Starting phenix.real_space_refine
on Wed Mar 12 09:13:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d7r_30610/03_2025/7d7r_30610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d7r_30610/03_2025/7d7r_30610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d7r_30610/03_2025/7d7r_30610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d7r_30610/03_2025/7d7r_30610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d7r_30610/03_2025/7d7r_30610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d7r_30610/03_2025/7d7r_30610.cif"
  }
  resolution = 4.0
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4864      2.51       5
     N    1368      2.21       5
     O    1426      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7680
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 3840
          Classifications: {'peptide': 580}
          Incomplete info: {'truncation_to_alanine': 216}
          Link IDs: {'PTRANS': 12, 'TRANS': 567}
          Chain breaks: 1
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 773
          Unresolved non-hydrogen angles: 992
          Unresolved non-hydrogen dihedrals: 622
          Unresolved non-hydrogen chiralities: 82
          Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 429
    Chain: "B"
      Number of atoms: 3840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 3840
          Classifications: {'peptide': 580}
          Incomplete info: {'truncation_to_alanine': 216}
          Link IDs: {'PTRANS': 12, 'TRANS': 567}
          Chain breaks: 1
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 773
          Unresolved non-hydrogen angles: 992
          Unresolved non-hydrogen dihedrals: 622
          Unresolved non-hydrogen chiralities: 82
          Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 429
  Time building chain proxies: 5.00, per 1000 atoms: 0.65
  Number of scatterers: 7680
  At special positions: 0
  Unit cell: (86.32, 107.12, 134.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O    1426      8.00
     N    1368      7.00
     C    4864      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: 1.81
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      68.7% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 261 through 297
      removed outlier: 3.947A  pdb=" N   ARG A 276 " --> pdb=" O   MET A 272 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
    Processing helix  chain 'A' and resid 306 through 321
      removed outlier: 4.207A  pdb=" N   LEU A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 353
      removed outlier: 4.020A  pdb=" N   ARG A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 363
      removed outlier: 3.970A  pdb=" N   GLY A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 390
      removed outlier: 3.516A  pdb=" N   VAL A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 409
    Processing helix  chain 'A' and resid 412 through 459
      removed outlier: 4.322A  pdb=" N   LYS A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE A 438 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ASN A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 471 through 523
      removed outlier: 4.148A  pdb=" N   LEU A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 542
      removed outlier: 3.613A  pdb=" N   PHE A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE A 537 " --> pdb=" O   PHE A 533 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 549
    Processing helix  chain 'A' and resid 550 through 568
      removed outlier: 3.740A  pdb=" N   GLN A 555 " --> pdb=" O   TYR A 551 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ASN A 563 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET A 564 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 637
    Processing helix  chain 'A' and resid 659 through 664
    Processing helix  chain 'A' and resid 680 through 686
    Processing helix  chain 'A' and resid 692 through 704
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 728 through 744
    Processing helix  chain 'A' and resid 758 through 774
    Processing helix  chain 'A' and resid 807 through 815
    Processing helix  chain 'A' and resid 816 through 827
      removed outlier: 4.106A  pdb=" N   ASP A 820 " --> pdb=" O   GLY A 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 253
    Processing helix  chain 'B' and resid 261 through 297
      removed outlier: 3.947A  pdb=" N   ARG B 276 " --> pdb=" O   MET B 272 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 306 through 321
      removed outlier: 4.206A  pdb=" N   LEU B 315 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 353
      removed outlier: 4.021A  pdb=" N   ARG B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 363
      removed outlier: 3.971A  pdb=" N   GLY B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 390
      removed outlier: 3.516A  pdb=" N   VAL B 369 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 409
    Processing helix  chain 'B' and resid 412 through 459
      removed outlier: 4.322A  pdb=" N   LYS B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE B 438 " --> pdb=" O   TRP B 434 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ASN B 459 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 466
    Processing helix  chain 'B' and resid 471 through 523
      removed outlier: 4.148A  pdb=" N   LEU B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 542
      removed outlier: 3.613A  pdb=" N   PHE B 533 " --> pdb=" O   ASP B 529 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE B 537 " --> pdb=" O   PHE B 533 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ILE B 538 " --> pdb=" O   GLY B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 549
    Processing helix  chain 'B' and resid 550 through 568
      removed outlier: 3.740A  pdb=" N   GLN B 555 " --> pdb=" O   TYR B 551 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ASN B 563 " --> pdb=" O   ILE B 559 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET B 564 " --> pdb=" O   ASP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 637
    Processing helix  chain 'B' and resid 659 through 664
    Processing helix  chain 'B' and resid 680 through 686
    Processing helix  chain 'B' and resid 692 through 704
    Processing helix  chain 'B' and resid 705 through 712
    Processing helix  chain 'B' and resid 728 through 744
    Processing helix  chain 'B' and resid 758 through 774
    Processing helix  chain 'B' and resid 807 through 815
    Processing helix  chain 'B' and resid 816 through 827
      removed outlier: 4.105A  pdb=" N   ASP B 820 " --> pdb=" O   GLY B 816 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 611 through 613
    Processing sheet with id=AA2, first strand: chain 'A' and resid 666 through 669
      removed outlier: 6.362A  pdb=" N   GLY A 667 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   ASP A 751 " --> pdb=" O   GLY A 667 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL A 669 " --> pdb=" O   ASP A 751 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   ILE A 748 " --> pdb=" O   ILE A 779 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   VAL A 781 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   LEU A 750 " --> pdb=" O   VAL A 781 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   LEU A 619 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   THR A 618 " --> pdb=" O   GLN A 793 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   LEU A 795 " --> pdb=" O   THR A 618 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ALA A 620 " --> pdb=" O   LEU A 795 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ILE A 797 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL A 622 " --> pdb=" O   ILE A 797 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ILE A 794 " --> pdb=" O   ARG A 805 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ARG A 805 " --> pdb=" O   ILE A 794 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   VAL A 796 " --> pdb=" O   VAL A 803 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 679
    Processing sheet with id=AA4, first strand: chain 'B' and resid 611 through 613
    Processing sheet with id=AA5, first strand: chain 'B' and resid 666 through 669
      removed outlier: 6.363A  pdb=" N   GLY B 667 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASP B 751 " --> pdb=" O   GLY B 667 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL B 669 " --> pdb=" O   ASP B 751 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   ILE B 748 " --> pdb=" O   ILE B 779 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   VAL B 781 " --> pdb=" O   ILE B 748 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   LEU B 750 " --> pdb=" O   VAL B 781 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   LEU B 619 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   THR B 618 " --> pdb=" O   GLN B 793 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   LEU B 795 " --> pdb=" O   THR B 618 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ALA B 620 " --> pdb=" O   LEU B 795 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   ILE B 797 " --> pdb=" O   ALA B 620 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL B 622 " --> pdb=" O   ILE B 797 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ILE B 794 " --> pdb=" O   ARG B 805 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ARG B 805 " --> pdb=" O   ILE B 794 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   VAL B 796 " --> pdb=" O   VAL B 803 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 678 through 679

    609 hydrogen bonds defined for protein.
    1791 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: 2.32

  Time building geometry restraints manager: 2.16 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: 2308
        1.34 -     1.45: 1217
        1.45 -     1.57: 4223
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 7786
  Sorted by residual:
  bond pdb=" C   PRO A 255 "
       pdb=" N   ARG A 256 "
    ideal  model  delta    sigma   weight residual
    1.325  1.270  0.055 1.41e-02 5.03e+03 1.54e+01
  bond pdb=" C   PRO B 255 "
       pdb=" N   ARG B 256 "
    ideal  model  delta    sigma   weight residual
    1.325  1.270  0.055 1.41e-02 5.03e+03 1.52e+01
  bond pdb=" C   ARG A 256 "
       pdb=" N   GLY A 257 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.46e-02 4.69e+03 4.93e+00
  bond pdb=" C   ARG B 256 "
       pdb=" N   GLY B 257 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.46e-02 4.69e+03 4.87e+00
  bond pdb=" C   ILE B 392 "
       pdb=" N   PRO B 393 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.18e+00
  ... (remaining 7781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 10116
        1.89 -     3.78: 426
        3.78 -     5.67: 60
        5.67 -     7.56: 23
        7.56 -     9.45: 17
  Bond angle restraints: 10642
  Sorted by residual:
  angle pdb=" N   VAL B 282 "
        pdb=" CA  VAL B 282 "
        pdb=" C   VAL B 282 "
      ideal   model   delta    sigma   weight residual
     108.88  117.15   -8.27 2.16e+00 2.14e-01 1.47e+01
  angle pdb=" N   VAL A 282 "
        pdb=" CA  VAL A 282 "
        pdb=" C   VAL A 282 "
      ideal   model   delta    sigma   weight residual
     108.88  117.10   -8.22 2.16e+00 2.14e-01 1.45e+01
  angle pdb=" C   GLU B 593 "
        pdb=" N   ASN B 594 "
        pdb=" CA  ASN B 594 "
      ideal   model   delta    sigma   weight residual
     122.82  128.22   -5.40 1.42e+00 4.96e-01 1.45e+01
  angle pdb=" C   GLU A 593 "
        pdb=" N   ASN A 594 "
        pdb=" CA  ASN A 594 "
      ideal   model   delta    sigma   weight residual
     122.82  128.17   -5.35 1.42e+00 4.96e-01 1.42e+01
  angle pdb=" N   MET A 542 "
        pdb=" CA  MET A 542 "
        pdb=" C   MET A 542 "
      ideal   model   delta    sigma   weight residual
     109.81  117.37   -7.56 2.21e+00 2.05e-01 1.17e+01
  ... (remaining 10637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 4067
       17.39 -    34.78: 346
       34.78 -    52.17: 66
       52.17 -    69.56: 19
       69.56 -    86.94: 4
  Dihedral angle restraints: 4502
    sinusoidal: 1186
      harmonic: 3316
  Sorted by residual:
  dihedral pdb=" CA  PRO A 713 "
           pdb=" C   PRO A 713 "
           pdb=" N   GLU A 714 "
           pdb=" CA  GLU A 714 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.75  -27.25     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  PRO B 713 "
           pdb=" C   PRO B 713 "
           pdb=" N   GLU B 714 "
           pdb=" CA  GLU B 714 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.75  -27.25     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  LEU B 568 "
           pdb=" C   LEU B 568 "
           pdb=" N   LYS B 569 "
           pdb=" CA  LYS B 569 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.56  -25.44     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 4499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 950
       0.054 -    0.109: 288
       0.109 -    0.163: 52
       0.163 -    0.217: 8
       0.217 -    0.271: 2
  Chirality restraints: 1300
  Sorted by residual:
  chirality pdb=" CA  ASP A 799 "
            pdb=" N   ASP A 799 "
            pdb=" C   ASP A 799 "
            pdb=" CB  ASP A 799 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  ASP B 799 "
            pdb=" N   ASP B 799 "
            pdb=" C   ASP B 799 "
            pdb=" CB  ASP B 799 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CG  LEU A 333 "
            pdb=" CB  LEU A 333 "
            pdb=" CD1 LEU A 333 "
            pdb=" CD2 LEU A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1297 not shown)

  Planarity restraints: 1394
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 388 "    0.015 2.00e-02 2.50e+03   2.90e-02 8.40e+00
        pdb=" C   VAL B 388 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   VAL B 388 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE B 389 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 388 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.32e+00
        pdb=" C   VAL A 388 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL A 388 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   PHE A 389 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 542 "    0.047 5.00e-02 4.00e+02   7.02e-02 7.88e+00
        pdb=" N   PRO A 543 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1391 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2105
        2.80 -     3.32: 7386
        3.32 -     3.85: 12446
        3.85 -     4.37: 13459
        4.37 -     4.90: 22502
  Nonbonded interactions: 57898
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 476 "
            pdb=" OE1 GLU B 346 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OE1 GLN A 316 "
            pdb=" OG1 THR A 320 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OE1 GLN B 316 "
            pdb=" OG1 THR B 320 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   SER B 490 "
            pdb=" OG  SER B 493 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   SER A 490 "
            pdb=" OG  SER A 493 "
     model   vdw
     2.311 3.040
  ... (remaining 57893 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.030
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.250
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6003
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      :  0.004   0.055   7786  Z= 0.282
  Angle     :  0.961   9.447  10642  Z= 0.529
  Chirality :  0.054   0.271   1300
  Planarity :  0.006   0.070   1394
  Dihedral  : 14.868  86.944   2374
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.65 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.95 %
    Favored  : 88.69 %
  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: -3.66 (0.19), residues: 1152
  helix: -2.08 (0.14), residues: 758
  sheet: -1.05 (0.58), residues: 82
  loop : -3.22 (0.27), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 334 
 HIS   0.004   0.002   HIS B 352 
 PHE   0.032   0.002   PHE A 460 
 TYR   0.026   0.003   TYR B 541 
 ARG   0.006   0.001   ARG A 330 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 227
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 LEU cc_start: 0.7870 (pp) cc_final: 0.7643 (pp)
REVERT: A  328 ASN cc_start: 0.8140 (m-40) cc_final: 0.7351 (m-40)
REVERT: A  330 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6589 (ttm110)
REVERT: A  464 LYS cc_start: 0.7621 (mptt) cc_final: 0.7419 (pttt)
REVERT: A  487 GLU cc_start: 0.7251 (tp30) cc_final: 0.6990 (tp30)
REVERT: A  532 LEU cc_start: 0.8246 (tp) cc_final: 0.8001 (tp)
REVERT: B  278 LEU cc_start: 0.7866 (pp) cc_final: 0.7640 (pp)
REVERT: B  290 VAL cc_start: 0.7941 (m) cc_final: 0.7713 (t)
REVERT: B  294 THR cc_start: 0.6162 (p) cc_final: 0.5504 (p)
REVERT: B  328 ASN cc_start: 0.8051 (m-40) cc_final: 0.7296 (m-40)
REVERT: B  464 LYS cc_start: 0.7803 (mptt) cc_final: 0.7558 (pttt)
REVERT: B  519 PHE cc_start: 0.6365 (m-80) cc_final: 0.6156 (m-80)
REVERT: B  525 LEU cc_start: 0.4824 (pt) cc_final: 0.4542 (mp)
REVERT: B  532 LEU cc_start: 0.8210 (tp) cc_final: 0.7804 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 227
  average time/residue: 0.2190
  time to fit residues: 64.6474
Evaluate side-chains
  152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 87 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 59 optimal weight:   10.0000
   chunk 46 optimal weight:   20.0000
   chunk 90 optimal weight:    0.1980
   chunk 35 optimal weight:    0.1980
   chunk 55 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:   40.0000
   overall best weight:    3.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 316 GLN
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 GLN
B 279 ASN
B 316 GLN
** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 539 GLN
B 555 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.158476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.151042 restraints weight = 29960.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.152471 restraints weight = 19051.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.153302 restraints weight = 12885.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6310
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7786  Z= 0.263
  Angle     :  0.690   6.958  10642  Z= 0.383
  Chirality :  0.044   0.133   1300
  Planarity :  0.005   0.050   1394
  Dihedral  :  5.620  25.477   1226
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.60 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.26 %
    Favored  : 76.82 %
  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: -1.86 (0.22), residues: 1152
  helix: -0.49 (0.17), residues: 786
  sheet: -0.92 (0.54), residues: 82
  loop : -3.19 (0.27), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 334 
 HIS   0.004   0.002   HIS B 361 
 PHE   0.028   0.003   PHE B 314 
 TYR   0.030   0.003   TYR B 541 
 ARG   0.005   0.001   ARG A 365 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.8062 (m) cc_final: 0.7808 (t)
REVERT: A  328 ASN cc_start: 0.7968 (m-40) cc_final: 0.7656 (m-40)
REVERT: A  350 PHE cc_start: 0.8430 (t80) cc_final: 0.8082 (t80)
REVERT: A  464 LYS cc_start: 0.8020 (mptt) cc_final: 0.7630 (pttt)
REVERT: A  509 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7827 (tt)
REVERT: A  561 MET cc_start: 0.6404 (ppp) cc_final: 0.6168 (tmm)
REVERT: B  290 VAL cc_start: 0.8037 (m) cc_final: 0.7796 (t)
REVERT: B  328 ASN cc_start: 0.7929 (m-40) cc_final: 0.7498 (m110)
REVERT: B  350 PHE cc_start: 0.8493 (t80) cc_final: 0.8089 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 165
  average time/residue: 0.1859
  time to fit residues: 41.7651
Evaluate side-chains
  155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:   50.0000
   chunk 8 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 352 HIS
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.160592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.153012 restraints weight = 30013.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.154478 restraints weight = 19228.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.155501 restraints weight = 13184.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6153
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7786  Z= 0.186
  Angle     :  0.657   8.878  10642  Z= 0.343
  Chirality :  0.042   0.130   1300
  Planarity :  0.004   0.051   1394
  Dihedral  :  5.047  23.868   1226
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.99 %
    Favored  : 75.73 %
  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: -0.80 (0.23), residues: 1152
  helix:  0.40 (0.17), residues: 780
  sheet: -0.91 (0.54), residues: 86
  loop : -2.89 (0.30), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 334 
 HIS   0.004   0.001   HIS A 361 
 PHE   0.017   0.002   PHE A 533 
 TYR   0.020   0.002   TYR A 541 
 ARG   0.006   0.000   ARG B 365 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7718 (m) cc_final: 0.7369 (t)
REVERT: A  350 PHE cc_start: 0.8238 (t80) cc_final: 0.7905 (t80)
REVERT: A  370 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7237 (tt)
REVERT: A  464 LYS cc_start: 0.7785 (mptt) cc_final: 0.7535 (pttt)
REVERT: A  570 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5989 (mm-30)
REVERT: B  290 VAL cc_start: 0.7835 (m) cc_final: 0.7504 (t)
REVERT: B  350 PHE cc_start: 0.8175 (t80) cc_final: 0.7854 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 174
  average time/residue: 0.1767
  time to fit residues: 43.2961
Evaluate side-chains
  167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:   30.0000
   chunk 14 optimal weight:    0.0670
   chunk 76 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 33 optimal weight:   20.0000
   chunk 34 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    1.4922

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.146793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.142520 restraints weight = 31818.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.142764 restraints weight = 26402.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.143123 restraints weight = 22919.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7786  Z= 0.182
  Angle     :  0.668   9.782  10642  Z= 0.342
  Chirality :  0.042   0.129   1300
  Planarity :  0.004   0.077   1394
  Dihedral  :  4.727  22.219   1226
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 24.64 %
    Favored  : 71.53 %
  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: 1152
  helix:  0.89 (0.18), residues: 780
  sheet: -0.73 (0.54), residues: 86
  loop : -2.70 (0.32), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 334 
 HIS   0.004   0.001   HIS B 361 
 PHE   0.013   0.002   PHE A 314 
 TYR   0.049   0.002   TYR A 424 
 ARG   0.004   0.000   ARG B 439 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7609 (m) cc_final: 0.7386 (t)
REVERT: A  350 PHE cc_start: 0.7822 (t80) cc_final: 0.7556 (t80)
REVERT: A  370 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6743 (tt)
REVERT: A  442 MET cc_start: 0.5567 (ttm) cc_final: 0.5362 (ttp)
REVERT: B  290 VAL cc_start: 0.7743 (m) cc_final: 0.7452 (t)
REVERT: B  350 PHE cc_start: 0.7905 (t80) cc_final: 0.7618 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 180
  average time/residue: 0.1588
  time to fit residues: 40.1034
Evaluate side-chains
  163 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  460 PHE
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 62 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:   20.0000
   chunk 79 optimal weight:    0.9990
   chunk 97 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.156858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.149221 restraints weight = 30069.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.150676 restraints weight = 19338.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.151667 restraints weight = 13222.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6236
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7786  Z= 0.277
  Angle     :  0.742   8.893  10642  Z= 0.394
  Chirality :  0.045   0.174   1300
  Planarity :  0.004   0.037   1394
  Dihedral  :  5.140  25.056   1226
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.73 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 25.00 %
    Favored  : 69.89 %
  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: -0.42 (0.24), residues: 1152
  helix:  0.77 (0.18), residues: 778
  sheet: -1.20 (0.50), residues: 86
  loop : -2.86 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 334 
 HIS   0.006   0.002   HIS A 361 
 PHE   0.018   0.002   PHE A 533 
 TYR   0.017   0.002   TYR B 551 
 ARG   0.008   0.001   ARG A 330 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7701 (m) cc_final: 0.7444 (t)
REVERT: A  330 ARG cc_start: 0.7489 (ttm110) cc_final: 0.6987 (ttp-110)
REVERT: A  384 LEU cc_start: 0.8755 (pp) cc_final: 0.8552 (pp)
REVERT: B  290 VAL cc_start: 0.7912 (m) cc_final: 0.7561 (t)
REVERT: B  350 PHE cc_start: 0.8284 (t80) cc_final: 0.8075 (t80)
  outliers start: 28
  outliers final: 18
  residues processed: 165
  average time/residue: 0.1904
  time to fit residues: 43.3547
Evaluate side-chains
  155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  460 PHE
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 101 optimal weight:    0.3980
   chunk 45 optimal weight:   20.0000
   chunk 92 optimal weight:   30.0000
   chunk 110 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 38 optimal weight:   30.0000
   chunk 88 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0370
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A 459 ASN
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.147778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.144742 restraints weight = 31683.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.144689 restraints weight = 36624.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.144690 restraints weight = 36820.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6029
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7786  Z= 0.178
  Angle     :  0.709  11.623  10642  Z= 0.357
  Chirality :  0.042   0.158   1300
  Planarity :  0.004   0.052   1394
  Dihedral  :  4.465  19.673   1226
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 28.28 %
    Favored  : 68.07 %
  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:  0.28 (0.25), residues: 1152
  helix:  1.26 (0.18), residues: 780
  sheet: -0.62 (0.53), residues: 84
  loop : -2.60 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 412 
 HIS   0.005   0.002   HIS A 361 
 PHE   0.020   0.001   PHE B 408 
 TYR   0.022   0.002   TYR A 465 
 ARG   0.004   0.000   ARG A 330 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 PHE cc_start: 0.2962 (OUTLIER) cc_final: -0.2371 (m-80)
REVERT: A  424 TYR cc_start: 0.7132 (m-80) cc_final: 0.6910 (m-80)
REVERT: A  442 MET cc_start: 0.5823 (ttm) cc_final: 0.5488 (ttm)
REVERT: A  464 LYS cc_start: 0.7340 (mmtm) cc_final: 0.6828 (pttt)
REVERT: A  502 ASN cc_start: 0.5717 (m-40) cc_final: 0.5336 (t0)
REVERT: A  570 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5513 (mt-10)
REVERT: B  290 VAL cc_start: 0.7957 (m) cc_final: 0.7742 (t)
REVERT: B  311 PHE cc_start: 0.3028 (OUTLIER) cc_final: -0.1401 (m-10)
REVERT: B  330 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6932 (ttm110)
REVERT: B  502 ASN cc_start: 0.5879 (m-40) cc_final: 0.5387 (t0)
REVERT: B  505 ILE cc_start: 0.7556 (mt) cc_final: 0.7199 (tp)
  outliers start: 20
  outliers final: 11
  residues processed: 185
  average time/residue: 0.1884
  time to fit residues: 47.9860
Evaluate side-chains
  166 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  564 MET
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain B residue  311 PHE
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 52 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0020
   chunk 86 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 103 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.9794

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.159133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.151659 restraints weight = 29987.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.153126 restraints weight = 19358.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.153981 restraints weight = 13318.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6150
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7786  Z= 0.212
  Angle     :  0.708  13.297  10642  Z= 0.363
  Chirality :  0.043   0.153   1300
  Planarity :  0.004   0.056   1394
  Dihedral  :  4.471  19.780   1226
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 28.65 %
    Favored  : 67.15 %
  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:  0.35 (0.25), residues: 1152
  helix:  1.34 (0.18), residues: 778
  sheet: -0.78 (0.53), residues: 88
  loop : -2.56 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 334 
 HIS   0.005   0.001   HIS A 361 
 PHE   0.014   0.002   PHE B 408 
 TYR   0.028   0.002   TYR B 541 
 ARG   0.011   0.001   ARG B 276 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 PHE cc_start: 0.3593 (OUTLIER) cc_final: -0.1869 (m-80)
REVERT: A  384 LEU cc_start: 0.8768 (pp) cc_final: 0.8420 (pp)
REVERT: A  502 ASN cc_start: 0.5574 (m-40) cc_final: 0.5223 (t0)
REVERT: B  290 VAL cc_start: 0.7906 (m) cc_final: 0.7670 (t)
REVERT: B  502 ASN cc_start: 0.5584 (m-40) cc_final: 0.5308 (t0)
  outliers start: 23
  outliers final: 18
  residues processed: 164
  average time/residue: 0.1824
  time to fit residues: 41.4796
Evaluate side-chains
  156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 104 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 113 optimal weight:    0.0980
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.159747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.152320 restraints weight = 30503.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.153763 restraints weight = 19372.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.154832 restraints weight = 13159.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7786  Z= 0.197
  Angle     :  0.716  13.246  10642  Z= 0.365
  Chirality :  0.044   0.192   1300
  Planarity :  0.004   0.052   1394
  Dihedral  :  4.391  18.066   1226
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 29.20 %
    Favored  : 67.15 %
  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:  0.48 (0.25), residues: 1152
  helix:  1.42 (0.18), residues: 772
  sheet: -0.77 (0.54), residues: 88
  loop : -2.37 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 334 
 HIS   0.005   0.002   HIS A 361 
 PHE   0.018   0.002   PHE A 533 
 TYR   0.022   0.002   TYR B 541 
 ARG   0.011   0.001   ARG A 276 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7712 (m) cc_final: 0.7431 (t)
REVERT: A  311 PHE cc_start: 0.3486 (OUTLIER) cc_final: -0.1965 (m-80)
REVERT: A  384 LEU cc_start: 0.8681 (pp) cc_final: 0.8447 (pp)
REVERT: A  502 ASN cc_start: 0.5463 (m-40) cc_final: 0.5193 (t0)
REVERT: B  290 VAL cc_start: 0.7903 (m) cc_final: 0.7573 (t)
REVERT: B  464 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7407 (pttt)
REVERT: B  502 ASN cc_start: 0.5479 (m-40) cc_final: 0.5275 (t0)
REVERT: B  505 ILE cc_start: 0.7218 (mt) cc_final: 0.6952 (tp)
  outliers start: 20
  outliers final: 18
  residues processed: 168
  average time/residue: 0.1788
  time to fit residues: 41.1669
Evaluate side-chains
  164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  569 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 114 optimal weight:    1.9990
   chunk 98 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.159612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.152182 restraints weight = 30617.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.153689 restraints weight = 19462.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.154634 restraints weight = 13102.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6108
moved from start:          0.4594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7786  Z= 0.199
  Angle     :  0.726  14.299  10642  Z= 0.369
  Chirality :  0.043   0.193   1300
  Planarity :  0.004   0.046   1394
  Dihedral  :  4.288  17.814   1226
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 28.47 %
    Favored  : 67.88 %
  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:  0.68 (0.25), residues: 1152
  helix:  1.50 (0.18), residues: 768
  sheet: -0.16 (0.67), residues: 60
  loop : -2.04 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 334 
 HIS   0.005   0.002   HIS A 361 
 PHE   0.024   0.002   PHE B 325 
 TYR   0.022   0.002   TYR A 476 
 ARG   0.010   0.001   ARG A 276 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7756 (m) cc_final: 0.7481 (t)
REVERT: A  311 PHE cc_start: 0.3515 (OUTLIER) cc_final: -0.1784 (m-80)
REVERT: A  384 LEU cc_start: 0.8730 (pp) cc_final: 0.8408 (pp)
REVERT: A  502 ASN cc_start: 0.5512 (m-40) cc_final: 0.5250 (t0)
REVERT: B  290 VAL cc_start: 0.7852 (m) cc_final: 0.7550 (t)
REVERT: B  330 ARG cc_start: 0.7085 (ttm110) cc_final: 0.6797 (ttm110)
REVERT: B  464 LYS cc_start: 0.7790 (mmtm) cc_final: 0.7414 (pttt)
REVERT: B  505 ILE cc_start: 0.7180 (mt) cc_final: 0.6923 (tp)
REVERT: B  561 MET cc_start: 0.5865 (tmm) cc_final: 0.5600 (tmm)
  outliers start: 20
  outliers final: 19
  residues processed: 162
  average time/residue: 0.1751
  time to fit residues: 39.6163
Evaluate side-chains
  164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  346 GLU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  569 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 36 optimal weight:   20.0000
   chunk 110 optimal weight:   20.0000
   chunk 102 optimal weight:   30.0000
   chunk 47 optimal weight:    0.0980
   chunk 114 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 115 optimal weight:   20.0000
   chunk 86 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   chunk 103 optimal weight:   20.0000
   overall best weight:    2.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.143221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.139184 restraints weight = 32271.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.139555 restraints weight = 26558.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.139625 restraints weight = 22378.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6109
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7786  Z= 0.256
  Angle     :  0.763  14.709  10642  Z= 0.395
  Chirality :  0.045   0.196   1300
  Planarity :  0.004   0.086   1394
  Dihedral  :  4.669  21.369   1226
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 29.38 %
    Favored  : 66.79 %
  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:  0.31 (0.25), residues: 1152
  helix:  1.23 (0.18), residues: 772
  sheet: -0.26 (0.87), residues: 44
  loop : -2.18 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 334 
 HIS   0.006   0.002   HIS A 361 
 PHE   0.019   0.002   PHE B 350 
 TYR   0.053   0.003   TYR B 424 
 ARG   0.014   0.001   ARG A 276 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7844 (m) cc_final: 0.7573 (t)
REVERT: A  384 LEU cc_start: 0.8636 (pp) cc_final: 0.8367 (pp)
REVERT: B  290 VAL cc_start: 0.7939 (m) cc_final: 0.7630 (t)
REVERT: B  505 ILE cc_start: 0.7466 (mt) cc_final: 0.7221 (tp)
REVERT: B  561 MET cc_start: 0.5634 (tmm) cc_final: 0.5379 (tmm)
  outliers start: 21
  outliers final: 18
  residues processed: 152
  average time/residue: 0.1643
  time to fit residues: 35.4516
Evaluate side-chains
  151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  346 GLU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:   20.0000
   chunk 77 optimal weight:    0.8980
   chunk 106 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 112 optimal weight:   40.0000
   chunk 43 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 361 HIS
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.157473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.150143 restraints weight = 30510.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.151614 restraints weight = 19391.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.152631 restraints weight = 13152.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6160
moved from start:          0.4884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7786  Z= 0.225
  Angle     :  0.750  14.500  10642  Z= 0.385
  Chirality :  0.044   0.197   1300
  Planarity :  0.004   0.067   1394
  Dihedral  :  4.541  20.944   1226
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 30.29 %
    Favored  : 66.24 %
  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:  0.35 (0.25), residues: 1152
  helix:  1.25 (0.18), residues: 776
  sheet: -0.40 (0.89), residues: 44
  loop : -2.14 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 334 
 HIS   0.005   0.002   HIS A 361 
 PHE   0.018   0.002   PHE B 325 
 TYR   0.018   0.002   TYR B 541 
 ARG   0.012   0.001   ARG B 276 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2267.46 seconds
wall clock time: 40 minutes 13.64 seconds (2413.64 seconds total)