Starting phenix.real_space_refine
on Sat Jan 18 01:14:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xaj_38200/01_2025/8xaj_38200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xaj_38200/01_2025/8xaj_38200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xaj_38200/01_2025/8xaj_38200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xaj_38200/01_2025/8xaj_38200.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xaj_38200/01_2025/8xaj_38200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xaj_38200/01_2025/8xaj_38200.cif"
  }
  resolution = 3.29
  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=   0.017 sd=   0.074
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: 5
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     S      52      5.16       5
     C    7776      2.51       5
     N    1847      2.21       5
     O    1986      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 11668
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 705, 5645
          Classifications: {'peptide': 705}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 36, 'TRANS': 668}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "B"
      Number of atoms: 5645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 705, 5645
          Classifications: {'peptide': 705}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 36, 'TRANS': 668}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "A"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 378
          Unusual residues: {'PCW': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N   PCW A 801 " occ=0.00
      ... (52 atoms not shown)
      pdb=" P   PCW A 801 " occ=0.00
    residue:
      pdb=" N   PCW A 802 " occ=0.00
      ... (52 atoms not shown)
      pdb=" P   PCW A 802 " occ=0.00
    residue:
      pdb=" N   PCW A 803 " occ=0.00
      ... (52 atoms not shown)
      pdb=" P   PCW A 803 " occ=0.00
    residue:
      pdb=" N   PCW A 804 " occ=0.00
      ... (52 atoms not shown)
      pdb=" P   PCW A 804 " occ=0.00
    residue:
      pdb=" N   PCW A 805 " occ=0.00
      ... (52 atoms not shown)
      pdb=" P   PCW A 805 " occ=0.00
    residue:
      pdb=" N   PCW A 806 " occ=0.00
      ... (52 atoms not shown)
      pdb=" P   PCW A 806 " occ=0.00
    residue:
      pdb=" N   PCW A 807 " occ=0.00
      ... (52 atoms not shown)
      pdb=" P   PCW A 807 " occ=0.00
  Time building chain proxies: 6.97, per 1000 atoms: 0.60
  Number of scatterers: 11668
  At special positions: 0
  Unit cell: (98.115, 148.755, 99.17, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       7     15.00
     O    1986      8.00
     N    1847      7.00
     C    7776      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=7, symmetry=0
  Number of additional bonds: simple=7, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.38
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2712

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 2 sheets defined
      67.4% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 25
    Processing helix  chain 'A' and resid 26 through 28
      No H-bonds generated for 'chain 'A' and resid 26 through 28'
    Processing helix  chain 'A' and resid 39 through 43
      removed outlier: 4.155A  pdb=" N   TRP A  42 " --> pdb=" O   PHE A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 92 through 125
      removed outlier: 4.592A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 133 through 141
      removed outlier: 3.795A  pdb=" N   LEU A 136 " --> pdb=" O   ALA A 133 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   ASN A 138 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL A 139 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 158 through 194
      removed outlier: 3.874A  pdb=" N   HIS A 162 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 228
    Processing helix  chain 'A' and resid 243 through 269
    Processing helix  chain 'A' and resid 291 through 313
      removed outlier: 3.937A  pdb=" N   GLU A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLU A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL A 313 " --> pdb=" O   ARG A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'A' and resid 367 through 388
    Processing helix  chain 'A' and resid 390 through 400
    Processing helix  chain 'A' and resid 408 through 412
      removed outlier: 3.732A  pdb=" N   LEU A 412 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 452
      Proline residue:  A 430  - end of helix
      removed outlier: 3.664A  pdb=" N   LEU A 434 " --> pdb=" O   PRO A 430 " (cutoff:3.500A)
      Proline residue:  A 442  - end of helix
      removed outlier: 3.760A  pdb=" N   GLU A 452 " --> pdb=" O   MET A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 482
    Processing helix  chain 'A' and resid 485 through 495
    Processing helix  chain 'A' and resid 500 through 532
      Proline residue:  A 510  - end of helix
      removed outlier: 4.593A  pdb=" N   THR A 514 " --> pdb=" O   PRO A 510 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   PHE A 515 " --> pdb=" O   MET A 511 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A 532 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 548
      removed outlier: 4.025A  pdb=" N   LEU A 538 " --> pdb=" O   MET A 534 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A 543 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ALA A 546 " --> pdb=" O   HIS A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 583
    Processing helix  chain 'A' and resid 589 through 612
      removed outlier: 4.241A  pdb=" N   PHE A 593 " --> pdb=" O   MET A 589 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 595 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ARG A 606 " --> pdb=" O   TYR A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 649
    Processing helix  chain 'A' and resid 654 through 676
      Proline residue:  A 662  - end of helix
    Processing helix  chain 'A' and resid 677 through 681
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 709
      removed outlier: 3.747A  pdb=" N   TYR A 707 " --> pdb=" O   ASN A 703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 26 through 28
      No H-bonds generated for 'chain 'B' and resid 26 through 28'
    Processing helix  chain 'B' and resid 39 through 43
      removed outlier: 4.154A  pdb=" N   TRP B  42 " --> pdb=" O   PHE B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 92 through 125
      removed outlier: 4.592A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
      Proline residue:  B 122  - end of helix
    Processing helix  chain 'B' and resid 133 through 141
      removed outlier: 3.794A  pdb=" N   LEU B 136 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   ASN B 138 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   VAL B 139 " --> pdb=" O   LEU B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 152
    Processing helix  chain 'B' and resid 158 through 194
      removed outlier: 3.875A  pdb=" N   HIS B 162 " --> pdb=" O   ARG B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 201
    Processing helix  chain 'B' and resid 216 through 228
    Processing helix  chain 'B' and resid 243 through 269
    Processing helix  chain 'B' and resid 291 through 313
      removed outlier: 3.936A  pdb=" N   GLU B 310 " --> pdb=" O   SER B 306 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLU B 311 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   VAL B 313 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 339
    Processing helix  chain 'B' and resid 367 through 388
    Processing helix  chain 'B' and resid 390 through 400
    Processing helix  chain 'B' and resid 408 through 412
      removed outlier: 3.732A  pdb=" N   LEU B 412 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 452
      Proline residue:  B 430  - end of helix
      removed outlier: 3.664A  pdb=" N   LEU B 434 " --> pdb=" O   PRO B 430 " (cutoff:3.500A)
      Proline residue:  B 442  - end of helix
      removed outlier: 3.761A  pdb=" N   GLU B 452 " --> pdb=" O   MET B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 482
    Processing helix  chain 'B' and resid 485 through 495
    Processing helix  chain 'B' and resid 500 through 532
      Proline residue:  B 510  - end of helix
      removed outlier: 4.593A  pdb=" N   THR B 514 " --> pdb=" O   PRO B 510 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   PHE B 515 " --> pdb=" O   MET B 511 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE B 532 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 548
      removed outlier: 4.024A  pdb=" N   LEU B 538 " --> pdb=" O   MET B 534 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 543 " --> pdb=" O   ILE B 539 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B 546 " --> pdb=" O   HIS B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 583
    Processing helix  chain 'B' and resid 589 through 612
      removed outlier: 4.241A  pdb=" N   PHE B 593 " --> pdb=" O   MET B 589 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B 595 " --> pdb=" O   LEU B 591 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ARG B 606 " --> pdb=" O   TYR B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 649
    Processing helix  chain 'B' and resid 654 through 676
      Proline residue:  B 662  - end of helix
    Processing helix  chain 'B' and resid 677 through 681
    Processing helix  chain 'B' and resid 684 through 699
    Processing helix  chain 'B' and resid 703 through 709
      removed outlier: 3.746A  pdb=" N   TYR B 707 " --> pdb=" O   ASN B 703 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238
    Processing sheet with id=AA2, first strand: chain 'B' and resid 235 through 238

    685 hydrogen bonds defined for protein.
    1983 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.34

  Time building geometry restraints manager: 3.77 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1762
        1.31 -     1.44: 3314
        1.44 -     1.56: 6753
        1.56 -     1.69: 52
        1.69 -     1.81: 96
  Bond restraints: 11977
  Sorted by residual:
  bond pdb=" C14 PCW A 804 "
       pdb=" C15 PCW A 804 "
    ideal  model  delta    sigma   weight residual
    1.523  1.630 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" C11 PCW A 807 "
       pdb=" O3  PCW A 807 "
    ideal  model  delta    sigma   weight residual
    1.326  1.429 -0.103 2.00e-02 2.50e+03 2.64e+01
  bond pdb=" C11 PCW A 804 "
       pdb=" O3  PCW A 804 "
    ideal  model  delta    sigma   weight residual
    1.326  1.428 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C11 PCW A 806 "
       pdb=" O3  PCW A 806 "
    ideal  model  delta    sigma   weight residual
    1.326  1.428 -0.102 2.00e-02 2.50e+03 2.58e+01
  bond pdb=" C11 PCW A 801 "
       pdb=" O3  PCW A 801 "
    ideal  model  delta    sigma   weight residual
    1.326  1.427 -0.101 2.00e-02 2.50e+03 2.55e+01
  ... (remaining 11972 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 15796
        2.88 -     5.76: 330
        5.76 -     8.64: 58
        8.64 -    11.52: 23
       11.52 -    14.40: 14
  Bond angle restraints: 16221
  Sorted by residual:
  angle pdb=" O3P PCW A 802 "
        pdb=" P   PCW A 802 "
        pdb=" O4P PCW A 802 "
      ideal   model   delta    sigma   weight residual
      96.85  111.25  -14.40 3.00e+00 1.11e-01 2.30e+01
  angle pdb=" C5  PCW A 803 "
        pdb=" N   PCW A 803 "
        pdb=" C7  PCW A 803 "
      ideal   model   delta    sigma   weight residual
     107.31  120.91  -13.60 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" C5  PCW A 802 "
        pdb=" N   PCW A 802 "
        pdb=" C7  PCW A 802 "
      ideal   model   delta    sigma   weight residual
     107.31  120.83  -13.52 3.00e+00 1.11e-01 2.03e+01
  angle pdb=" C   ARG B 675 "
        pdb=" CA  ARG B 675 "
        pdb=" CB  ARG B 675 "
      ideal   model   delta    sigma   weight residual
     111.03  102.78    8.25 1.87e+00 2.86e-01 1.95e+01
  angle pdb=" O3P PCW A 801 "
        pdb=" P   PCW A 801 "
        pdb=" O4P PCW A 801 "
      ideal   model   delta    sigma   weight residual
      96.85  109.97  -13.12 3.00e+00 1.11e-01 1.91e+01
  ... (remaining 16216 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.56: 6939
       34.56 -    69.12: 196
       69.12 -   103.68: 18
      103.68 -   138.24: 4
      138.24 -   172.80: 2
  Dihedral angle restraints: 7159
    sinusoidal: 2985
      harmonic: 4174
  Sorted by residual:
  dihedral pdb=" CA  ARG B 682 "
           pdb=" C   ARG B 682 "
           pdb=" N   TYR B 683 "
           pdb=" CA  TYR B 683 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.82  -27.18     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  ARG A 682 "
           pdb=" C   ARG A 682 "
           pdb=" N   TYR A 683 "
           pdb=" CA  TYR A 683 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.83  -27.17     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  VAL B 612 "
           pdb=" C   VAL B 612 "
           pdb=" N   TYR B 613 "
           pdb=" CA  TYR B 613 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.17   25.83     0      5.00e+00 4.00e-02 2.67e+01
  ... (remaining 7156 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1449
       0.058 -    0.116: 290
       0.116 -    0.174: 40
       0.174 -    0.232: 10
       0.232 -    0.290: 4
  Chirality restraints: 1793
  Sorted by residual:
  chirality pdb=" C2  PCW A 807 "
            pdb=" C1  PCW A 807 "
            pdb=" C3  PCW A 807 "
            pdb=" O2  PCW A 807 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.61    0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" C2  PCW A 805 "
            pdb=" C1  PCW A 805 "
            pdb=" C3  PCW A 805 "
            pdb=" O2  PCW A 805 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.58    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" C2  PCW A 804 "
            pdb=" C1  PCW A 804 "
            pdb=" C3  PCW A 804 "
            pdb=" O2  PCW A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.56    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1790 not shown)

  Planarity restraints: 2002
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 PCW A 804 "    0.022 2.00e-02 2.50e+03   3.97e-02 1.58e+01
        pdb=" C39 PCW A 804 "   -0.050 2.00e-02 2.50e+03
        pdb=" C40 PCW A 804 "    0.052 2.00e-02 2.50e+03
        pdb=" C41 PCW A 804 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  84 "    0.059 5.00e-02 4.00e+02   8.93e-02 1.28e+01
        pdb=" N   PRO A  85 "   -0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A  85 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A  85 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  84 "   -0.059 5.00e-02 4.00e+02   8.93e-02 1.27e+01
        pdb=" N   PRO B  85 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO B  85 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B  85 "   -0.050 5.00e-02 4.00e+02
  ... (remaining 1999 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 8
        2.22 -     2.89: 4656
        2.89 -     3.56: 17669
        3.56 -     4.23: 25752
        4.23 -     4.90: 44600
  Nonbonded interactions: 92685
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 188 "
            pdb=" O   ALA A 620 "
     model   vdw
     1.547 3.120
  nonbonded pdb=" NH1 ARG B 188 "
            pdb=" O   ALA B 620 "
     model   vdw
     1.550 3.120
  nonbonded pdb=" NH1 ARG A 188 "
            pdb=" C   ALA A 620 "
     model   vdw
     2.088 3.350
  nonbonded pdb=" NH1 ARG B 188 "
            pdb=" C   ALA B 620 "
     model   vdw
     2.092 3.350
  nonbonded pdb=" ND2 ASN A 257 "
            pdb=" OD2 ASP A 554 "
     model   vdw
     2.194 3.120
  ... (remaining 92680 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 3 through 718)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.97
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.690
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
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      :  0.009   0.107  11977  Z= 0.572
  Angle     :  1.091  14.398  16221  Z= 0.519
  Chirality :  0.050   0.290   1793
  Planarity :  0.007   0.089   2002
  Dihedral  : 16.782 172.801   4447
  Min Nonbonded Distance : 1.547

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.52 (0.22), residues: 1402
  helix:  0.13 (0.18), residues: 832
  sheet:  None (None), residues: 0
  loop : -2.81 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 624 
 HIS   0.004   0.001   HIS A  90 
 PHE   0.017   0.002   PHE B 598 
 TYR   0.030   0.002   TYR B 181 
 ARG   0.014   0.001   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.9221 (tptm) cc_final: 0.8987 (tptp)
REVERT: A  307 LYS cc_start: 0.8231 (tptp) cc_final: 0.7897 (tptp)
REVERT: A  650 HIS cc_start: 0.7976 (m170) cc_final: 0.7753 (m170)
REVERT: B  165 MET cc_start: 0.8072 (mmp) cc_final: 0.7587 (mmp)
REVERT: B  167 TYR cc_start: 0.8730 (m-80) cc_final: 0.8447 (m-80)
REVERT: B  300 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8374 (mtmt)
REVERT: B  303 LYS cc_start: 0.9190 (tptm) cc_final: 0.8952 (mmmm)
REVERT: B  307 LYS cc_start: 0.8374 (tptp) cc_final: 0.8018 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2602
  time to fit residues: 71.8181
Evaluate side-chains
  155 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 109 optimal weight:    5.9990
   chunk 42 optimal weight:    0.3980
   chunk 66 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0770
   chunk 127 optimal weight:    0.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 257 ASN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 GLN
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 257 ASN
B 574 GLN
B 639 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.178741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138205 restraints weight = 17940.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 2.46
r_work: 0.3556 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11977  Z= 0.200
  Angle     :  0.713   7.908  16221  Z= 0.366
  Chirality :  0.044   0.158   1793
  Planarity :  0.006   0.068   2002
  Dihedral  : 14.574 150.609   1831
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  8.57 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.23), residues: 1402
  helix:  1.17 (0.19), residues: 812
  sheet: -2.05 (0.87), residues: 34
  loop : -2.90 (0.25), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 624 
 HIS   0.002   0.001   HIS B 607 
 PHE   0.033   0.002   PHE A  72 
 TYR   0.027   0.002   TYR B 181 
 ARG   0.013   0.001   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8497 (pp30)
REVERT: A  303 LYS cc_start: 0.9279 (tptm) cc_final: 0.8972 (tptp)
REVERT: A  307 LYS cc_start: 0.8564 (tptp) cc_final: 0.8130 (tptp)
REVERT: A  451 PHE cc_start: 0.8324 (t80) cc_final: 0.8079 (t80)
REVERT: A  613 TYR cc_start: 0.6902 (m-80) cc_final: 0.6257 (m-80)
REVERT: A  650 HIS cc_start: 0.8094 (m170) cc_final: 0.7855 (m170)
REVERT: B  125 TRP cc_start: 0.7822 (t60) cc_final: 0.7463 (t-100)
REVERT: B  165 MET cc_start: 0.8145 (mmp) cc_final: 0.7848 (mmp)
REVERT: B  182 GLU cc_start: 0.7729 (tt0) cc_final: 0.7435 (tt0)
REVERT: B  303 LYS cc_start: 0.9271 (tptm) cc_final: 0.8960 (tptp)
REVERT: B  307 LYS cc_start: 0.8626 (tptp) cc_final: 0.8236 (tptp)
REVERT: B  437 PHE cc_start: 0.7821 (t80) cc_final: 0.7597 (t80)
REVERT: B  521 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6267 (mpp)
REVERT: B  613 TYR cc_start: 0.6953 (m-80) cc_final: 0.6394 (m-80)
  outliers start: 14
  outliers final: 5
  residues processed: 190
  average time/residue: 0.2170
  time to fit residues: 60.7649
Evaluate side-chains
  169 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 163
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASN
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  521 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 96 optimal weight:   50.0000
   chunk 6 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 127 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    0.1980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 ASN
B 489 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.178817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138646 restraints weight = 18132.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.44
r_work: 0.3574 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11977  Z= 0.201
  Angle     :  0.666   8.013  16221  Z= 0.342
  Chirality :  0.043   0.160   1793
  Planarity :  0.006   0.061   2002
  Dihedral  : 14.142 152.186   1831
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.26 %
    Favored  : 86.72 %
  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 (0.24), residues: 1402
  helix:  1.38 (0.19), residues: 824
  sheet: -1.10 (1.12), residues: 22
  loop : -2.72 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 624 
 HIS   0.002   0.001   HIS B 232 
 PHE   0.030   0.001   PHE A 389 
 TYR   0.025   0.002   TYR B 181 
 ARG   0.010   0.000   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7380 (mmt) cc_final: 0.7102 (mmp)
REVERT: A   86 GLU cc_start: 0.7915 (tp30) cc_final: 0.7663 (tp30)
REVERT: A  297 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5939 (mp0)
REVERT: A  303 LYS cc_start: 0.9248 (tptm) cc_final: 0.8930 (tptp)
REVERT: A  304 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7077 (pm20)
REVERT: A  307 LYS cc_start: 0.8598 (tptp) cc_final: 0.8171 (tptp)
REVERT: A  613 TYR cc_start: 0.7175 (m-80) cc_final: 0.6448 (m-80)
REVERT: B   70 MET cc_start: 0.7025 (mmt) cc_final: 0.6818 (mmp)
REVERT: B  124 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7672 (t0)
REVERT: B  125 TRP cc_start: 0.8077 (t60) cc_final: 0.7705 (t-100)
REVERT: B  165 MET cc_start: 0.8097 (mmp) cc_final: 0.7769 (mmp)
REVERT: B  182 GLU cc_start: 0.7633 (tt0) cc_final: 0.7396 (tt0)
REVERT: B  200 ASP cc_start: 0.8849 (p0) cc_final: 0.8620 (p0)
REVERT: B  297 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6475 (mp0)
REVERT: B  303 LYS cc_start: 0.9262 (tptm) cc_final: 0.8930 (tptp)
REVERT: B  304 GLU cc_start: 0.7660 (mp0) cc_final: 0.7438 (pm20)
REVERT: B  307 LYS cc_start: 0.8650 (tptp) cc_final: 0.8283 (tptp)
REVERT: B  613 TYR cc_start: 0.7147 (m-80) cc_final: 0.6509 (m-80)
  outliers start: 24
  outliers final: 11
  residues processed: 187
  average time/residue: 0.2146
  time to fit residues: 59.5155
Evaluate side-chains
  176 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue  124 ASN
Chi-restraints excluded: chain B residue  146 LYS
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  549 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 44 optimal weight:    0.2980
   chunk 136 optimal weight:    0.6980
   chunk 133 optimal weight:    6.9990
   chunk 135 optimal weight:    1.9990
   chunk 123 optimal weight:    0.3980
   chunk 91 optimal weight:    0.5980
   chunk 100 optimal weight:    0.0980
   chunk 131 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
** A 574 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 = 0.4178 r_free = 0.4178 target = 0.181632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.141334 restraints weight = 17972.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.51
r_work: 0.3593 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11977  Z= 0.169
  Angle     :  0.636   7.805  16221  Z= 0.326
  Chirality :  0.042   0.158   1793
  Planarity :  0.005   0.058   2002
  Dihedral  : 13.716 162.782   1831
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.53 %
    Favored  : 84.37 %
  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: -0.13 (0.24), residues: 1402
  helix:  1.51 (0.19), residues: 826
  sheet: -0.90 (1.13), residues: 22
  loop : -2.70 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 624 
 HIS   0.002   0.000   HIS B 628 
 PHE   0.032   0.001   PHE A  72 
 TYR   0.024   0.001   TYR B 181 
 ARG   0.010   0.000   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7210 (mmt) cc_final: 0.6935 (mmp)
REVERT: A   86 GLU cc_start: 0.7904 (tp30) cc_final: 0.7629 (tp30)
REVERT: A  200 ASP cc_start: 0.8615 (p0) cc_final: 0.8147 (p0)
REVERT: A  297 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6021 (mp0)
REVERT: A  303 LYS cc_start: 0.9254 (tptm) cc_final: 0.8934 (tptp)
REVERT: A  307 LYS cc_start: 0.8627 (tptp) cc_final: 0.8091 (tptp)
REVERT: A  437 PHE cc_start: 0.7721 (t80) cc_final: 0.7510 (t80)
REVERT: A  589 MET cc_start: 0.8175 (mmm) cc_final: 0.7906 (mmm)
REVERT: A  613 TYR cc_start: 0.7143 (m-80) cc_final: 0.6420 (m-80)
REVERT: B  125 TRP cc_start: 0.8167 (t60) cc_final: 0.7736 (t-100)
REVERT: B  165 MET cc_start: 0.7999 (mmp) cc_final: 0.7786 (mmp)
REVERT: B  182 GLU cc_start: 0.7627 (tt0) cc_final: 0.7396 (tt0)
REVERT: B  297 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6525 (mp0)
REVERT: B  303 LYS cc_start: 0.9267 (tptm) cc_final: 0.8960 (tptp)
REVERT: B  307 LYS cc_start: 0.8657 (tptp) cc_final: 0.8295 (tptp)
REVERT: B  613 TYR cc_start: 0.7082 (m-80) cc_final: 0.6567 (m-80)
  outliers start: 25
  outliers final: 14
  residues processed: 197
  average time/residue: 0.2143
  time to fit residues: 62.8108
Evaluate side-chains
  185 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  489 GLN
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  549 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   chunk 126 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0070
   chunk 43 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 124 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN
B 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.179905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.139969 restraints weight = 17762.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.47
r_work: 0.3571 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11977  Z= 0.203
  Angle     :  0.648   7.932  16221  Z= 0.333
  Chirality :  0.043   0.192   1793
  Planarity :  0.005   0.056   2002
  Dihedral  : 13.397 173.008   1831
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.87 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.24), residues: 1402
  helix:  1.55 (0.19), residues: 832
  sheet: -0.79 (1.15), residues: 22
  loop : -2.60 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 628 
 PHE   0.034   0.001   PHE B  72 
 TYR   0.027   0.001   TYR B 181 
 ARG   0.010   0.000   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.7976 (tp30) cc_final: 0.7633 (tp30)
REVERT: A  122 PRO cc_start: 0.8877 (Cg_exo) cc_final: 0.8513 (Cg_endo)
REVERT: A  127 ASN cc_start: 0.7766 (p0) cc_final: 0.7009 (m-40)
REVERT: A  297 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6068 (mp0)
REVERT: A  303 LYS cc_start: 0.9239 (tptm) cc_final: 0.8919 (tptp)
REVERT: A  307 LYS cc_start: 0.8644 (tptp) cc_final: 0.8111 (tptp)
REVERT: A  437 PHE cc_start: 0.7719 (t80) cc_final: 0.7491 (t80)
REVERT: A  521 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5366 (mpp)
REVERT: A  613 TYR cc_start: 0.7300 (m-80) cc_final: 0.6467 (m-80)
REVERT: A  709 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7742 (pp30)
REVERT: B  125 TRP cc_start: 0.8143 (t60) cc_final: 0.7684 (t-100)
REVERT: B  165 MET cc_start: 0.8096 (mmp) cc_final: 0.7821 (mmp)
REVERT: B  182 GLU cc_start: 0.7686 (tt0) cc_final: 0.7450 (tt0)
REVERT: B  297 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6370 (mp0)
REVERT: B  303 LYS cc_start: 0.9252 (tptm) cc_final: 0.8948 (tptp)
REVERT: B  307 LYS cc_start: 0.8720 (tptp) cc_final: 0.8367 (tptp)
REVERT: B  598 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6856 (m-10)
REVERT: B  613 TYR cc_start: 0.7243 (m-80) cc_final: 0.6625 (m-80)
  outliers start: 32
  outliers final: 17
  residues processed: 202
  average time/residue: 0.2121
  time to fit residues: 64.0829
Evaluate side-chains
  193 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  489 GLN
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  598 PHE
Chi-restraints excluded: chain B residue  653 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 101 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0270
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.9640

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN
** B 124 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 = 0.4155 r_free = 0.4155 target = 0.179616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.139804 restraints weight = 17969.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.50
r_work: 0.3563 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11977  Z= 0.209
  Angle     :  0.659   9.522  16221  Z= 0.335
  Chirality :  0.043   0.160   1793
  Planarity :  0.005   0.056   2002
  Dihedral  : 13.239 178.772   1831
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.47 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.24), residues: 1402
  helix:  1.56 (0.19), residues: 832
  sheet: -0.86 (1.13), residues: 22
  loop : -2.58 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 628 
 PHE   0.030   0.001   PHE A  72 
 TYR   0.028   0.001   TYR B 181 
 ARG   0.010   0.000   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 176
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7426 (mmt) cc_final: 0.7164 (mmp)
REVERT: A  122 PRO cc_start: 0.8907 (Cg_exo) cc_final: 0.8702 (Cg_endo)
REVERT: A  127 ASN cc_start: 0.7792 (p0) cc_final: 0.7051 (m-40)
REVERT: A  297 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6005 (mp0)
REVERT: A  303 LYS cc_start: 0.9245 (tptm) cc_final: 0.8924 (tptp)
REVERT: A  307 LYS cc_start: 0.8661 (tptp) cc_final: 0.8140 (tptp)
REVERT: A  437 PHE cc_start: 0.7661 (t80) cc_final: 0.7429 (t80)
REVERT: A  521 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5382 (mpp)
REVERT: A  613 TYR cc_start: 0.7358 (m-80) cc_final: 0.6538 (m-80)
REVERT: A  709 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7736 (pp30)
REVERT: B   44 LEU cc_start: 0.3493 (OUTLIER) cc_final: 0.3118 (mp)
REVERT: B  125 TRP cc_start: 0.8092 (t60) cc_final: 0.7696 (t-100)
REVERT: B  182 GLU cc_start: 0.7728 (tt0) cc_final: 0.7510 (tt0)
REVERT: B  297 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6395 (mp0)
REVERT: B  303 LYS cc_start: 0.9271 (tptm) cc_final: 0.8958 (tptp)
REVERT: B  307 LYS cc_start: 0.8731 (tptp) cc_final: 0.8369 (tptp)
REVERT: B  613 TYR cc_start: 0.7160 (m-80) cc_final: 0.6544 (m-80)
  outliers start: 28
  outliers final: 18
  residues processed: 193
  average time/residue: 0.2278
  time to fit residues: 65.5247
Evaluate side-chains
  194 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  489 GLN
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  653 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN
** B 124 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 = 0.4146 r_free = 0.4146 target = 0.178635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.138506 restraints weight = 18106.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.51
r_work: 0.3554 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11977  Z= 0.237
  Angle     :  0.673   9.967  16221  Z= 0.344
  Chirality :  0.044   0.182   1793
  Planarity :  0.005   0.054   2002
  Dihedral  : 13.030 176.102   1831
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.72 %
    Favored  : 80.76 %
  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:  0.04 (0.24), residues: 1402
  helix:  1.58 (0.19), residues: 832
  sheet: -0.84 (1.13), residues: 22
  loop : -2.56 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 624 
 HIS   0.004   0.001   HIS B 628 
 PHE   0.030   0.001   PHE B  72 
 TYR   0.029   0.002   TYR B 181 
 ARG   0.009   0.000   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 176
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7433 (mmt) cc_final: 0.7180 (mmp)
REVERT: A  122 PRO cc_start: 0.9011 (Cg_exo) cc_final: 0.8643 (Cg_endo)
REVERT: A  127 ASN cc_start: 0.7661 (p0) cc_final: 0.7008 (m-40)
REVERT: A  297 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5963 (mp0)
REVERT: A  303 LYS cc_start: 0.9252 (tptm) cc_final: 0.8931 (tptp)
REVERT: A  307 LYS cc_start: 0.8673 (tptp) cc_final: 0.8163 (tptp)
REVERT: A  521 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5343 (mpp)
REVERT: A  613 TYR cc_start: 0.7304 (m-80) cc_final: 0.6522 (m-80)
REVERT: B   44 LEU cc_start: 0.3354 (OUTLIER) cc_final: 0.2815 (mt)
REVERT: B  125 TRP cc_start: 0.8082 (t60) cc_final: 0.7714 (t-100)
REVERT: B  182 GLU cc_start: 0.7734 (tt0) cc_final: 0.7523 (tt0)
REVERT: B  297 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6446 (mp0)
REVERT: B  303 LYS cc_start: 0.9278 (tptm) cc_final: 0.8960 (tptp)
REVERT: B  307 LYS cc_start: 0.8730 (tptp) cc_final: 0.8358 (tptp)
REVERT: B  613 TYR cc_start: 0.7093 (m-80) cc_final: 0.6489 (m-80)
  outliers start: 30
  outliers final: 19
  residues processed: 194
  average time/residue: 0.2432
  time to fit residues: 70.2289
Evaluate side-chains
  191 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 1.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue   43 TYR
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  489 GLN
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  653 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 128 optimal weight:    0.9980
   chunk 123 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 113 optimal weight:    0.0980
   chunk 96 optimal weight:    8.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 397 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 = 0.4157 r_free = 0.4157 target = 0.179684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.139763 restraints weight = 18038.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.51
r_work: 0.3567 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  11977  Z= 0.213
  Angle     :  0.675   9.954  16221  Z= 0.345
  Chirality :  0.043   0.174   1793
  Planarity :  0.005   0.054   2002
  Dihedral  : 12.693 170.762   1831
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.65 %
    Favored  : 80.00 %
  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:  0.07 (0.24), residues: 1402
  helix:  1.63 (0.19), residues: 830
  sheet: -1.31 (1.20), residues: 20
  loop : -2.54 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 628 
 PHE   0.031   0.001   PHE B  72 
 TYR   0.029   0.001   TYR B 181 
 ARG   0.009   0.000   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 1.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7262 (mmt) cc_final: 0.6990 (mmp)
REVERT: A  127 ASN cc_start: 0.7745 (p0) cc_final: 0.6898 (m-40)
REVERT: A  297 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5953 (mp0)
REVERT: A  303 LYS cc_start: 0.9258 (tptm) cc_final: 0.8937 (tptp)
REVERT: A  307 LYS cc_start: 0.8699 (tptp) cc_final: 0.8266 (tptp)
REVERT: A  320 MET cc_start: 0.8391 (ptp) cc_final: 0.8045 (pmm)
REVERT: A  521 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5278 (mpp)
REVERT: A  613 TYR cc_start: 0.7299 (m-80) cc_final: 0.6509 (m-80)
REVERT: B   44 LEU cc_start: 0.3334 (OUTLIER) cc_final: 0.2857 (mt)
REVERT: B  125 TRP cc_start: 0.8068 (t60) cc_final: 0.7704 (t-100)
REVERT: B  182 GLU cc_start: 0.7716 (tt0) cc_final: 0.7512 (tt0)
REVERT: B  297 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6375 (mp0)
REVERT: B  303 LYS cc_start: 0.9287 (tptm) cc_final: 0.8961 (tptp)
REVERT: B  307 LYS cc_start: 0.8740 (tptp) cc_final: 0.8360 (tptp)
REVERT: B  613 TYR cc_start: 0.7085 (m-80) cc_final: 0.6465 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 193
  average time/residue: 0.2216
  time to fit residues: 63.4434
Evaluate side-chains
  196 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain B residue   43 TYR
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  489 GLN
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  653 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 121 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 104 optimal weight:    0.1980
   chunk 130 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 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 = 0.4117 r_free = 0.4117 target = 0.176105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.135803 restraints weight = 18070.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.50
r_work: 0.3519 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  11977  Z= 0.305
  Angle     :  0.721   9.995  16221  Z= 0.370
  Chirality :  0.045   0.201   1793
  Planarity :  0.006   0.053   2002
  Dihedral  : 12.505 167.132   1831
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.40 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.24), residues: 1402
  helix:  1.61 (0.19), residues: 818
  sheet: -1.28 (1.20), residues: 20
  loop : -2.50 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 117 
 HIS   0.004   0.001   HIS B  90 
 PHE   0.027   0.002   PHE A 389 
 TYR   0.032   0.002   TYR B 181 
 ARG   0.008   0.001   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 1.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7343 (mmt) cc_final: 0.7086 (mmp)
REVERT: A  122 PRO cc_start: 0.9001 (Cg_exo) cc_final: 0.8639 (Cg_endo)
REVERT: A  127 ASN cc_start: 0.7835 (p0) cc_final: 0.7072 (m-40)
REVERT: A  297 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5976 (mp0)
REVERT: A  303 LYS cc_start: 0.9260 (tptm) cc_final: 0.8937 (tptp)
REVERT: A  307 LYS cc_start: 0.8726 (tptp) cc_final: 0.8291 (tptp)
REVERT: A  320 MET cc_start: 0.8419 (ptp) cc_final: 0.8038 (pmm)
REVERT: A  521 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5353 (mpp)
REVERT: A  613 TYR cc_start: 0.7206 (m-80) cc_final: 0.6438 (m-80)
REVERT: B   44 LEU cc_start: 0.3523 (OUTLIER) cc_final: 0.2986 (mt)
REVERT: B  125 TRP cc_start: 0.8077 (t60) cc_final: 0.7696 (t-100)
REVERT: B  165 MET cc_start: 0.8088 (mmp) cc_final: 0.7610 (mmp)
REVERT: B  182 GLU cc_start: 0.7686 (tt0) cc_final: 0.7474 (tt0)
REVERT: B  263 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8567 (pp30)
REVERT: B  297 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6488 (mp0)
REVERT: B  303 LYS cc_start: 0.9287 (tptm) cc_final: 0.8945 (tptp)
REVERT: B  307 LYS cc_start: 0.8772 (tptp) cc_final: 0.8378 (tptp)
REVERT: B  613 TYR cc_start: 0.7112 (m-80) cc_final: 0.6496 (m-80)
  outliers start: 25
  outliers final: 19
  residues processed: 185
  average time/residue: 0.2250
  time to fit residues: 60.7697
Evaluate side-chains
  193 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  489 GLN
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  653 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 136 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 135 optimal weight:    0.6980
   chunk 110 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 66 optimal weight:    0.4980
   chunk 101 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 397 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 = 0.4162 r_free = 0.4162 target = 0.180379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.140386 restraints weight = 17996.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.52
r_work: 0.3578 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  11977  Z= 0.201
  Angle     :  0.693  10.899  16221  Z= 0.354
  Chirality :  0.043   0.177   1793
  Planarity :  0.005   0.053   2002
  Dihedral  : 12.251 164.171   1831
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.74 %
    Favored  : 79.33 %
  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:  0.11 (0.24), residues: 1402
  helix:  1.67 (0.19), residues: 828
  sheet: -1.37 (1.19), residues: 20
  loop : -2.53 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 624 
 HIS   0.004   0.001   HIS B 650 
 PHE   0.031   0.001   PHE A  72 
 TYR   0.029   0.001   TYR B 181 
 ARG   0.008   0.000   ARG B 630 

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

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

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2804 Ramachandran restraints generated.
    1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 179
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7223 (mmt) cc_final: 0.6950 (mmp)
REVERT: A  297 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5968 (mp0)
REVERT: A  303 LYS cc_start: 0.9240 (tptm) cc_final: 0.8921 (tptp)
REVERT: A  307 LYS cc_start: 0.8719 (tptp) cc_final: 0.8285 (tptp)
REVERT: A  320 MET cc_start: 0.8347 (ptp) cc_final: 0.8022 (pmm)
REVERT: A  521 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5243 (mpp)
REVERT: A  613 TYR cc_start: 0.7219 (m-80) cc_final: 0.6478 (m-80)
REVERT: B   44 LEU cc_start: 0.3353 (OUTLIER) cc_final: 0.2917 (mt)
REVERT: B  125 TRP cc_start: 0.8132 (t60) cc_final: 0.7713 (t-100)
REVERT: B  165 MET cc_start: 0.7848 (mmp) cc_final: 0.7543 (mmt)
REVERT: B  182 GLU cc_start: 0.7717 (tt0) cc_final: 0.7507 (tt0)
REVERT: B  263 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8550 (pp30)
REVERT: B  297 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6433 (mp0)
REVERT: B  303 LYS cc_start: 0.9271 (tptm) cc_final: 0.8957 (tptp)
REVERT: B  307 LYS cc_start: 0.8750 (tptp) cc_final: 0.8359 (tptp)
REVERT: B  547 PHE cc_start: 0.8526 (m-10) cc_final: 0.8320 (m-10)
REVERT: B  613 TYR cc_start: 0.7070 (m-80) cc_final: 0.6432 (m-80)
  outliers start: 23
  outliers final: 18
  residues processed: 193
  average time/residue: 0.2238
  time to fit residues: 63.8403
Evaluate side-chains
  193 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  709 GLN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  317 LYS
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  489 GLN
Chi-restraints excluded: chain B residue  517 ILE
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  549 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 129 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0010
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 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 = 0.4161 r_free = 0.4161 target = 0.180188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.140532 restraints weight = 17927.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.50
r_work: 0.3577 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.243  11977  Z= 0.347
  Angle     :  0.942  59.188  16221  Z= 0.520
  Chirality :  0.045   0.532   1793
  Planarity :  0.005   0.053   2002
  Dihedral  : 12.247 164.162   1831
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.49 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.07 %
  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:  0.11 (0.24), residues: 1402
  helix:  1.67 (0.19), residues: 828
  sheet: -1.37 (1.19), residues: 20
  loop : -2.53 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 624 
 HIS   0.003   0.001   HIS B 650 
 PHE   0.031   0.001   PHE A  72 
 TYR   0.029   0.001   TYR B 181 
 ARG   0.009   0.000   ARG B 630 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4739.01 seconds
wall clock time: 85 minutes 53.06 seconds (5153.06 seconds total)