Starting phenix.real_space_refine
on Fri Feb 14 23:29:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pqe_13591/02_2025/7pqe_13591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pqe_13591/02_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_13591/02_2025/7pqe_13591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pqe_13591/02_2025/7pqe_13591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pqe_13591/02_2025/7pqe_13591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pqe_13591/02_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.60, per 1000 atoms: 0.61
  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.10
  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: 3.75

  Time building geometry restraints manager: 2.91 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:             1.870
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     26.780
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.180
-------------------------------------------------------------------------------
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= 0.367
  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 

*********************** 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  : 1.195 
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: 0.2374
  time to fit residues: 53.5399
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  : 1.291 
-------------------------------------------------------------------------------
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 = 0.100894 restraints weight = 14130.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.101387 restraints weight = 11504.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
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= 0.171
  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 

*********************** 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  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8418 (tp30) cc_final: 0.7974 (tp30)
REVERT: A  785 MET cc_start: 0.8054 (tpp) cc_final: 0.7579 (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: 0.8354 (t80)
REVERT: B  105 GLU cc_start: 0.7205 (mp0) cc_final: 0.6710 (pm20)
  outliers start: 14
  outliers final: 7
  residues processed: 168
  average time/residue: 0.2011
  time to fit residues: 49.6787
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  : 1.351 
-------------------------------------------------------------------------------
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:    0.0030
   chunk 44 optimal weight:    0.9990
   chunk 133 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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
C 361 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.129831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.101003 restraints weight = 19123.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.101619 restraints weight = 14782.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.101886 restraints weight = 12956.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10968  Z= 0.176
  Angle     :  0.510   7.113  14836  Z= 0.268
  Chirality :  0.039   0.152   1650
  Planarity :  0.004   0.043   1919
  Dihedral  :  4.147  19.397   1470
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  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: -0.02 (0.24), residues: 1347
  helix:  1.27 (0.20), residues: 723
  sheet: -1.97 (0.50), residues: 97
  loop : -1.44 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   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 

*********************** 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  : 1.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8448 (tp30) cc_final: 0.8057 (tp30)
REVERT: A  295 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7342 (mp0)
REVERT: C  210 TRP cc_start: 0.8600 (t-100) cc_final: 0.8326 (t-100)
REVERT: C  295 ARG cc_start: 0.6733 (ttm110) cc_final: 0.6320 (tpt-90)
REVERT: C  353 THR cc_start: 0.8807 (m) cc_final: 0.8486 (p)
REVERT: C  756 MET cc_start: 0.8005 (mmt) cc_final: 0.7717 (mmm)
REVERT: B    7 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: B   17 PHE cc_start: 0.8861 (t80) cc_final: 0.8405 (t80)
REVERT: B  105 GLU cc_start: 0.7252 (mp0) cc_final: 0.6643 (pm20)
  outliers start: 15
  outliers final: 9
  residues processed: 161
  average time/residue: 0.2168
  time to fit residues: 51.2619
Evaluate side-chains
  138 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 108 optimal weight:    0.2980
   chunk 26 optimal weight:    9.9990
   chunk 70 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 158 ASN
C 361 ASN
C 611 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.128320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.098321 restraints weight = 18859.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.099273 restraints weight = 15142.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.100046 restraints weight = 11466.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2155

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= 0.168
  Angle     :  0.497   7.109  14836  Z= 0.260
  Chirality :  0.039   0.152   1650
  Planarity :  0.004   0.042   1919
  Dihedral  :  3.998  17.703   1470
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 10.08 %
    Favored  : 88.08 %
  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:  0.18 (0.24), residues: 1347
  helix:  1.41 (0.20), residues: 723
  sheet: -1.81 (0.51), residues: 97
  loop : -1.33 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 549 
 HIS   0.005   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 

*********************** 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
  174 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8494 (tp30) cc_final: 0.8041 (tp30)
REVERT: A  295 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7475 (mp0)
REVERT: A  785 MET cc_start: 0.8020 (tpp) cc_final: 0.7469 (tpt)
REVERT: C  210 TRP cc_start: 0.8581 (t-100) cc_final: 0.8301 (t-100)
REVERT: C  295 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6287 (tpt-90)
REVERT: C  768 GLN cc_start: 0.7842 (tp40) cc_final: 0.7642 (tp40)
REVERT: B    7 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: B   17 PHE cc_start: 0.8837 (t80) cc_final: 0.8423 (t80)
REVERT: B  105 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6644 (pm20)
  outliers start: 21
  outliers final: 14
  residues processed: 166
  average time/residue: 0.2147
  time to fit residues: 51.8029
Evaluate side-chains
  152 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 1.447 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 90 optimal weight:    0.0170
   chunk 61 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0020
   chunk 58 optimal weight:    0.0870
   chunk 20 optimal weight:    0.6980
   chunk 133 optimal weight:    9.9990
   chunk 102 optimal weight:    0.5980
   chunk 129 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.2604

-------------------------------------------------------------------------------
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 611 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.130658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.100091 restraints weight = 18853.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.101317 restraints weight = 14334.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.102424 restraints weight = 11147.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  10968  Z= 0.142
  Angle     :  0.497   7.159  14836  Z= 0.258
  Chirality :  0.038   0.167   1650
  Planarity :  0.004   0.040   1919
  Dihedral  :  3.810  17.685   1470
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  9.90 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.24), residues: 1347
  helix:  1.64 (0.20), residues: 722
  sheet: -1.44 (0.53), residues: 95
  loop : -1.32 (0.28), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 549 
 HIS   0.005   0.001   HIS C 171 
 PHE   0.024   0.001   PHE C 356 
 TYR   0.026   0.001   TYR A 256 
 ARG   0.004   0.000   ARG C 676 

*********************** 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
  178 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8506 (tp30) cc_final: 0.8062 (tp30)
REVERT: C  210 TRP cc_start: 0.8579 (t-100) cc_final: 0.8332 (t-100)
REVERT: C  295 ARG cc_start: 0.6600 (ttm110) cc_final: 0.6276 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8214 (tp30) cc_final: 0.7491 (tp30)
REVERT: C  756 MET cc_start: 0.7833 (mmt) cc_final: 0.7631 (mmm)
REVERT: C  768 GLN cc_start: 0.7756 (tp40) cc_final: 0.7553 (tp40)
REVERT: B    7 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: B   17 PHE cc_start: 0.8797 (t80) cc_final: 0.8487 (t80)
REVERT: B   33 LEU cc_start: 0.8200 (tp) cc_final: 0.7830 (tp)
REVERT: B  105 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6639 (pm20)
  outliers start: 21
  outliers final: 15
  residues processed: 169
  average time/residue: 0.2045
  time to fit residues: 52.2400
Evaluate side-chains
  156 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
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  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   40 LEU
Chi-restraints excluded: chain B residue   80 THR
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:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 111 optimal weight:    0.0040
   chunk 86 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 110 optimal weight:    4.9990
   chunk 116 optimal weight:    0.6980
   chunk 1 optimal weight:    0.1980
   chunk 77 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   overall best weight:    0.5192

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.129288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.098529 restraints weight = 18845.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.099080 restraints weight = 15018.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.100296 restraints weight = 11179.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2608

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= 0.166
  Angle     :  0.502   7.176  14836  Z= 0.260
  Chirality :  0.039   0.171   1650
  Planarity :  0.003   0.039   1919
  Dihedral  :  3.787  16.228   1470
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.39 %
    Favored  : 86.77 %
  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:  0.50 (0.24), residues: 1347
  helix:  1.71 (0.20), residues: 722
  sheet: -1.36 (0.52), residues: 97
  loop : -1.31 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 572 
 PHE   0.015   0.001   PHE C 475 
 TYR   0.018   0.001   TYR A 256 
 ARG   0.004   0.000   ARG C 676 

*********************** 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
  169 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLU cc_start: 0.8467 (tp30) cc_final: 0.7860 (tp30)
REVERT: A  785 MET cc_start: 0.7937 (tpp) cc_final: 0.7419 (tpt)
REVERT: C  210 TRP cc_start: 0.8655 (t-100) cc_final: 0.8415 (t-100)
REVERT: C  295 ARG cc_start: 0.6616 (ttm110) cc_final: 0.6271 (tpt-90)
REVERT: C  480 GLU cc_start: 0.8239 (tp30) cc_final: 0.7496 (tp30)
REVERT: B    7 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: B   17 PHE cc_start: 0.8817 (t80) cc_final: 0.8480 (t80)
REVERT: B   33 LEU cc_start: 0.8200 (tp) cc_final: 0.7796 (tp)
REVERT: B   52 MET cc_start: 0.7843 (tpp) cc_final: 0.7510 (tpp)
REVERT: B   53 ILE cc_start: 0.8481 (pt) cc_final: 0.8266 (pt)
REVERT: B   57 ASP cc_start: 0.4311 (t0) cc_final: 0.4049 (p0)
REVERT: B  105 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6652 (pm20)
  outliers start: 21
  outliers final: 16
  residues processed: 160
  average time/residue: 0.2132
  time to fit residues: 50.8998
Evaluate side-chains
  152 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 115 optimal weight:    0.0370
   chunk 86 optimal weight:    0.6980
   chunk 123 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 82 optimal weight:   10.0000
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.3748 r_free = 0.3748 target = 0.129521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.099118 restraints weight = 19059.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.100122 restraints weight = 14669.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.101088 restraints weight = 10929.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10968  Z= 0.166
  Angle     :  0.509   7.525  14836  Z= 0.261
  Chirality :  0.039   0.178   1650
  Planarity :  0.004   0.039   1919
  Dihedral  :  3.748  16.792   1470
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.92 %
    Favored  : 86.24 %
  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:  0.58 (0.24), residues: 1347
  helix:  1.78 (0.20), residues: 722
  sheet: -1.30 (0.52), residues: 97
  loop : -1.28 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 549 
 HIS   0.006   0.001   HIS C 246 
 PHE   0.016   0.001   PHE C 174 
 TYR   0.035   0.002   TYR A 361 
 ARG   0.003   0.000   ARG C 676 

*********************** 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
  160 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.7809 (m) cc_final: 0.7523 (t)
REVERT: A  294 GLU cc_start: 0.8499 (tp30) cc_final: 0.8114 (tp30)
REVERT: A  543 MET cc_start: 0.7513 (tmm) cc_final: 0.6731 (ppp)
REVERT: C  210 TRP cc_start: 0.8661 (t-100) cc_final: 0.8404 (t-100)
REVERT: C  295 ARG cc_start: 0.6646 (ttm110) cc_final: 0.6296 (tpt-90)
REVERT: C  299 ASN cc_start: 0.7929 (t0) cc_final: 0.7630 (t0)
REVERT: C  480 GLU cc_start: 0.8239 (tp30) cc_final: 0.7456 (tp30)
REVERT: C  576 PHE cc_start: 0.8208 (t80) cc_final: 0.7995 (t80)
REVERT: C  756 MET cc_start: 0.7814 (mmt) cc_final: 0.7612 (mmm)
REVERT: B    7 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: B   17 PHE cc_start: 0.8838 (t80) cc_final: 0.8466 (t80)
REVERT: B   33 LEU cc_start: 0.8197 (tp) cc_final: 0.7780 (tp)
REVERT: B  105 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6947 (pm20)
  outliers start: 21
  outliers final: 16
  residues processed: 151
  average time/residue: 0.2144
  time to fit residues: 48.2358
Evaluate side-chains
  148 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  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  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:    0.0170
   chunk 89 optimal weight:    0.0020
   chunk 130 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 131 optimal weight:    0.0070
   chunk 114 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 113 optimal weight:    0.8980
   overall best weight:    0.3044

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.131007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.101255 restraints weight = 18834.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.101776 restraints weight = 10949.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.101677 restraints weight = 8693.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3001

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= 0.141
  Angle     :  0.512   8.467  14836  Z= 0.261
  Chirality :  0.038   0.184   1650
  Planarity :  0.003   0.038   1919
  Dihedral  :  3.702  17.557   1470
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.71 %
    Favored  : 85.54 %
  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:  0.64 (0.24), residues: 1347
  helix:  1.84 (0.20), residues: 721
  sheet: -1.25 (0.52), residues: 97
  loop : -1.28 (0.27), 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   0.018   0.001   PHE C 174 
 TYR   0.023   0.001   TYR A 361 
 ARG   0.004   0.000   ARG A 274 

*********************** 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
  169 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.8086 (m) cc_final: 0.7752 (t)
REVERT: A  294 GLU cc_start: 0.8608 (tp30) cc_final: 0.8140 (tp30)
REVERT: A  543 MET cc_start: 0.7786 (tmm) cc_final: 0.7057 (tmm)
REVERT: A  547 ASP cc_start: 0.8282 (p0) cc_final: 0.7476 (p0)
REVERT: A  548 TYR cc_start: 0.8725 (t80) cc_final: 0.8402 (t80)
REVERT: A  785 MET cc_start: 0.7932 (tpp) cc_final: 0.7403 (tpt)
REVERT: C  210 TRP cc_start: 0.8648 (t-100) cc_final: 0.8413 (t-100)
REVERT: C  295 ARG cc_start: 0.6549 (ttm110) cc_final: 0.6262 (tpt-90)
REVERT: C  299 ASN cc_start: 0.7849 (t0) cc_final: 0.7624 (t0)
REVERT: C  480 GLU cc_start: 0.8171 (tp30) cc_final: 0.7483 (tp30)
REVERT: C  576 PHE cc_start: 0.8335 (t80) cc_final: 0.8117 (t80)
REVERT: B    7 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: B   17 PHE cc_start: 0.8835 (t80) cc_final: 0.8521 (t80)
REVERT: B   33 LEU cc_start: 0.8087 (tp) cc_final: 0.7756 (tp)
REVERT: B   57 ASP cc_start: 0.4809 (t0) cc_final: 0.4356 (p0)
REVERT: B  105 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7024 (pm20)
  outliers start: 20
  outliers final: 17
  residues processed: 161
  average time/residue: 0.1982
  time to fit residues: 47.8455
Evaluate side-chains
  158 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  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  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:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0270
   chunk 74 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 116 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 50 optimal weight:    0.1980
   chunk 35 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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 = 0.3762 r_free = 0.3762 target = 0.130618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.101105 restraints weight = 18921.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.101974 restraints weight = 12737.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.102282 restraints weight = 10428.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.3060

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= 0.169
  Angle     :  0.527   8.262  14836  Z= 0.267
  Chirality :  0.039   0.184   1650
  Planarity :  0.003   0.038   1919
  Dihedral  :  3.750  22.473   1470
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.80 %
    Favored  : 85.36 %
  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:  1.87 (0.20), residues: 720
  sheet: -1.12 (0.52), residues: 97
  loop : -1.30 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 572 
 PHE   0.026   0.001   PHE A 448 
 TYR   0.020   0.001   TYR A 246 
 ARG   0.015   0.000   ARG C 127 

*********************** 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
  155 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.7976 (m) cc_final: 0.7674 (t)
REVERT: A  294 GLU cc_start: 0.8532 (tp30) cc_final: 0.8145 (tp30)
REVERT: A  547 ASP cc_start: 0.8074 (p0) cc_final: 0.7870 (p0)
REVERT: A  548 TYR cc_start: 0.8746 (t80) cc_final: 0.8474 (t80)
REVERT: A  785 MET cc_start: 0.7910 (tpp) cc_final: 0.7194 (mtm)
REVERT: C  210 TRP cc_start: 0.8685 (t-100) cc_final: 0.8459 (t-100)
REVERT: C  295 ARG cc_start: 0.6634 (ttm110) cc_final: 0.6325 (tpt-90)
REVERT: C  299 ASN cc_start: 0.7883 (t0) cc_final: 0.7605 (t0)
REVERT: C  480 GLU cc_start: 0.8195 (tp30) cc_final: 0.7492 (tp30)
REVERT: C  576 PHE cc_start: 0.8263 (t80) cc_final: 0.8045 (t80)
REVERT: B    7 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: B   17 PHE cc_start: 0.8837 (t80) cc_final: 0.8483 (t80)
REVERT: B   33 LEU cc_start: 0.8082 (tp) cc_final: 0.7667 (tp)
REVERT: B  105 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7001 (pm20)
  outliers start: 21
  outliers final: 17
  residues processed: 147
  average time/residue: 0.2095
  time to fit residues: 46.0373
Evaluate side-chains
  150 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  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  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:    4.9990
   chunk 50 optimal weight:    0.0040
   chunk 90 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 102 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 128 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.3774 r_free = 0.3774 target = 0.131794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.102296 restraints weight = 19009.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.102979 restraints weight = 12437.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.103661 restraints weight = 10654.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10968  Z= 0.167
  Angle     :  0.519   8.580  14836  Z= 0.263
  Chirality :  0.039   0.190   1650
  Planarity :  0.003   0.038   1919
  Dihedral  :  3.740  22.039   1470
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.88 %
    Favored  : 85.36 %
  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:  1.91 (0.20), residues: 720
  sheet: -1.06 (0.52), residues: 97
  loop : -1.30 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 572 
 PHE   0.025   0.001   PHE A 448 
 TYR   0.020   0.001   TYR A 246 
 ARG   0.004   0.000   ARG A 274 

********************** 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
  151 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 1.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 SER cc_start: 0.8066 (m) cc_final: 0.7762 (t)
REVERT: A  294 GLU cc_start: 0.8552 (tp30) cc_final: 0.8188 (tp30)
REVERT: A  543 MET cc_start: 0.7723 (tmm) cc_final: 0.7419 (tmm)
REVERT: A  547 ASP cc_start: 0.8230 (p0) cc_final: 0.7974 (p0)
REVERT: A  785 MET cc_start: 0.7910 (tpp) cc_final: 0.7186 (mtm)
REVERT: C  210 TRP cc_start: 0.8723 (t-100) cc_final: 0.8461 (t-100)
REVERT: C  295 ARG cc_start: 0.6641 (ttm110) cc_final: 0.6436 (tpt-90)
REVERT: C  299 ASN cc_start: 0.7886 (t0) cc_final: 0.7597 (t0)
REVERT: C  480 GLU cc_start: 0.8202 (tp30) cc_final: 0.7507 (tp30)
REVERT: B    7 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: B   17 PHE cc_start: 0.8870 (t80) cc_final: 0.8492 (t80)
REVERT: B   33 LEU cc_start: 0.8105 (tp) cc_final: 0.7624 (tp)
REVERT: B  105 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7003 (pm20)
  outliers start: 20
  outliers final: 17
  residues processed: 143
  average time/residue: 0.2117
  time to fit residues: 45.1119
Evaluate side-chains
  144 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  276 HIS
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  797 HIS
Chi-restraints excluded: chain A residue  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  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:    0.9980
   chunk 108 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 118 optimal weight:    0.8980
   chunk 82 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 111 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 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 = 0.3740 r_free = 0.3740 target = 0.129014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.099390 restraints weight = 18859.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.100571 restraints weight = 13344.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.101708 restraints weight = 10617.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3007

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= 0.220
  Angle     :  0.549   7.603  14836  Z= 0.277
  Chirality :  0.040   0.189   1650
  Planarity :  0.004   0.060   1919
  Dihedral  :  3.857  22.370   1470
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.97 %
    Favored  : 85.01 %
  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:  0.66 (0.24), residues: 1347
  helix:  1.86 (0.20), residues: 720
  sheet: -1.00 (0.52), residues: 97
  loop : -1.31 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 549 
 HIS   0.004   0.001   HIS C 572 
 PHE   0.025   0.001   PHE A 448 
 TYR   0.045   0.002   TYR A 246 
 ARG   0.013   0.000   ARG C 127 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3124.37 seconds
wall clock time: 57 minutes 4.00 seconds (3424.00 seconds total)