Starting phenix.real_space_refine
on Mon Jul 28 22:53:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pqe_13591/07_2025/7pqe_13591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pqe_13591/07_2025/7pqe_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pqe_13591/07_2025/7pqe_13591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pqe_13591/07_2025/7pqe_13591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pqe_13591/07_2025/7pqe_13591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pqe_13591/07_2025/7pqe_13591.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 5}
          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: 6.62, per 1000 atoms: 0.62
  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.56
  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: 5.46

  Time building geometry restraints manager: 3.03 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:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     28.090
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.070
  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:3.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.590
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.23), 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
 TRP   0.050   0.003   TRP A 432 
 HIS   0.007   0.001   HIS C 246 
 PHE   0.018   0.002   PHE C 475 
 TYR   0.018   0.002   TYR C 599 
 ARG   0.009   0.001   ARG C 293 

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

*********************** 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  : 1.383 
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: 0.3206
  time to fit residues: 70.0501
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  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    0.7980
   chunk 102 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0870
   chunk 69 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0980
   chunk 64 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0570
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.2876

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.129955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.101020 restraints weight = 18912.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.100893 restraints weight = 14134.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.101360 restraints weight = 11511.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10968  Z= 0.120
  Angle     :  0.543   8.458  14836  Z= 0.289
  Chirality :  0.039   0.152   1650
  Planarity :  0.004   0.044   1919
  Dihedral  :  4.358  21.520   1470
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  5.96 %
    Favored  : 92.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.24), residues: 1347
  helix:  1.01 (0.20), residues: 723
  sheet: -2.11 (0.50), residues: 98
  loop : -1.56 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 432 
 HIS   0.005   0.001   HIS C 572 
 PHE   0.019   0.001   PHE C 475 
 TYR   0.014   0.001   TYR C 702 
 ARG   0.007   0.000   ARG C 676 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  550)
  hydrogen bonds       : angle       4.26144 ( 1608)
  covalent geometry    : bond        0.00266 (10968)
  covalent geometry    : angle       0.54287 (14836)

*********************** 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
  175 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 1.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8417 (tp30) cc_final: 0.7975 (tp30)
REVERT: A  785 MET cc_start: 0.8055 (tpp) cc_final: 0.7580 (tpt)
REVERT: C  295 ARG cc_start: 0.6723 (ttm110) cc_final: 0.6335 (tpt-90)
REVERT: C  353 THR cc_start: 0.8820 (m) cc_final: 0.8509 (p)
REVERT: C  480 GLU cc_start: 0.8204 (tp30) cc_final: 0.7640 (tp30)
REVERT: B   17 PHE cc_start: 0.8861 (t80) cc_final: 0.8355 (t80)
REVERT: B  105 GLU cc_start: 0.7204 (mp0) cc_final: 0.6710 (pm20)
  outliers start: 14
  outliers final: 7
  residues processed: 168
  average time/residue: 0.2762
  time to fit residues: 69.1640
Evaluate side-chains
  137 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
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 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 6 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0000
   chunk 69 optimal weight:    0.9990
   chunk 131 optimal weight:    0.0770
   chunk 44 optimal weight:    4.9990
   chunk 133 optimal weight:    8.9990
   chunk 4 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.5944

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
A 885 GLN
C 158 ASN
C 180 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.129516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.100650 restraints weight = 19138.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.100667 restraints weight = 15257.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.101440 restraints weight = 13632.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10968  Z= 0.126
  Angle     :  0.513   7.115  14836  Z= 0.269
  Chirality :  0.039   0.153   1650
  Planarity :  0.004   0.043   1919
  Dihedral  :  4.153  19.391   1470
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.50 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1347
  helix:  1.26 (0.20), residues: 723
  sheet: -1.98 (0.50), residues: 97
  loop : -1.44 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 210 
 HIS   0.005   0.001   HIS C 572 
 PHE   0.017   0.001   PHE C 475 
 TYR   0.012   0.001   TYR A 347 
 ARG   0.004   0.000   ARG C 676 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  550)
  hydrogen bonds       : angle       3.99761 ( 1608)
  covalent geometry    : bond        0.00289 (10968)
  covalent geometry    : angle       0.51268 (14836)

*********************** 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
  165 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8428 (tp30) cc_final: 0.8032 (tp30)
REVERT: A  295 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7347 (mp0)
REVERT: A  543 MET cc_start: 0.7682 (ppp) cc_final: 0.7360 (ppp)
REVERT: C  210 TRP cc_start: 0.8583 (t-100) cc_final: 0.8330 (t-100)
REVERT: C  295 ARG cc_start: 0.6762 (ttm110) cc_final: 0.6327 (tpt-90)
REVERT: C  353 THR cc_start: 0.8802 (m) cc_final: 0.8479 (p)
REVERT: C  756 MET cc_start: 0.8015 (mmt) cc_final: 0.7740 (mmm)
REVERT: B    7 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: B   17 PHE cc_start: 0.8861 (t80) cc_final: 0.8418 (t80)
REVERT: B  105 GLU cc_start: 0.7239 (mp0) cc_final: 0.6638 (pm20)
  outliers start: 15
  outliers final: 10
  residues processed: 161
  average time/residue: 0.2178
  time to fit residues: 51.3314
Evaluate side-chains
  141 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
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  892 VAL
Chi-restraints excluded: chain C residue  121 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 71 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 116 optimal weight:    0.8980
   chunk 108 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 70 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
C 158 ASN
C 180 ASN
C 611 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.127683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.097414 restraints weight = 18928.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.098298 restraints weight = 15475.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.099393 restraints weight = 11748.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2041

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= 0.132
  Angle     :  0.513   7.120  14836  Z= 0.268
  Chirality :  0.039   0.153   1650
  Planarity :  0.004   0.042   1919
  Dihedral  :  4.073  18.119   1470
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 10.25 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.24), residues: 1347
  helix:  1.36 (0.20), residues: 724
  sheet: -1.84 (0.51), residues: 97
  loop : -1.36 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 
 PHE   0.019   0.001   PHE C 425 
 TYR   0.015   0.001   TYR A 256 
 ARG   0.004   0.000   ARG C 676 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  550)
  hydrogen bonds       : angle       3.88933 ( 1608)
  covalent geometry    : bond        0.00308 (10968)
  covalent geometry    : angle       0.51324 (14836)

*********************** 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
  167 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LEU cc_start: 0.9214 (tp) cc_final: 0.9009 (tp)
REVERT: A  294 GLU cc_start: 0.8448 (tp30) cc_final: 0.8035 (tp30)
REVERT: A  295 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7491 (mp0)
REVERT: A  543 MET cc_start: 0.7725 (ppp) cc_final: 0.7386 (ppp)
REVERT: A  785 MET cc_start: 0.7964 (tpp) cc_final: 0.7445 (tpt)
REVERT: C  210 TRP cc_start: 0.8616 (t-100) cc_final: 0.8325 (t-100)
REVERT: C  295 ARG cc_start: 0.6731 (ttm110) cc_final: 0.6325 (tpt-90)
REVERT: B    7 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: B   17 PHE cc_start: 0.8844 (t80) cc_final: 0.8410 (t80)
REVERT: B  105 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6649 (pm20)
  outliers start: 21
  outliers final: 14
  residues processed: 159
  average time/residue: 0.2085
  time to fit residues: 48.8787
Evaluate side-chains
  151 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
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  865 VAL
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  265 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 90 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0040
   chunk 58 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0980
   chunk 133 optimal weight:    0.7980
   chunk 102 optimal weight:    0.5980
   chunk 129 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.4192

-------------------------------------------------------------------------------
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 158 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 = 0.3735 r_free = 0.3735 target = 0.128756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.098678 restraints weight = 18879.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.098693 restraints weight = 15103.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.099723 restraints weight = 12736.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10968  Z= 0.108
  Angle     :  0.500   7.167  14836  Z= 0.259
  Chirality :  0.038   0.152   1650
  Planarity :  0.004   0.041   1919
  Dihedral  :  3.915  17.975   1470
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 10.69 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.24), residues: 1347
  helix:  1.52 (0.20), residues: 723
  sheet: -1.48 (0.54), residues: 95
  loop : -1.29 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 
 PHE   0.021   0.001   PHE C 356 
 TYR   0.022   0.001   TYR A 256 
 ARG   0.004   0.000   ARG C 676 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03336 (  550)
  hydrogen bonds       : angle       3.77192 ( 1608)
  covalent geometry    : bond        0.00244 (10968)
  covalent geometry    : angle       0.50021 (14836)

*********************** 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
  173 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8475 (tp30) cc_final: 0.8017 (tp30)
REVERT: A  295 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7520 (mp0)
REVERT: C  210 TRP cc_start: 0.8627 (t-100) cc_final: 0.8329 (t-100)
REVERT: C  295 ARG cc_start: 0.6701 (ttm110) cc_final: 0.6294 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8239 (tp30) cc_final: 0.7498 (tp30)
REVERT: C  756 MET cc_start: 0.7902 (mmt) cc_final: 0.7653 (mmm)
REVERT: C  836 ASN cc_start: 0.8499 (t0) cc_final: 0.8296 (t0)
REVERT: B    7 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7760 (tm-30)
REVERT: B   17 PHE cc_start: 0.8821 (t80) cc_final: 0.8471 (t80)
REVERT: B  105 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6635 (pm20)
  outliers start: 22
  outliers final: 14
  residues processed: 165
  average time/residue: 0.2220
  time to fit residues: 54.8277
Evaluate side-chains
  154 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
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  121 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  265 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   chunk 111 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 29 optimal weight:    0.4980
   chunk 110 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 4 optimal weight:    0.2980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 158 ASN
C 180 ASN
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.128722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.097961 restraints weight = 18872.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.098729 restraints weight = 14096.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.100111 restraints weight = 10889.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10968  Z= 0.120
  Angle     :  0.508   7.168  14836  Z= 0.262
  Chirality :  0.039   0.173   1650
  Planarity :  0.004   0.040   1919
  Dihedral  :  3.866  16.496   1470
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.39 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.24), residues: 1347
  helix:  1.64 (0.20), residues: 721
  sheet: -1.35 (0.52), residues: 97
  loop : -1.33 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 
 PHE   0.016   0.001   PHE C 475 
 TYR   0.025   0.001   TYR A 256 
 ARG   0.004   0.000   ARG C 676 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03360 (  550)
  hydrogen bonds       : angle       3.72238 ( 1608)
  covalent geometry    : bond        0.00276 (10968)
  covalent geometry    : angle       0.50810 (14836)

*********************** 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
  170 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8501 (tp30) cc_final: 0.7935 (tp30)
REVERT: A  295 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7647 (mp0)
REVERT: A  484 PRO cc_start: 0.7436 (Cg_exo) cc_final: 0.7217 (Cg_endo)
REVERT: A  548 TYR cc_start: 0.8729 (t80) cc_final: 0.8377 (t80)
REVERT: C  210 TRP cc_start: 0.8673 (t-100) cc_final: 0.8420 (t-100)
REVERT: C  295 ARG cc_start: 0.6694 (ttm110) cc_final: 0.6330 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8240 (tp30) cc_final: 0.7479 (tp30)
REVERT: C  675 PHE cc_start: 0.8206 (t80) cc_final: 0.7814 (t80)
REVERT: C  768 GLN cc_start: 0.7868 (tp40) cc_final: 0.7650 (tp40)
REVERT: C  836 ASN cc_start: 0.8558 (t0) cc_final: 0.8351 (t0)
REVERT: B    7 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: B   17 PHE cc_start: 0.8850 (t80) cc_final: 0.8432 (t80)
REVERT: B   33 LEU cc_start: 0.8295 (tp) cc_final: 0.7975 (tp)
REVERT: B   52 MET cc_start: 0.7896 (tpp) cc_final: 0.7482 (mmt)
REVERT: B   53 ILE cc_start: 0.8535 (pt) cc_final: 0.8316 (pt)
REVERT: B  105 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6666 (pm20)
  outliers start: 22
  outliers final: 15
  residues processed: 160
  average time/residue: 0.2217
  time to fit residues: 53.5041
Evaluate side-chains
  153 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
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  892 VAL
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  265 SER
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  515 VAL
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   80 THR
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 115 optimal weight:    0.0970
   chunk 86 optimal weight:    0.5980
   chunk 123 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 180 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 = 0.3715 r_free = 0.3715 target = 0.127083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.096740 restraints weight = 19154.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.097236 restraints weight = 15063.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.098335 restraints weight = 11348.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10968  Z= 0.157
  Angle     :  0.539   7.383  14836  Z= 0.276
  Chirality :  0.040   0.157   1650
  Planarity :  0.004   0.039   1919
  Dihedral  :  3.984  17.331   1470
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.24), residues: 1347
  helix:  1.56 (0.20), residues: 726
  sheet: -1.34 (0.52), residues: 97
  loop : -1.28 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 549 
 HIS   0.005   0.001   HIS C 246 
 PHE   0.016   0.001   PHE B  20 
 TYR   0.021   0.002   TYR A 256 
 ARG   0.003   0.000   ARG C 676 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  550)
  hydrogen bonds       : angle       3.81129 ( 1608)
  covalent geometry    : bond        0.00368 (10968)
  covalent geometry    : angle       0.53865 (14836)

*********************** 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: 24
    poor density    : 140
  time to evaluate  : 1.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.7882 (m) cc_final: 0.7592 (t)
REVERT: A  294 GLU cc_start: 0.8497 (tp30) cc_final: 0.8184 (tp30)
REVERT: A  295 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7556 (mp0)
REVERT: C  295 ARG cc_start: 0.6794 (ttm110) cc_final: 0.6462 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8290 (tp30) cc_final: 0.7529 (tp30)
REVERT: C  675 PHE cc_start: 0.8246 (t80) cc_final: 0.7850 (t80)
REVERT: B    7 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7837 (tm-30)
REVERT: B   17 PHE cc_start: 0.8899 (t80) cc_final: 0.8462 (t80)
REVERT: B  105 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6948 (pm20)
  outliers start: 24
  outliers final: 18
  residues processed: 156
  average time/residue: 0.2488
  time to fit residues: 57.9646
Evaluate side-chains
  149 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
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  121 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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 25 optimal weight:    0.1980
   chunk 89 optimal weight:    1.9990
   chunk 130 optimal weight:   20.0000
   chunk 4 optimal weight:    7.9990
   chunk 131 optimal weight:    6.9990
   chunk 114 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3737 r_free = 0.3737 target = 0.128798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.097628 restraints weight = 19068.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.099184 restraints weight = 15164.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.100069 restraints weight = 11420.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10968  Z= 0.130
  Angle     :  0.532   8.622  14836  Z= 0.272
  Chirality :  0.039   0.155   1650
  Planarity :  0.004   0.040   1919
  Dihedral  :  3.926  18.420   1470
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.71 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.24), residues: 1347
  helix:  1.69 (0.20), residues: 720
  sheet: -1.25 (0.52), residues: 97
  loop : -1.35 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 572 
 PHE   0.017   0.001   PHE C 174 
 TYR   0.018   0.002   TYR A 476 
 ARG   0.003   0.000   ARG C 676 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03412 (  550)
  hydrogen bonds       : angle       3.73234 ( 1608)
  covalent geometry    : bond        0.00302 (10968)
  covalent geometry    : angle       0.53225 (14836)

*********************** 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: 21
    poor density    : 134
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.8017 (m) cc_final: 0.7710 (t)
REVERT: A  294 GLU cc_start: 0.8500 (tp30) cc_final: 0.8135 (tp30)
REVERT: A  295 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7656 (mp0)
REVERT: A  785 MET cc_start: 0.7969 (tpp) cc_final: 0.7266 (mtt)
REVERT: A  791 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7734 (tm-30)
REVERT: C  295 ARG cc_start: 0.6782 (ttm110) cc_final: 0.6489 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8284 (tp30) cc_final: 0.7525 (tp30)
REVERT: C  675 PHE cc_start: 0.8195 (t80) cc_final: 0.7788 (t80)
REVERT: C  756 MET cc_start: 0.7824 (mmt) cc_final: 0.7594 (mmm)
REVERT: C  836 ASN cc_start: 0.8585 (t0) cc_final: 0.8377 (t0)
REVERT: B    7 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: B   17 PHE cc_start: 0.8868 (t80) cc_final: 0.8387 (t80)
REVERT: B   33 LEU cc_start: 0.8375 (tp) cc_final: 0.8083 (tp)
REVERT: B  105 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7018 (pm20)
  outliers start: 21
  outliers final: 16
  residues processed: 147
  average time/residue: 0.2132
  time to fit residues: 46.7278
Evaluate side-chains
  148 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
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  892 VAL
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain C residue  154 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   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 38 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   chunk 116 optimal weight:    0.0870
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0980
   chunk 35 optimal weight:    0.0870
   chunk 109 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.4536

-------------------------------------------------------------------------------
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 = 0.3750 r_free = 0.3750 target = 0.129684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.098936 restraints weight = 18960.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.100911 restraints weight = 14473.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.101501 restraints weight = 11239.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10968  Z= 0.110
  Angle     :  0.529   8.410  14836  Z= 0.269
  Chirality :  0.039   0.158   1650
  Planarity :  0.003   0.039   1919
  Dihedral  :  3.851  17.374   1470
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.24), residues: 1347
  helix:  1.73 (0.20), residues: 721
  sheet: -1.14 (0.54), residues: 95
  loop : -1.32 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 
 PHE   0.019   0.001   PHE C 174 
 TYR   0.019   0.001   TYR A 476 
 ARG   0.004   0.000   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (  550)
  hydrogen bonds       : angle       3.64500 ( 1608)
  covalent geometry    : bond        0.00254 (10968)
  covalent geometry    : angle       0.52937 (14836)

*********************** 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
  161 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.8116 (m) cc_final: 0.7802 (t)
REVERT: A  294 GLU cc_start: 0.8512 (tp30) cc_final: 0.8076 (tp30)
REVERT: A  785 MET cc_start: 0.7966 (tpp) cc_final: 0.7236 (mtt)
REVERT: A  791 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7772 (tm-30)
REVERT: C  210 TRP cc_start: 0.8682 (t-100) cc_final: 0.8396 (t-100)
REVERT: C  295 ARG cc_start: 0.6721 (ttm110) cc_final: 0.6396 (tpt-90)
REVERT: C  299 ASN cc_start: 0.7929 (t0) cc_final: 0.7639 (t0)
REVERT: C  480 GLU cc_start: 0.8216 (tp30) cc_final: 0.7466 (tp30)
REVERT: C  675 PHE cc_start: 0.8174 (t80) cc_final: 0.7779 (t80)
REVERT: C  756 MET cc_start: 0.7856 (mmt) cc_final: 0.7630 (mmm)
REVERT: C  836 ASN cc_start: 0.8569 (t0) cc_final: 0.8358 (t0)
REVERT: B    7 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: B   17 PHE cc_start: 0.8861 (t80) cc_final: 0.8487 (t80)
REVERT: B   33 LEU cc_start: 0.8255 (tp) cc_final: 0.7875 (tp)
REVERT: B   57 ASP cc_start: 0.4462 (t0) cc_final: 0.4061 (p0)
REVERT: B  105 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7016 (pm20)
  outliers start: 20
  outliers final: 17
  residues processed: 153
  average time/residue: 0.2397
  time to fit residues: 56.0506
Evaluate side-chains
  148 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
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  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  121 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  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 59 optimal weight:    0.0020
   chunk 50 optimal weight:    0.0020
   chunk 90 optimal weight:    0.1980
   chunk 25 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 102 optimal weight:    0.8980
   chunk 3 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 128 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    0.3396

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.132392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.102735 restraints weight = 18949.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.102338 restraints weight = 12333.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.102875 restraints weight = 10093.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3023

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= 0.102
  Angle     :  0.518   8.809  14836  Z= 0.264
  Chirality :  0.039   0.190   1650
  Planarity :  0.004   0.039   1919
  Dihedral  :  3.715  18.277   1470
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 7.60
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.24), residues: 1347
  helix:  1.82 (0.20), residues: 721
  sheet: -1.01 (0.53), residues: 97
  loop : -1.25 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 171 
 PHE   0.022   0.001   PHE C 174 
 TYR   0.020   0.001   TYR C 222 
 ARG   0.003   0.000   ARG C 676 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03143 (  550)
  hydrogen bonds       : angle       3.59613 ( 1608)
  covalent geometry    : bond        0.00231 (10968)
  covalent geometry    : angle       0.51764 (14836)

********************** 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
  157 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.8122 (m) cc_final: 0.7799 (t)
REVERT: A  294 GLU cc_start: 0.8493 (tp30) cc_final: 0.8100 (tp30)
REVERT: A  785 MET cc_start: 0.7945 (tpp) cc_final: 0.7253 (mtm)
REVERT: A  791 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7759 (tm-30)
REVERT: C  210 TRP cc_start: 0.8653 (t-100) cc_final: 0.8385 (t-100)
REVERT: C  295 ARG cc_start: 0.6644 (ttm110) cc_final: 0.6362 (tpt-90)
REVERT: C  299 ASN cc_start: 0.7890 (t0) cc_final: 0.7607 (t0)
REVERT: C  480 GLU cc_start: 0.8197 (tp30) cc_final: 0.7458 (tp30)
REVERT: C  675 PHE cc_start: 0.8162 (t80) cc_final: 0.7763 (t80)
REVERT: B    7 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7624 (tm-30)
REVERT: B   17 PHE cc_start: 0.8831 (t80) cc_final: 0.8459 (t80)
REVERT: B   33 LEU cc_start: 0.8131 (tp) cc_final: 0.7657 (tp)
REVERT: B   57 ASP cc_start: 0.4656 (t0) cc_final: 0.4324 (p0)
REVERT: B  105 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7031 (pm20)
  outliers start: 20
  outliers final: 18
  residues processed: 150
  average time/residue: 0.2135
  time to fit residues: 48.3648
Evaluate side-chains
  151 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
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  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain C residue  121 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 63 optimal weight:    0.5980
   chunk 108 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 118 optimal weight:    0.0270
   chunk 82 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 111 optimal weight:    0.0270
   chunk 66 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.3696

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.132375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.103892 restraints weight = 18692.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.103068 restraints weight = 12051.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.103377 restraints weight = 9894.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3167

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= 0.106
  Angle     :  0.543   7.891  14836  Z= 0.273
  Chirality :  0.039   0.193   1650
  Planarity :  0.004   0.039   1919
  Dihedral  :  3.713  20.354   1470
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.85 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.24), residues: 1347
  helix:  1.81 (0.20), residues: 727
  sheet: -0.93 (0.53), residues: 97
  loop : -1.20 (0.28), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 243 
 PHE   0.021   0.001   PHE A 448 
 TYR   0.016   0.001   TYR A 476 
 ARG   0.016   0.000   ARG C 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03129 (  550)
  hydrogen bonds       : angle       3.57587 ( 1608)
  covalent geometry    : bond        0.00242 (10968)
  covalent geometry    : angle       0.54282 (14836)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4467.59 seconds
wall clock time: 82 minutes 1.79 seconds (4921.79 seconds total)