Starting phenix.real_space_refine
on Tue Jul 29 17:45:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xaj_38200/07_2025/8xaj_38200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xaj_38200/07_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_38200/07_2025/8xaj_38200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xaj_38200/07_2025/8xaj_38200.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xaj_38200/07_2025/8xaj_38200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xaj_38200/07_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): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.50, per 1000 atoms: 0.64
  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: 2.89
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.00
  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: 3.25

  Time building geometry restraints manager: 3.47 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:             1.200
  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:             0.020
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.780
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.040
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.080
-------------------------------------------------------------------------------
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  11984  Z= 0.426
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13776 (  685)
  hydrogen bonds       : angle       6.87951 ( 1983)
  covalent geometry    : bond        0.00860 (11977)
  covalent geometry    : angle       1.09119 (16221)
  Misc. bond           : bond        0.04136 (    7)

*********************** 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  : 1.241 
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: 0.2360
  time to fit residues: 65.5940
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  : 1.167 
-------------------------------------------------------------------------------
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 = 43)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138207 restraints weight = 17940.517|
|-----------------------------------------------------------------------------|
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  11984  Z= 0.145
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04315 (  685)
  hydrogen bonds       : angle       4.89888 ( 1983)
  covalent geometry    : bond        0.00310 (11977)
  covalent geometry    : angle       0.71299 (16221)
  Misc. bond           : bond        0.00156 (    7)

*********************** 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  : 1.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8498 (pp30)
REVERT: A  303 LYS cc_start: 0.9279 (tptm) cc_final: 0.8971 (tptp)
REVERT: A  307 LYS cc_start: 0.8563 (tptp) cc_final: 0.8128 (tptp)
REVERT: A  451 PHE cc_start: 0.8323 (t80) cc_final: 0.8079 (t80)
REVERT: A  613 TYR cc_start: 0.6903 (m-80) cc_final: 0.6257 (m-80)
REVERT: A  650 HIS cc_start: 0.8093 (m170) cc_final: 0.7854 (m170)
REVERT: B  125 TRP cc_start: 0.7821 (t60) cc_final: 0.7462 (t-100)
REVERT: B  165 MET cc_start: 0.8144 (mmp) cc_final: 0.7847 (mmp)
REVERT: B  182 GLU cc_start: 0.7727 (tt0) cc_final: 0.7433 (tt0)
REVERT: B  303 LYS cc_start: 0.9270 (tptm) cc_final: 0.8960 (tptp)
REVERT: B  307 LYS cc_start: 0.8625 (tptp) cc_final: 0.8235 (tptp)
REVERT: B  437 PHE cc_start: 0.7822 (t80) cc_final: 0.7596 (t80)
REVERT: B  521 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6266 (mpp)
REVERT: B  593 PHE cc_start: 0.6948 (m-10) cc_final: 0.6748 (m-80)
REVERT: B  613 TYR cc_start: 0.6955 (m-80) cc_final: 0.6394 (m-80)
  outliers start: 14
  outliers final: 5
  residues processed: 190
  average time/residue: 0.2101
  time to fit residues: 58.9163
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  : 1.142 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 127 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 118 optimal weight:    0.1980
   chunk 46 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    0.0980
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.180695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.140232 restraints weight = 18210.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.52
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: 0.7309
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11984  Z= 0.133
  Angle     :  0.653   7.862  16221  Z= 0.334
  Chirality :  0.043   0.161   1793
  Planarity :  0.006   0.061   2002
  Dihedral  : 14.053 154.909   1831
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.09 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.24), residues: 1402
  helix:  1.44 (0.19), residues: 824
  sheet: -1.11 (1.12), residues: 22
  loop : -2.73 (0.26), 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 232 
 PHE   0.031   0.001   PHE B  72 
 TYR   0.024   0.001   TYR B 181 
 ARG   0.010   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03891 (  685)
  hydrogen bonds       : angle       4.64484 ( 1983)
  covalent geometry    : bond        0.00282 (11977)
  covalent geometry    : angle       0.65286 (16221)
  Misc. bond           : bond        0.00123 (    7)

*********************** 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
  202 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7401 (mmt) cc_final: 0.7120 (mmp)
REVERT: A   86 GLU cc_start: 0.7923 (tp30) cc_final: 0.7676 (tp30)
REVERT: A  200 ASP cc_start: 0.8652 (p0) cc_final: 0.8225 (p0)
REVERT: A  297 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5953 (mp0)
REVERT: A  303 LYS cc_start: 0.9266 (tptm) cc_final: 0.8944 (tptp)
REVERT: A  307 LYS cc_start: 0.8615 (tptp) cc_final: 0.8178 (tptp)
REVERT: A  589 MET cc_start: 0.8163 (mmm) cc_final: 0.7838 (mmm)
REVERT: A  613 TYR cc_start: 0.7130 (m-80) cc_final: 0.6380 (m-80)
REVERT: B   70 MET cc_start: 0.7120 (mmt) cc_final: 0.6878 (mmp)
REVERT: B  124 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7636 (t0)
REVERT: B  125 TRP cc_start: 0.8024 (t60) cc_final: 0.7660 (t-100)
REVERT: B  165 MET cc_start: 0.7973 (mmp) cc_final: 0.7661 (mmp)
REVERT: B  182 GLU cc_start: 0.7602 (tt0) cc_final: 0.7366 (tt0)
REVERT: B  297 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6460 (mp0)
REVERT: B  303 LYS cc_start: 0.9270 (tptm) cc_final: 0.8960 (tptp)
REVERT: B  304 GLU cc_start: 0.7712 (mp0) cc_final: 0.7472 (mp0)
REVERT: B  307 LYS cc_start: 0.8651 (tptp) cc_final: 0.8279 (tptp)
REVERT: B  613 TYR cc_start: 0.7000 (m-80) cc_final: 0.6403 (m-80)
  outliers start: 24
  outliers final: 12
  residues processed: 193
  average time/residue: 0.2077
  time to fit residues: 59.9466
Evaluate side-chains
  182 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 136 optimal weight:    2.9990
   chunk 133 optimal weight:    6.9990
   chunk 135 optimal weight:    0.5980
   chunk 123 optimal weight:    7.9990
   chunk 91 optimal weight:    0.2980
   chunk 100 optimal weight:    0.0040
   chunk 131 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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**
A 709 GLN
B 124 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.181343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.141213 restraints weight = 17863.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.49
r_work: 0.3588 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11984  Z= 0.129
  Angle     :  0.638   7.774  16221  Z= 0.327
  Chirality :  0.042   0.159   1793
  Planarity :  0.005   0.057   2002
  Dihedral  : 13.682 163.820   1831
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.87 %
    Favored  : 84.12 %
  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:  1.53 (0.19), residues: 826
  sheet: -0.94 (1.12), residues: 22
  loop : -2.68 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 624 
 HIS   0.002   0.001   HIS A 650 
 PHE   0.032   0.001   PHE A  72 
 TYR   0.024   0.001   TYR B 181 
 ARG   0.011   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 (  685)
  hydrogen bonds       : angle       4.53789 ( 1983)
  covalent geometry    : bond        0.00278 (11977)
  covalent geometry    : angle       0.63815 (16221)
  Misc. bond           : bond        0.00112 (    7)

*********************** 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
  204 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7194 (mmt) cc_final: 0.6922 (mmp)
REVERT: A   86 GLU cc_start: 0.7913 (tp30) cc_final: 0.7627 (tp30)
REVERT: A  122 PRO cc_start: 0.8857 (Cg_exo) cc_final: 0.8506 (Cg_endo)
REVERT: A  200 ASP cc_start: 0.8671 (p0) cc_final: 0.8277 (p0)
REVERT: A  297 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6007 (mp0)
REVERT: A  303 LYS cc_start: 0.9250 (tptm) cc_final: 0.8930 (tptp)
REVERT: A  307 LYS cc_start: 0.8627 (tptp) cc_final: 0.8091 (tptp)
REVERT: A  437 PHE cc_start: 0.7732 (t80) cc_final: 0.7499 (t80)
REVERT: A  613 TYR cc_start: 0.7121 (m-80) cc_final: 0.6373 (m-80)
REVERT: A  709 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7738 (pp30)
REVERT: B  125 TRP cc_start: 0.8151 (t60) cc_final: 0.7709 (t-100)
REVERT: B  165 MET cc_start: 0.7964 (mmp) cc_final: 0.7654 (mmp)
REVERT: B  182 GLU cc_start: 0.7630 (tt0) cc_final: 0.7398 (tt0)
REVERT: B  297 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6498 (mp0)
REVERT: B  303 LYS cc_start: 0.9272 (tptm) cc_final: 0.8961 (tptp)
REVERT: B  307 LYS cc_start: 0.8659 (tptp) cc_final: 0.8296 (tptp)
REVERT: B  613 TYR cc_start: 0.6924 (m-80) cc_final: 0.6509 (m-80)
  outliers start: 24
  outliers final: 13
  residues processed: 196
  average time/residue: 0.2080
  time to fit residues: 61.0416
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  : 1.192 
-------------------------------------------------------------------------------
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  517 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  549 VAL
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  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:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   chunk 108 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 124 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.178714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.138107 restraints weight = 17884.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.50
r_work: 0.3548 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11984  Z= 0.165
  Angle     :  0.665   7.942  16221  Z= 0.342
  Chirality :  0.044   0.176   1793
  Planarity :  0.006   0.056   2002
  Dihedral  : 13.445 172.243   1831
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.29 %
    Favored  : 82.27 %
  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:  1.50 (0.19), residues: 830
  sheet: -0.82 (1.13), residues: 22
  loop : -2.61 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 624 
 HIS   0.004   0.001   HIS B 628 
 PHE   0.032   0.002   PHE B  72 
 TYR   0.030   0.002   TYR B 181 
 ARG   0.009   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  685)
  hydrogen bonds       : angle       4.58473 ( 1983)
  covalent geometry    : bond        0.00379 (11977)
  covalent geometry    : angle       0.66496 (16221)
  Misc. bond           : bond        0.00099 (    7)

*********************** 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
  207 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 178
  time to evaluate  : 1.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7237 (mmt) cc_final: 0.6960 (mmp)
REVERT: A   86 GLU cc_start: 0.7976 (tp30) cc_final: 0.7625 (tp30)
REVERT: A  127 ASN cc_start: 0.7783 (p0) cc_final: 0.7046 (m-40)
REVERT: A  297 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5983 (mp0)
REVERT: A  303 LYS cc_start: 0.9257 (tptm) cc_final: 0.8939 (tptp)
REVERT: A  307 LYS cc_start: 0.8660 (tptp) cc_final: 0.8126 (tptp)
REVERT: A  437 PHE cc_start: 0.7728 (t80) cc_final: 0.7482 (t80)
REVERT: A  521 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5485 (mpp)
REVERT: A  613 TYR cc_start: 0.7324 (m-80) cc_final: 0.6511 (m-80)
REVERT: A  709 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7672 (pp30)
REVERT: B  125 TRP cc_start: 0.8049 (t60) cc_final: 0.7658 (t-100)
REVERT: B  165 MET cc_start: 0.8102 (mmp) cc_final: 0.7879 (mmp)
REVERT: B  182 GLU cc_start: 0.7709 (tt0) cc_final: 0.7487 (tt0)
REVERT: B  297 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6350 (mp0)
REVERT: B  303 LYS cc_start: 0.9258 (tptm) cc_final: 0.8950 (tptp)
REVERT: B  307 LYS cc_start: 0.8720 (tptp) cc_final: 0.8358 (tptp)
REVERT: B  598 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6865 (m-10)
REVERT: B  613 TYR cc_start: 0.7238 (m-80) cc_final: 0.6736 (m-80)
  outliers start: 29
  outliers final: 16
  residues processed: 195
  average time/residue: 0.2654
  time to fit residues: 76.8934
Evaluate side-chains
  194 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 173
  time to evaluate  : 1.737 
-------------------------------------------------------------------------------
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  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:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 101 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 489 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.177319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.136871 restraints weight = 18044.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.49
r_work: 0.3532 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11984  Z= 0.178
  Angle     :  0.684   8.948  16221  Z= 0.351
  Chirality :  0.044   0.203   1793
  Planarity :  0.006   0.054   2002
  Dihedral  : 13.278 178.995   1831
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.39 %
    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: -0.02 (0.24), residues: 1402
  helix:  1.58 (0.19), residues: 818
  sheet: -0.86 (1.13), residues: 22
  loop : -2.56 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 624 
 HIS   0.004   0.001   HIS B 628 
 PHE   0.029   0.002   PHE B  72 
 TYR   0.031   0.002   TYR A 181 
 ARG   0.009   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03998 (  685)
  hydrogen bonds       : angle       4.64577 ( 1983)
  covalent geometry    : bond        0.00416 (11977)
  covalent geometry    : angle       0.68395 (16221)
  Misc. bond           : bond        0.00091 (    7)

*********************** 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
  200 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 1.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7267 (mmt) cc_final: 0.6990 (mmp)
REVERT: A   86 GLU cc_start: 0.8009 (tp30) cc_final: 0.7676 (tp30)
REVERT: A  127 ASN cc_start: 0.7767 (p0) cc_final: 0.7077 (m-40)
REVERT: A  263 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8461 (pp30)
REVERT: A  297 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6058 (mp0)
REVERT: A  303 LYS cc_start: 0.9258 (tptm) cc_final: 0.8935 (tptp)
REVERT: A  307 LYS cc_start: 0.8683 (tptp) cc_final: 0.8174 (tptp)
REVERT: A  320 MET cc_start: 0.8426 (ptp) cc_final: 0.8055 (pmm)
REVERT: A  437 PHE cc_start: 0.7748 (t80) cc_final: 0.7496 (t80)
REVERT: A  613 TYR cc_start: 0.7410 (m-80) cc_final: 0.6578 (m-80)
REVERT: B  125 TRP cc_start: 0.8067 (t60) cc_final: 0.7718 (t-100)
REVERT: B  182 GLU cc_start: 0.7712 (tt0) cc_final: 0.7497 (tt0)
REVERT: B  297 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6341 (mp0)
REVERT: B  303 LYS cc_start: 0.9275 (tptm) cc_final: 0.8965 (tptp)
REVERT: B  307 LYS cc_start: 0.8758 (tptp) cc_final: 0.8392 (tptp)
REVERT: B  598 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.7000 (m-10)
REVERT: B  613 TYR cc_start: 0.7158 (m-80) cc_final: 0.6544 (m-80)
  outliers start: 29
  outliers final: 20
  residues processed: 188
  average time/residue: 0.3131
  time to fit residues: 89.5472
Evaluate side-chains
  195 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
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  121 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 129 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 489 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.178372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.137962 restraints weight = 18106.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.51
r_work: 0.3545 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11984  Z= 0.152
  Angle     :  0.667   9.321  16221  Z= 0.342
  Chirality :  0.043   0.169   1793
  Planarity :  0.005   0.054   2002
  Dihedral  : 13.040 175.869   1831
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.55 %
    Favored  : 80.84 %
  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:  1.64 (0.19), residues: 818
  sheet: -0.93 (1.12), residues: 22
  loop : -2.55 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 624 
 HIS   0.004   0.001   HIS B 628 
 PHE   0.030   0.001   PHE B  72 
 TYR   0.030   0.002   TYR B 181 
 ARG   0.009   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03845 (  685)
  hydrogen bonds       : angle       4.58264 ( 1983)
  covalent geometry    : bond        0.00348 (11977)
  covalent geometry    : angle       0.66698 (16221)
  Misc. bond           : bond        0.00084 (    7)

*********************** 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
  209 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 1.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7280 (mmt) cc_final: 0.7009 (mmp)
REVERT: A   86 GLU cc_start: 0.8093 (tp30) cc_final: 0.7726 (tp30)
REVERT: A  122 PRO cc_start: 0.8997 (Cg_exo) cc_final: 0.8658 (Cg_endo)
REVERT: A  127 ASN cc_start: 0.7693 (p0) cc_final: 0.7050 (m-40)
REVERT: A  297 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5983 (mp0)
REVERT: A  303 LYS cc_start: 0.9252 (tptm) cc_final: 0.8929 (tptp)
REVERT: A  307 LYS cc_start: 0.8685 (tptp) cc_final: 0.8181 (tptp)
REVERT: A  320 MET cc_start: 0.8400 (ptp) cc_final: 0.8047 (pmm)
REVERT: A  521 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5292 (mpp)
REVERT: A  613 TYR cc_start: 0.7332 (m-80) cc_final: 0.6537 (m-80)
REVERT: A  709 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7759 (pp30)
REVERT: B   44 LEU cc_start: 0.3616 (OUTLIER) cc_final: 0.2995 (mt)
REVERT: B  125 TRP cc_start: 0.8034 (t60) cc_final: 0.7732 (t-100)
REVERT: B  182 GLU cc_start: 0.7724 (tt0) cc_final: 0.7517 (tt0)
REVERT: B  200 ASP cc_start: 0.8899 (p0) cc_final: 0.8617 (p0)
REVERT: B  297 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6385 (mp0)
REVERT: B  303 LYS cc_start: 0.9281 (tptm) cc_final: 0.8967 (tptp)
REVERT: B  307 LYS cc_start: 0.8751 (tptp) cc_final: 0.8376 (tptp)
REVERT: B  613 TYR cc_start: 0.7131 (m-80) cc_final: 0.6480 (m-80)
REVERT: B  689 MET cc_start: 0.8894 (tpp) cc_final: 0.8542 (tpt)
  outliers start: 31
  outliers final: 19
  residues processed: 196
  average time/residue: 0.4262
  time to fit residues: 128.7148
Evaluate side-chains
  191 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 2.130 
-------------------------------------------------------------------------------
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  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  482 ILE
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:    0.9990
   chunk 123 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0000
   chunk 101 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 96 optimal weight:   50.0000
   overall best weight:    1.3390

-------------------------------------------------------------------------------
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**
B 489 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.178104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137445 restraints weight = 18157.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.53
r_work: 0.3539 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  11984  Z= 0.166
  Angle     :  0.684   9.923  16221  Z= 0.352
  Chirality :  0.044   0.172   1793
  Planarity :  0.005   0.053   2002
  Dihedral  : 12.822 172.052   1831
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.48 %
    Favored  : 80.17 %
  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:  1.61 (0.19), residues: 818
  sheet: -1.39 (1.18), residues: 20
  loop : -2.51 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 624 
 HIS   0.004   0.001   HIS B 628 
 PHE   0.029   0.002   PHE B  72 
 TYR   0.031   0.002   TYR B 181 
 ARG   0.009   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  685)
  hydrogen bonds       : angle       4.61238 ( 1983)
  covalent geometry    : bond        0.00387 (11977)
  covalent geometry    : angle       0.68414 (16221)
  Misc. bond           : bond        0.00079 (    7)

*********************** 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
  203 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 2.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.7910 (tp30) cc_final: 0.7618 (tp30)
REVERT: A  122 PRO cc_start: 0.9031 (Cg_exo) cc_final: 0.8686 (Cg_endo)
REVERT: A  127 ASN cc_start: 0.7734 (p0) cc_final: 0.7080 (m-40)
REVERT: A  297 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5990 (mp0)
REVERT: A  303 LYS cc_start: 0.9249 (tptm) cc_final: 0.8931 (tptp)
REVERT: A  307 LYS cc_start: 0.8704 (tptp) cc_final: 0.8274 (tptp)
REVERT: A  320 MET cc_start: 0.8394 (ptp) cc_final: 0.8073 (pmm)
REVERT: A  521 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.5369 (mpp)
REVERT: A  613 TYR cc_start: 0.7271 (m-80) cc_final: 0.6552 (m-80)
REVERT: B   44 LEU cc_start: 0.3682 (OUTLIER) cc_final: 0.3304 (mp)
REVERT: B  125 TRP cc_start: 0.8071 (t60) cc_final: 0.7732 (t-100)
REVERT: B  182 GLU cc_start: 0.7789 (tt0) cc_final: 0.7589 (tt0)
REVERT: B  200 ASP cc_start: 0.8803 (p0) cc_final: 0.8556 (p0)
REVERT: B  297 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6489 (mp0)
REVERT: B  303 LYS cc_start: 0.9279 (tptm) cc_final: 0.8961 (tptp)
REVERT: B  307 LYS cc_start: 0.8752 (tptp) cc_final: 0.8380 (tptp)
REVERT: B  613 TYR cc_start: 0.7115 (m-80) cc_final: 0.6521 (m-80)
  outliers start: 28
  outliers final: 19
  residues processed: 189
  average time/residue: 0.2355
  time to fit residues: 67.5256
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  : 1.156 
-------------------------------------------------------------------------------
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  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  389 PHE
Chi-restraints excluded: chain B residue  482 ILE
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:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 104 optimal weight:    0.3980
   chunk 130 optimal weight:    3.9990
   chunk 109 optimal weight:    0.0370
   chunk 41 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.4864

-------------------------------------------------------------------------------
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**
B 489 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.176789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.136542 restraints weight = 18019.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.51
r_work: 0.3530 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  11984  Z= 0.176
  Angle     :  0.707  10.984  16221  Z= 0.363
  Chirality :  0.045   0.192   1793
  Planarity :  0.006   0.053   2002
  Dihedral  : 12.557 167.814   1831
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.73 %
    Favored  : 79.92 %
  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: -0.00 (0.24), residues: 1402
  helix:  1.55 (0.19), residues: 820
  sheet: -1.38 (1.18), residues: 20
  loop : -2.46 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 624 
 HIS   0.004   0.001   HIS B 628 
 PHE   0.029   0.002   PHE A  72 
 TYR   0.031   0.002   TYR B 181 
 ARG   0.008   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  685)
  hydrogen bonds       : angle       4.65586 ( 1983)
  covalent geometry    : bond        0.00415 (11977)
  covalent geometry    : angle       0.70720 (16221)
  Misc. bond           : bond        0.00073 (    7)

*********************** 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
  199 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 171
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7503 (mmt) cc_final: 0.7276 (mmp)
REVERT: A   86 GLU cc_start: 0.7951 (tp30) cc_final: 0.7642 (tp30)
REVERT: A  122 PRO cc_start: 0.8997 (Cg_exo) cc_final: 0.8643 (Cg_endo)
REVERT: A  127 ASN cc_start: 0.7830 (p0) cc_final: 0.7087 (m-40)
REVERT: A  297 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5983 (mp0)
REVERT: A  303 LYS cc_start: 0.9264 (tptm) cc_final: 0.8943 (tptp)
REVERT: A  307 LYS cc_start: 0.8733 (tptp) cc_final: 0.8295 (tptp)
REVERT: A  320 MET cc_start: 0.8401 (ptp) cc_final: 0.8047 (pmm)
REVERT: A  521 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5340 (mpp)
REVERT: A  613 TYR cc_start: 0.7344 (m-80) cc_final: 0.6550 (m-80)
REVERT: B   44 LEU cc_start: 0.3610 (OUTLIER) cc_final: 0.3353 (mp)
REVERT: B  125 TRP cc_start: 0.8054 (t60) cc_final: 0.7720 (t-100)
REVERT: B  182 GLU cc_start: 0.7733 (tt0) cc_final: 0.7515 (tt0)
REVERT: B  297 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6469 (mp0)
REVERT: B  303 LYS cc_start: 0.9286 (tptm) cc_final: 0.8952 (tptp)
REVERT: B  307 LYS cc_start: 0.8771 (tptp) cc_final: 0.8377 (tptp)
REVERT: B  613 TYR cc_start: 0.7116 (m-80) cc_final: 0.6504 (m-80)
REVERT: B  689 MET cc_start: 0.8899 (tpp) cc_final: 0.8555 (tpt)
  outliers start: 28
  outliers final: 19
  residues processed: 186
  average time/residue: 0.2202
  time to fit residues: 61.4601
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  : 1.387 
-------------------------------------------------------------------------------
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  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  389 PHE
Chi-restraints excluded: chain B residue  482 ILE
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:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 135 optimal weight:    0.9980
   chunk 110 optimal weight:    8.9990
   chunk 6 optimal weight:    0.6980
   chunk 111 optimal weight:    0.0980
   chunk 105 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.180979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.140938 restraints weight = 18035.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.52
r_work: 0.3583 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11984  Z= 0.135
  Angle     :  0.673  11.213  16221  Z= 0.343
  Chirality :  0.043   0.170   1793
  Planarity :  0.005   0.053   2002
  Dihedral  : 12.266 164.418   1831
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.49 %
    Favored  : 79.75 %
  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:  0.10 (0.24), residues: 1402
  helix:  1.54 (0.19), residues: 844
  sheet: -1.42 (1.19), residues: 20
  loop : -2.42 (0.28), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 650 
 PHE   0.032   0.001   PHE A  72 
 TYR   0.029   0.001   TYR B 181 
 ARG   0.009   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03642 (  685)
  hydrogen bonds       : angle       4.52408 ( 1983)
  covalent geometry    : bond        0.00301 (11977)
  covalent geometry    : angle       0.67314 (16221)
  Misc. bond           : bond        0.00072 (    7)

********************** 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: 21
    poor density    : 181
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.7505 (mmt) cc_final: 0.7280 (mmp)
REVERT: A   86 GLU cc_start: 0.7813 (tp30) cc_final: 0.7490 (tp30)
REVERT: A  124 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7369 (t0)
REVERT: A  297 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5981 (mp0)
REVERT: A  303 LYS cc_start: 0.9247 (tptm) cc_final: 0.8931 (tptp)
REVERT: A  307 LYS cc_start: 0.8710 (tptp) cc_final: 0.8277 (tptp)
REVERT: A  320 MET cc_start: 0.8333 (ptp) cc_final: 0.8053 (pmm)
REVERT: A  521 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5391 (mpp)
REVERT: A  559 MET cc_start: 0.2433 (ptt) cc_final: 0.2045 (ptp)
REVERT: A  613 TYR cc_start: 0.7307 (m-80) cc_final: 0.6588 (m-80)
REVERT: B   44 LEU cc_start: 0.3733 (OUTLIER) cc_final: 0.3232 (mt)
REVERT: B  125 TRP cc_start: 0.8171 (t60) cc_final: 0.7785 (t-100)
REVERT: B  297 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6427 (mp0)
REVERT: B  303 LYS cc_start: 0.9286 (tptm) cc_final: 0.8953 (tptp)
REVERT: B  307 LYS cc_start: 0.8758 (tptp) cc_final: 0.8365 (tptp)
REVERT: B  613 TYR cc_start: 0.7086 (m-80) cc_final: 0.6456 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 193
  average time/residue: 0.2053
  time to fit residues: 59.0510
Evaluate side-chains
  191 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASN
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  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  482 ILE
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:    7.9990
   chunk 106 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 129 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0010
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.7790

-------------------------------------------------------------------------------
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**
** 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 = 0.4165 r_free = 0.4165 target = 0.180548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.141084 restraints weight = 17942.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.48
r_work: 0.3584 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.153  11984  Z= 0.206
  Angle     :  1.123  59.178  16221  Z= 0.655
  Chirality :  0.047   0.610   1793
  Planarity :  0.005   0.053   2002
  Dihedral  : 12.277 164.406   1831
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.70 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 19.16 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.15 %
  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:  0.08 (0.24), residues: 1402
  helix:  1.53 (0.19), residues: 844
  sheet: -1.41 (1.18), residues: 20
  loop : -2.43 (0.28), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.003   0.001   HIS A 650 
 PHE   0.034   0.001   PHE A 169 
 TYR   0.029   0.001   TYR B 181 
 ARG   0.009   0.000   ARG B 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03645 (  685)
  hydrogen bonds       : angle       4.52271 ( 1983)
  covalent geometry    : bond        0.00421 (11977)
  covalent geometry    : angle       1.12292 (16221)
  Misc. bond           : bond        0.00069 (    7)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5952.06 seconds
wall clock time: 108 minutes 39.32 seconds (6519.32 seconds total)