorted by residual:
  chirality pdb=" CA  GLU A 295 "
            pdb=" N   GLU A 295 "
            pdb=" C   GLU A 295 "
            pdb=" CB  GLU A 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  VAL A 334 "
            pdb=" CA  VAL A 334 "
            pdb=" CG1 VAL A 334 "
            pdb=" CG2 VAL A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  PHE C 475 "
            pdb=" N   PHE C 475 "
            pdb=" C   PHE C 475 "
            pdb=" CB  PHE C 475 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.29e-01
  ... (remaining 1647 not shown)

  Planarity restraints: 1919
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 432 "    0.020 2.00e-02 2.50e+03   1.89e-02 8.97e+00
        pdb=" CG  TRP A 432 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 432 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 432 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 432 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 432 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 432 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 432 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 432 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 432 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 628 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO C 629 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO C 629 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 629 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 581 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.12e+00
        pdb=" N   PRO A 582 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 582 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 582 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1916 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 217
        2.67 -     3.22: 10874
        3.22 -     3.78: 16950
        3.78 -     4.34: 23028
        4.34 -     4.90: 37389
  Nonbonded interactions: 88458
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 306 "
            pdb=" OG1 THR C 750 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" OH  TYR C 326 "
            pdb=" OG  SER C 546 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OD1 ASP A 237 "
            pdb=" OG1 THR A 239 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OG  SER C 399 "
            pdb=" OD2 ASP C 473 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OG  SER C 220 "
            pdb=" OD1 ASP C 793 "
     model   vdw
     2.153 3.040
  ... (remaining 88453 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.180
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
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      :  0.006   0.065  10968  Z= 0.246
  Angle     :  0.676   8.386  14836  Z= 0.384
  Chirality :  0.043   0.263   1650
  Planarity :  0.004   0.045   1919
  Dihedral  : 13.131  86.914   4035
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.35 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.23), residues: 1347
  helix:  0.37 (0.19), residues: 720
  sheet: -2.40 (0.51), residues: 95
  loop : -1.89 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 293 
 TYR   0.018   0.002   TYR C 599 
 PHE   0.018   0.002   PHE C 475 
 TRP   0.050   0.003   TRP A 432 
 HIS   0.007   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 (10968)
  covalent geometry    : angle       0.67575 (14836)
  hydrogen bonds       : bond        0.13371 (  550)
  hydrogen bonds       : angle       5.96569 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  241 LEU cc_start: 0.9008 (tp) cc_final: 0.8780 (tp)
REVERT: C  295 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6463 (tpt-90)
REVERT: C  353 THR cc_start: 0.8870 (m) cc_final: 0.8609 (p)
REVERT: C  783 SER cc_start: 0.8881 (m) cc_final: 0.8629 (m)
REVERT: B   73 MET cc_start: 0.8341 (mmm) cc_final: 0.7483 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1072
  time to fit residues: 24.3096
Evaluate side-chains
  119 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
A 550 ASN
C 158 ASN
C 180 ASN
C 361 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.128185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.097950 restraints weight = 19051.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.098886 restraints weight = 13985.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.100040 restraints weight = 10915.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.100226 restraints weight = 8649.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.100358 restraints weight = 8185.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10968  Z= 0.149
  Angle     :  0.563   8.739  14836  Z= 0.298
  Chirality :  0.040   0.151   1650
  Planarity :  0.004   0.045   1919
  Dihedral  :  4.474  21.373   1470
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  6.22 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.23), residues: 1347
  helix:  0.90 (0.20), residues: 723
  sheet: -2.16 (0.51), residues: 97
  loop : -1.66 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 676 
 TYR   0.015   0.001   TYR C 599 
 PHE   0.018   0.001   PHE C 475 
 TRP   0.022   0.002   TRP A 432 
 HIS   0.005   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10968)
  covalent geometry    : angle       0.56313 (14836)
  hydrogen bonds       : bond        0.04007 (  550)
  hydrogen bonds       : angle       4.33693 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8447 (tp30) cc_final: 0.7989 (tp30)
REVERT: A  548 TYR cc_start: 0.8792 (t80) cc_final: 0.8585 (t80)
REVERT: A  785 MET cc_start: 0.8054 (tpp) cc_final: 0.7581 (tpt)
REVERT: C  295 ARG cc_start: 0.6832 (ttm110) cc_final: 0.6485 (tpt-90)
REVERT: C  353 THR cc_start: 0.8852 (m) cc_final: 0.8531 (p)
REVERT: C  425 PHE cc_start: 0.7055 (t80) cc_final: 0.6848 (t80)
REVERT: C  480 GLU cc_start: 0.8233 (tp30) cc_final: 0.7678 (tp30)
REVERT: B    7 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7891 (tm-30)
REVERT: B   17 PHE cc_start: 0.8930 (t80) cc_final: 0.8335 (t80)
REVERT: B  105 GLU cc_start: 0.7236 (mp0) cc_final: 0.6710 (pm20)
  outliers start: 17
  outliers final: 10
  residues processed: 159
  average time/residue: 0.0908
  time to fit residues: 21.3900
Evaluate side-chains
  134 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue  108 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 132 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0170
   chunk 124 optimal weight:    4.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 885 GLN
C 158 ASN
C 180 ASN
C 259 GLN
C 361 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.128546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.099386 restraints weight = 19134.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.099260 restraints weight = 15437.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.100395 restraints weight = 13166.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.100719 restraints weight = 10245.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.101075 restraints weight = 9211.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10968  Z= 0.134
  Angle     :  0.519   7.101  14836  Z= 0.272
  Chirality :  0.039   0.153   1650
  Planarity :  0.004   0.044   1919
  Dihedral  :  4.209  19.527   1470
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.59 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.24), residues: 1347
  helix:  1.22 (0.20), residues: 723
  sheet: -1.98 (0.50), residues: 97
  loop : -1.47 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 352 
 TYR   0.012   0.001   TYR A 347 
 PHE   0.017   0.001   PHE C 475 
 TRP   0.021   0.002   TRP A 549 
 HIS   0.007   0.001   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10968)
  covalent geometry    : angle       0.51873 (14836)
  hydrogen bonds       : bond        0.03663 (  550)
  hydrogen bonds       : angle       4.03726 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.6726 (m90)
REVERT: A  294 GLU cc_start: 0.8467 (tp30) cc_final: 0.8042 (tp30)
REVERT: A  295 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7342 (mp0)
REVERT: A  543 MET cc_start: 0.7716 (ppp) cc_final: 0.7399 (ppp)
REVERT: A  548 TYR cc_start: 0.8779 (t80) cc_final: 0.8403 (t80)
REVERT: A  791 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: C  295 ARG cc_start: 0.6779 (ttm110) cc_final: 0.6385 (tpt-90)
REVERT: C  353 THR cc_start: 0.8825 (m) cc_final: 0.8456 (p)
REVERT: B   17 PHE cc_start: 0.8885 (t80) cc_final: 0.8417 (t80)
REVERT: B  105 GLU cc_start: 0.7252 (mp0) cc_final: 0.6973 (pm20)
  outliers start: 15
  outliers final: 9
  residues processed: 156
  average time/residue: 0.0877
  time to fit residues: 20.5972
Evaluate side-chains
  144 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  707 GLU
Chi-restraints excluded: chain B residue    6 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 130 optimal weight:   20.0000
   chunk 119 optimal weight:    2.9990
   chunk 59 optimal weight:    0.3980
   chunk 134 optimal weight:   30.0000
   chunk 113 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 2 optimal weight:   10.0000
   chunk 105 optimal weight:    0.6980
   chunk 127 optimal weight:    9.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 158 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.127025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.097418 restraints weight = 19311.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.096586 restraints weight = 16736.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.097976 restraints weight = 14927.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.098502 restraints weight = 10989.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.098527 restraints weight = 10798.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10968  Z= 0.153
  Angle     :  0.524   7.133  14836  Z= 0.273
  Chirality :  0.040   0.154   1650
  Planarity :  0.004   0.043   1919
  Dihedral  :  4.141  17.997   1470
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 10.17 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.24), residues: 1347
  helix:  1.29 (0.20), residues: 724
  sheet: -1.90 (0.50), residues: 97
  loop : -1.40 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 676 
 TYR   0.029   0.002   TYR A 256 
 PHE   0.020   0.001   PHE C 425 
 TRP   0.020   0.001   TRP A 549 
 HIS   0.004   0.001   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10968)
  covalent geometry    : angle       0.52380 (14836)
  hydrogen bonds       : bond        0.03660 (  550)
  hydrogen bonds       : angle       3.94429 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.6762 (m90)
REVERT: A  294 GLU cc_start: 0.8477 (tp30) cc_final: 0.8053 (tp30)
REVERT: A  295 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7457 (mp0)
REVERT: A  543 MET cc_start: 0.7776 (ppp) cc_final: 0.7395 (ppp)
REVERT: A  548 TYR cc_start: 0.8812 (t80) cc_final: 0.8359 (t80)
REVERT: A  785 MET cc_start: 0.8068 (tpp) cc_final: 0.7544 (tpt)
REVERT: A  791 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: C  222 TYR cc_start: 0.9061 (m-10) cc_final: 0.8631 (m-80)
REVERT: C  295 ARG cc_start: 0.6804 (ttm110) cc_final: 0.6369 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8298 (tp30) cc_final: 0.7563 (tp30)
REVERT: B    7 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7778 (tm-30)
REVERT: B   17 PHE cc_start: 0.8866 (t80) cc_final: 0.8400 (t80)
REVERT: B  105 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6701 (pm20)
  outliers start: 22
  outliers final: 14
  residues processed: 157
  average time/residue: 0.0882
  time to fit residues: 20.6218
Evaluate side-chains
  146 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  538 SER
Chi-restraints excluded: chain C residue  696 MET
Chi-restraints excluded: chain C residue  707 GLU
Chi-restraints excluded: chain C residue  773 LEU
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue  105 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 130 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0770
   chunk 133 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0370
   chunk 104 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0870
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.3594

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 ASN
C 158 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.129026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.098652 restraints weight = 19045.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.099327 restraints weight = 15577.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.100159 restraints weight = 11629.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.100492 restraints weight = 9501.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.100674 restraints weight = 8962.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10968  Z= 0.105
  Angle     :  0.499   7.163  14836  Z= 0.259
  Chirality :  0.038   0.152   1650
  Planarity :  0.004   0.042   1919
  Dihedral  :  3.928  18.110   1470
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.57 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.24), residues: 1347
  helix:  1.48 (0.20), residues: 724
  sheet: -1.53 (0.52), residues: 97
  loop : -1.29 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 676 
 TYR   0.029   0.001   TYR A 256 
 PHE   0.027   0.001   PHE C 356 
 TRP   0.023   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (10968)
  covalent geometry    : angle       0.49930 (14836)
  hydrogen bonds       : bond        0.03348 (  550)
  hydrogen bonds       : angle       3.76482 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.6703 (m90)
REVERT: A  294 GLU cc_start: 0.8472 (tp30) cc_final: 0.7966 (tp30)
REVERT: A  295 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7570 (mp0)
REVERT: A  791 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7764 (tm-30)
REVERT: C  210 TRP cc_start: 0.8740 (t-100) cc_final: 0.8460 (t-100)
REVERT: C  295 ARG cc_start: 0.6729 (ttm110) cc_final: 0.6318 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8236 (tp30) cc_final: 0.7511 (tp30)
REVERT: C  756 MET cc_start: 0.7912 (mmt) cc_final: 0.7667 (mmm)
REVERT: B    7 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7682 (tm-30)
REVERT: B   17 PHE cc_start: 0.8800 (t80) cc_final: 0.8470 (t80)
REVERT: B  105 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6685 (pm20)
  outliers start: 22
  outliers final: 13
  residues processed: 167
  average time/residue: 0.0912
  time to fit residues: 22.8701
Evaluate side-chains
  149 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  451 THR
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  538 SER
Chi-restraints excluded: chain C residue  696 MET
Chi-restraints excluded: chain C residue  707 GLU
Chi-restraints excluded: chain C residue  773 LEU
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue  105 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 128 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0060
   chunk 31 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 126 optimal weight:    9.9990
   chunk 89 optimal weight:    0.0980
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 ASN
C 158 ASN
C 180 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.129460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098510 restraints weight = 19001.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.099780 restraints weight = 14673.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.100830 restraints weight = 11228.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.100816 restraints weight = 10283.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.101210 restraints weight = 8676.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10968  Z= 0.108
  Angle     :  0.497   7.315  14836  Z= 0.258
  Chirality :  0.038   0.159   1650
  Planarity :  0.004   0.040   1919
  Dihedral  :  3.814  16.713   1470
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.09 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.24), residues: 1347
  helix:  1.59 (0.20), residues: 726
  sheet: -1.36 (0.53), residues: 97
  loop : -1.21 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 676 
 TYR   0.014   0.001   TYR A 347 
 PHE   0.016   0.001   PHE C 475 
 TRP   0.016   0.001   TRP A 549 
 HIS   0.005   0.001   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (10968)
  covalent geometry    : angle       0.49685 (14836)
  hydrogen bonds       : bond        0.03291 (  550)
  hydrogen bonds       : angle       3.69839 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8478 (tp30) cc_final: 0.7866 (tp30)
REVERT: A  295 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7570 (mp0)
REVERT: C  210 TRP cc_start: 0.8730 (t-100) cc_final: 0.8449 (t-100)
REVERT: C  295 ARG cc_start: 0.6666 (ttm110) cc_final: 0.6332 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8249 (tp30) cc_final: 0.7478 (tp30)
REVERT: B    7 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: B   17 PHE cc_start: 0.8797 (t80) cc_final: 0.8427 (t80)
REVERT: B   33 LEU cc_start: 0.8315 (tp) cc_final: 0.8025 (tp)
REVERT: B   52 MET cc_start: 0.7736 (tpp) cc_final: 0.7525 (tpp)
REVERT: B   53 ILE cc_start: 0.8545 (pt) cc_final: 0.8321 (pt)
REVERT: B  105 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6687 (pm20)
  outliers start: 21
  outliers final: 15
  residues processed: 155
  average time/residue: 0.0926
  time to fit residues: 21.4188
Evaluate side-chains
  152 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  451 THR
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  696 MET
Chi-restraints excluded: chain C residue  707 GLU
Chi-restraints excluded: chain C residue  773 LEU
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue  105 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 108 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 122 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 98 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.128410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098416 restraints weight = 19071.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.099383 restraints weight = 15335.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.100572 restraints weight = 12743.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.100508 restraints weight = 10004.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.100845 restraints weight = 9147.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10968  Z= 0.123
  Angle     :  0.512   7.784  14836  Z= 0.264
  Chirality :  0.039   0.153   1650
  Planarity :  0.004   0.040   1919
  Dihedral  :  3.821  17.943   1470
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.71 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.24), residues: 1347
  helix:  1.59 (0.20), residues: 728
  sheet: -1.30 (0.53), residues: 97
  loop : -1.17 (0.28), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 676 
 TYR   0.021   0.001   TYR A 246 
 PHE   0.015   0.001   PHE C 475 
 TRP   0.018   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10968)
  covalent geometry    : angle       0.51213 (14836)
  hydrogen bonds       : bond        0.03332 (  550)
  hydrogen bonds       : angle       3.70405 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8474 (tp30) cc_final: 0.8086 (tp30)
REVERT: A  295 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7578 (mp0)
REVERT: C  210 TRP cc_start: 0.8749 (t-100) cc_final: 0.8464 (t-100)
REVERT: C  295 ARG cc_start: 0.6706 (ttm110) cc_final: 0.6379 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8258 (tp30) cc_final: 0.7470 (tp30)
REVERT: C  756 MET cc_start: 0.7852 (mmt) cc_final: 0.7623 (mmm)
REVERT: C  768 GLN cc_start: 0.7834 (tp40) cc_final: 0.7624 (tp40)
REVERT: B    7 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7734 (tm-30)
REVERT: B   17 PHE cc_start: 0.8827 (t80) cc_final: 0.8489 (t80)
REVERT: B   33 LEU cc_start: 0.8318 (tp) cc_final: 0.8009 (tp)
REVERT: B  105 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6670 (pm20)
  outliers start: 25
  outliers final: 20
  residues processed: 154
  average time/residue: 0.0925
  time to fit residues: 21.1634
Evaluate side-chains
  154 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  202 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  451 THR
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  696 MET
Chi-restraints excluded: chain C residue  707 GLU
Chi-restraints excluded: chain C residue  773 LEU
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  105 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 109 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 110 optimal weight:    0.2980
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.128940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.097842 restraints weight = 19073.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.099572 restraints weight = 14788.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.100208 restraints weight = 11130.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.100640 restraints weight = 9531.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.100751 restraints weight = 8459.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10968  Z= 0.126
  Angle     :  0.521   8.552  14836  Z= 0.267
  Chirality :  0.039   0.153   1650
  Planarity :  0.004   0.039   1919
  Dihedral  :  3.828  18.723   1470
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.71 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.24), residues: 1347
  helix:  1.70 (0.20), residues: 721
  sheet: -1.25 (0.52), residues: 97
  loop : -1.24 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 676 
 TYR   0.016   0.001   TYR A 246 
 PHE   0.017   0.001   PHE C 174 
 TRP   0.018   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10968)
  covalent geometry    : angle       0.52098 (14836)
  hydrogen bonds       : bond        0.03347 (  550)
  hydrogen bonds       : angle       3.70549 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.7972 (m) cc_final: 0.7671 (t)
REVERT: A  294 GLU cc_start: 0.8520 (tp30) cc_final: 0.8155 (tp30)
REVERT: A  295 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7646 (mp0)
REVERT: C  295 ARG cc_start: 0.6737 (ttm110) cc_final: 0.6432 (tpt-90)
REVERT: C  299 ASN cc_start: 0.7953 (t0) cc_final: 0.7653 (t0)
REVERT: C  480 GLU cc_start: 0.8265 (tp30) cc_final: 0.7509 (tp30)
REVERT: C  768 GLN cc_start: 0.7866 (tp40) cc_final: 0.7655 (tp40)
REVERT: B    7 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7775 (tm-30)
REVERT: B   17 PHE cc_start: 0.8860 (t80) cc_final: 0.8458 (t80)
REVERT: B   33 LEU cc_start: 0.8318 (tp) cc_final: 0.8043 (tp)
REVERT: B   57 ASP cc_start: 0.4663 (t0) cc_final: 0.4147 (p0)
REVERT: B  105 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6713 (pm20)
  outliers start: 24
  outliers final: 19
  residues processed: 145
  average time/residue: 0.0879
  time to fit residues: 19.2511
Evaluate side-chains
  148 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  425 PHE
Chi-restraints excluded: chain C residue  451 THR
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  696 MET
Chi-restraints excluded: chain C residue  707 GLU
Chi-restraints excluded: chain C residue  773 LEU
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  105 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 126 optimal weight:    0.3980
   chunk 113 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 60 optimal weight:    0.1980
   chunk 63 optimal weight:    0.7980
   chunk 34 optimal weight:    0.4980
   chunk 72 optimal weight:    7.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.129759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.098935 restraints weight = 19022.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.099946 restraints weight = 14626.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.100823 restraints weight = 11416.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.101097 restraints weight = 10840.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.101221 restraints weight = 9474.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10968  Z= 0.113
  Angle     :  0.522   8.759  14836  Z= 0.266
  Chirality :  0.039   0.152   1650
  Planarity :  0.004   0.039   1919
  Dihedral  :  3.801  17.749   1470
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.71 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.24), residues: 1347
  helix:  1.76 (0.20), residues: 720
  sheet: -1.20 (0.52), residues: 97
  loop : -1.25 (0.28), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 676 
 TYR   0.024   0.001   TYR A 246 
 PHE   0.019   0.001   PHE C 174 
 TRP   0.021   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10968)
  covalent geometry    : angle       0.52165 (14836)
  hydrogen bonds       : bond        0.03237 (  550)
  hydrogen bonds       : angle       3.65351 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.8054 (m) cc_final: 0.7751 (t)
REVERT: A  294 GLU cc_start: 0.8500 (tp30) cc_final: 0.8091 (tp30)
REVERT: A  785 MET cc_start: 0.7923 (tpp) cc_final: 0.7231 (mtt)
REVERT: C  210 TRP cc_start: 0.8767 (t-100) cc_final: 0.8496 (t-100)
REVERT: C  222 TYR cc_start: 0.9153 (m-10) cc_final: 0.8788 (m-80)
REVERT: C  295 ARG cc_start: 0.6723 (ttm110) cc_final: 0.6406 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8209 (tp30) cc_final: 0.7454 (tp30)
REVERT: C  768 GLN cc_start: 0.7807 (tp40) cc_final: 0.7596 (tp40)
REVERT: B    7 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: B   17 PHE cc_start: 0.8832 (t80) cc_final: 0.8438 (t80)
REVERT: B   33 LEU cc_start: 0.8283 (tp) cc_final: 0.7952 (tp)
REVERT: B   57 ASP cc_start: 0.4539 (t0) cc_final: 0.4140 (p0)
REVERT: B  105 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6701 (pm20)
  outliers start: 24
  outliers final: 18
  residues processed: 146
  average time/residue: 0.0910
  time to fit residues: 19.7545
Evaluate side-chains
  143 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  425 PHE
Chi-restraints excluded: chain C residue  451 THR
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  696 MET
Chi-restraints excluded: chain C residue  707 GLU
Chi-restraints excluded: chain C residue  773 LEU
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  105 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0270
   chunk 7 optimal weight:    0.0000
   chunk 31 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 121 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0770
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.3200

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 430 GLN
A 550 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.132436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.102873 restraints weight = 18907.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.102821 restraints weight = 11688.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.103324 restraints weight = 9713.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.103607 restraints weight = 8543.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.103849 restraints weight = 8063.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10968  Z= 0.101
  Angle     :  0.516   8.865  14836  Z= 0.263
  Chirality :  0.038   0.151   1650
  Planarity :  0.004   0.039   1919
  Dihedral  :  3.730  17.966   1470
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.06 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.24), residues: 1347
  helix:  1.79 (0.20), residues: 726
  sheet: -1.06 (0.53), residues: 97
  loop : -1.22 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 515 
 TYR   0.025   0.001   TYR A 246 
 PHE   0.019   0.001   PHE C 174 
 TRP   0.021   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10968)
  covalent geometry    : angle       0.51641 (14836)
  hydrogen bonds       : bond        0.03108 (  550)
  hydrogen bonds       : angle       3.60097 ( 1608)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.8148 (m) cc_final: 0.7825 (t)
REVERT: A  294 GLU cc_start: 0.8552 (tp30) cc_final: 0.7873 (tp30)
REVERT: A  432 TRP cc_start: 0.8312 (m100) cc_final: 0.8086 (m100)
REVERT: A  785 MET cc_start: 0.7934 (tpp) cc_final: 0.7212 (mtm)
REVERT: C  210 TRP cc_start: 0.8707 (t-100) cc_final: 0.8422 (t-100)
REVERT: C  295 ARG cc_start: 0.6702 (ttm110) cc_final: 0.6448 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8178 (tp30) cc_final: 0.7441 (tp30)
REVERT: C  768 GLN cc_start: 0.7752 (tp40) cc_final: 0.7520 (tp40)
REVERT: C  773 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7568 (tp)
REVERT: B    7 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7732 (tm-30)
REVERT: B   17 PHE cc_start: 0.8825 (t80) cc_final: 0.8440 (t80)
REVERT: B   33 LEU cc_start: 0.8150 (tp) cc_final: 0.7710 (tp)
REVERT: B  105 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6746 (pm20)
  outliers start: 21
  outliers final: 17
  residues processed: 154
  average time/residue: 0.0863
  time to fit residues: 20.1447
Evaluate side-chains
  143 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  296 LEU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  451 THR
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  696 MET
Chi-restraints excluded: chain C residue  707 GLU
Chi-restraints excluded: chain C residue  773 LEU
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  105 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 98 optimal weight:    0.6980
   chunk 123 optimal weight:    0.6980
   chunk 125 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 132 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.130331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.100212 restraints weight = 19081.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.100529 restraints weight = 14439.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.101875 restraints weight = 11273.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.102171 restraints weight = 9143.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.102331 restraints weight = 8147.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10968  Z= 0.135
  Angle     :  0.549   8.111  14836  Z= 0.279
  Chirality :  0.039   0.155   1650
  Planarity :  0.004   0.038   1919
  Dihedral  :  3.792  16.860   1470
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.32 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.24), residues: 1347
  helix:  1.82 (0.20), residues: 719
  sheet: -0.98 (0.53), residues: 97
  loop : -1.26 (0.28), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C 127 
 TYR   0.016   0.001   TYR A 246 
 PHE   0.016   0.001   PHE C 174 
 TRP   0.022   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (10968)
  covalent geometry    : angle       0.54893 (14836)
  hydrogen bonds       : bond        0.03276 (  550)
  hydrogen bonds       : angle       3.67591 ( 1608)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1655.14 seconds
wall clock time: 29 minutes 26.92 seconds (1766.92 seconds total)