Starting phenix.real_space_refine
on Wed Jul 30 14:36:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kx9_23063/07_2025/7kx9_23063.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kx9_23063/07_2025/7kx9_23063.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2025/7kx9_23063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2025/7kx9_23063.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2025/7kx9_23063.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2025/7kx9_23063.cif"
  }
  resolution = 3.5
  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=   0.003 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 25 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     Mg      2      5.21       5
     S      33      5.16       5
     C    4015      2.51       5
     N    1170      2.21       5
     O    1318      1.98       5
     H    5846      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12424
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 11133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 734, 11133
          Classifications: {'peptide': 734}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 38, 'TRANS': 695}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 201
          Unresolved non-hydrogen angles: 254
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 104
    Chain: "B"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 774
          Classifications: {'RNA': 24}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 7, 'rna3p': 16}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "C"
      Number of atoms: 515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 515
          Classifications: {'RNA': 16}
          Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 15}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 8.69, per 1000 atoms: 0.70
  Number of scatterers: 12424
  At special positions: 0
  Unit cell: (79.35, 109.25, 75.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      33     16.00
     P      40     15.00
     Mg      2     11.99
     O    1318      8.00
     N    1170      7.00
     C    4015      6.00
     H    5846      1.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 5.53
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1398

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 11 sheets defined
      33.9% alpha, 16.2% beta
      10 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 7.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 267 through 277
      removed outlier: 3.644A  pdb=" N   GLU A 277 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 347
      removed outlier: 3.708A  pdb=" N   ARG A 345 " --> pdb=" O   LYS A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 412
    Processing helix  chain 'A' and resid 458 through 460
      No H-bonds generated for 'chain 'A' and resid 458 through 460'
    Processing helix  chain 'A' and resid 465 through 474
    Processing helix  chain 'A' and resid 521 through 527
    Processing helix  chain 'A' and resid 528 through 539
      removed outlier: 3.641A  pdb=" N   VAL A 536 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   HIS A 537 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 558
    Processing helix  chain 'A' and resid 559 through 570
      removed outlier: 3.551A  pdb=" N   SER A 563 " --> pdb=" O   THR A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 610
    Processing helix  chain 'A' and resid 631 through 646
    Processing helix  chain 'A' and resid 647 through 650
    Processing helix  chain 'A' and resid 665 through 677
    Processing helix  chain 'A' and resid 692 through 705
    Processing helix  chain 'A' and resid 717 through 721
      removed outlier: 4.297A  pdb=" N   GLN A 721 " --> pdb=" O   THR A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 739
      removed outlier: 3.560A  pdb=" N   LEU A 734 " --> pdb=" O   GLN A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 819
    Processing helix  chain 'A' and resid 836 through 851
      removed outlier: 4.021A  pdb=" N   VAL A 840 " --> pdb=" O   ARG A 836 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   SER A 841 " --> pdb=" O   GLU A 837 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   VAL A 845 " --> pdb=" O   SER A 841 " (cutoff:3.500A)
      Proline residue:  A 846  - end of helix
      removed outlier: 3.883A  pdb=" N   CYS A 851 " --> pdb=" O   GLN A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 856
      removed outlier: 3.616A  pdb=" N   PHE A 855 " --> pdb=" O   PHE A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 941
    Processing helix  chain 'A' and resid 942 through 944
      No H-bonds generated for 'chain 'A' and resid 942 through 944'
    Processing helix  chain 'A' and resid 955 through 969
      removed outlier: 3.651A  pdb=" N   ASN A 959 " --> pdb=" O   PRO A 955 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238
    Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579
      removed outlier: 3.804A  pdb=" N   LEU A 578 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 247
      removed outlier: 4.439A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL A 390 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA A 379 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP A 392 " --> pdb=" O   VAL A 377 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TRP A 373 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   TYR A 376 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TYR A 357 " --> pdb=" O   GLN A 350 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 288
      removed outlier: 3.504A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 294 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER A 322 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 309
    Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 441
      removed outlier: 3.512A  pdb=" N   ARG A 438 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 444 through 445
    Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 456
    Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 598
      removed outlier: 3.678A  pdb=" N   ALA A 746 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 660 through 661
      removed outlier: 7.529A  pdb=" N   VAL A 661 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   PHE A 627 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ALA A 624 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   VAL A 687 " --> pdb=" O   ALA A 624 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LEU A 626 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL A 684 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   LEU A 714 " --> pdb=" O   VAL A 684 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ILE A 686 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 775 through 777
      removed outlier: 6.957A  pdb=" N   MET A 755 " --> pdb=" O   ILE A 826 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   PHE A 828 " --> pdb=" O   MET A 755 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL A 757 " --> pdb=" O   PHE A 828 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   LEU A 863 " --> pdb=" O   ASP A 925 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   ASP A 925 " --> pdb=" O   LEU A 863 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   VAL A 865 " --> pdb=" O   ILE A 923 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ILE A 923 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)

    216 hydrogen bonds defined for protein.
    600 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      18 stacking parallelities
  Total time for adding SS restraints: 6.23

  Time building geometry restraints manager: 5.36 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5834
        1.03 -     1.23: 40
        1.23 -     1.42: 2910
        1.42 -     1.61: 3808
        1.61 -     1.81: 54
  Bond restraints: 12646
  Sorted by residual:
  bond pdb=" C2  OMG B  24 "
       pdb=" N3  OMG B  24 "
    ideal  model  delta    sigma   weight residual
    1.308  1.478 -0.170 2.00e-02 2.50e+03 7.27e+01
  bond pdb=" N3  OMG B  24 "
       pdb=" C4  OMG B  24 "
    ideal  model  delta    sigma   weight residual
    1.341  1.493 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" C2  OMG B  24 "
       pdb=" N2  OMG B  24 "
    ideal  model  delta    sigma   weight residual
    1.344  1.487 -0.143 2.00e-02 2.50e+03 5.12e+01
  bond pdb=" C5  OMG B  24 "
       pdb=" C6  OMG B  24 "
    ideal  model  delta    sigma   weight residual
    1.424  1.544 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" N1  OMG B  24 "
       pdb=" C2  OMG B  24 "
    ideal  model  delta    sigma   weight residual
    1.365  1.439 -0.074 2.00e-02 2.50e+03 1.36e+01
  ... (remaining 12641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.48: 22689
        5.48 -    10.96: 13
       10.96 -    16.44: 0
       16.44 -    21.92: 0
       21.92 -    27.40: 4
  Bond angle restraints: 22706
  Sorted by residual:
  angle pdb=" O3'   U B  10 "
        pdb=" P     U B  11 "
        pdb=" OP1   U B  11 "
      ideal   model   delta    sigma   weight residual
     108.00   80.60   27.40 3.00e+00 1.11e-01 8.34e+01
  angle pdb=" C1' OMG B  24 "
        pdb=" N9  OMG B  24 "
        pdb=" C8  OMG B  24 "
      ideal   model   delta    sigma   weight residual
     127.59  100.49   27.10 3.00e+00 1.11e-01 8.16e+01
  angle pdb=" C1' OMG B  24 "
        pdb=" N9  OMG B  24 "
        pdb=" C4  OMG B  24 "
      ideal   model   delta    sigma   weight residual
     125.50  151.60  -26.10 3.00e+00 1.11e-01 7.57e+01
  angle pdb=" O3'   U B  10 "
        pdb=" P     U B  11 "
        pdb=" OP2   U B  11 "
      ideal   model   delta    sigma   weight residual
     108.00   83.25   24.75 3.00e+00 1.11e-01 6.80e+01
  angle pdb=" OP1   U B  11 "
        pdb=" P     U B  11 "
        pdb=" OP2   U B  11 "
      ideal   model   delta    sigma   weight residual
     119.60  130.39  -10.79 3.00e+00 1.11e-01 1.29e+01
  ... (remaining 22701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.09: 5570
       24.09 -    48.19: 330
       48.19 -    72.28: 87
       72.28 -    96.37: 19
       96.37 -   120.47: 4
  Dihedral angle restraints: 6010
    sinusoidal: 3505
      harmonic: 2505
  Sorted by residual:
  dihedral pdb=" CA  ARG A 286 "
           pdb=" C   ARG A 286 "
           pdb=" N   VAL A 287 "
           pdb=" CA  VAL A 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.66   20.34     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  SER A 850 "
           pdb=" C   SER A 850 "
           pdb=" N   CYS A 851 "
           pdb=" CA  CYS A 851 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.83  -20.17     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  HIS A 895 "
           pdb=" C   HIS A 895 "
           pdb=" N   THR A 896 "
           pdb=" CA  THR A 896 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.07   18.93     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 6007 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.384: 1088
       0.384 -    0.768: 0
       0.768 -    1.152: 0
       1.152 -    1.536: 0
       1.536 -    1.921: 1
  Chirality restraints: 1089
  Sorted by residual:
  chirality pdb=" P     U B  11 "
            pdb=" OP1   U B  11 "
            pdb=" OP2   U B  11 "
            pdb=" O5'   U B  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.49    1.92 2.00e-01 2.50e+01 9.22e+01
  chirality pdb=" C1'   G C  22 "
            pdb=" O4'   G C  22 "
            pdb=" C2'   G C  22 "
            pdb=" N9    G C  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.26    0.20 2.00e-01 2.50e+01 9.65e-01
  chirality pdb=" CA  MET A 398 "
            pdb=" N   MET A 398 "
            pdb=" C   MET A 398 "
            pdb=" CB  MET A 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 1086 not shown)

  Planarity restraints: 1718
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 860 "    0.029 5.00e-02 4.00e+02   4.44e-02 3.16e+00
        pdb=" N   PRO A 861 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 861 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 861 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 397 "   -0.008 2.00e-02 2.50e+03   1.59e-02 2.54e+00
        pdb=" C   VAL A 397 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL A 397 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   MET A 398 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  22 "    0.019 2.00e-02 2.50e+03   8.46e-03 2.50e+00
        pdb=" N9    G C  22 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    G C  22 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G C  22 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  22 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  22 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G C  22 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    G C  22 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G C  22 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  22 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    G C  22 "    0.000 2.00e-02 2.50e+03
        pdb=" C4    G C  22 "    0.001 2.00e-02 2.50e+03
        pdb=" H8    G C  22 "    0.001 2.00e-02 2.50e+03
        pdb=" H1    G C  22 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1715 not shown)

  Histogram of nonbonded interaction distances:
        1.17 -     1.86: 52
        1.86 -     2.54: 10717
        2.54 -     3.23: 36642
        3.23 -     3.91: 45816
        3.91 -     4.60: 73739
  Nonbonded interactions: 166966
  Sorted by model distance:
  nonbonded pdb="HH21 ARG A 953 "
            pdb=" OP2   U B   6 "
     model   vdw
     1.172 2.450
  nonbonded pdb=" HD1 HIS A 962 "
            pdb="MG    MG A1002 "
     model   vdw
     1.466 1.700
  nonbonded pdb=" HE2 TYR A 468 "
            pdb=" H3' OMG B  24 "
     model   vdw
     1.497 2.270
  nonbonded pdb="HE22 GLN A 735 "
            pdb="MG    MG A1001 "
     model   vdw
     1.547 1.700
  nonbonded pdb=" O   ASN A 663 "
            pdb=" HG  SER A 668 "
     model   vdw
     1.548 2.450
  ... (remaining 166961 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.180
  Construct map_model_manager:             0.470
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     47.960
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:5.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
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      :  0.012   0.790   6801  Z= 1.025
  Angle     :  0.934  27.403   9412  Z= 0.453
  Chirality :  0.074   1.921   1089
  Planarity :  0.005   0.044   1062
  Dihedral  : 17.248 120.468   2747
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.54 %
    Favored  : 88.46 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.17 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.70 (0.30), residues: 728
  helix: -0.96 (0.34), residues: 224
  sheet: -3.45 (0.34), residues: 187
  loop : -2.83 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 623 
 HIS   0.009   0.001   HIS A 487 
 PHE   0.009   0.001   PHE A 340 
 TYR   0.011   0.002   TYR A 435 
 ARG   0.010   0.001   ARG A 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23118 (  241)
  hydrogen bonds       : angle       8.95913 (  650)
  covalent geometry    : bond        0.00777 ( 6800)
  covalent geometry    : angle       0.93373 ( 9412)
  Misc. bond           : bond        0.79026 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  86 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 1.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  621 LEU cc_start: 0.8702 (mt) cc_final: 0.8457 (mt)
REVERT: A  908 GLN cc_start: 0.7761 (tp40) cc_final: 0.7422 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 85
  average time/residue: 0.5313
  time to fit residues: 61.2467
Evaluate side-chains
  68 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0770
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    2.9342

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

Flipped N/Q/H residues before XYZ refinement:
A 640 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.148060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.103505 restraints weight = 25884.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.109718 restraints weight = 12443.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.113537 restraints weight = 8168.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6801  Z= 0.156
  Angle     :  0.752  27.245   9412  Z= 0.351
  Chirality :  0.071   1.899   1089
  Planarity :  0.005   0.085   1062
  Dihedral  : 17.567 116.420   1402
  Min Nonbonded Distance : 1.765

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  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: -2.89 (0.30), residues: 728
  helix: -0.01 (0.34), residues: 220
  sheet: -2.92 (0.37), residues: 171
  loop : -2.65 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 569 
 HIS   0.005   0.001   HIS A 458 
 PHE   0.015   0.001   PHE A 406 
 TYR   0.011   0.001   TYR A 376 
 ARG   0.007   0.001   ARG A 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05952 (  241)
  hydrogen bonds       : angle       6.32710 (  650)
  covalent geometry    : bond        0.00350 ( 6800)
  covalent geometry    : angle       0.75225 ( 9412)
  Misc. bond           : bond        0.00579 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 MET cc_start: 0.7302 (mmp) cc_final: 0.6815 (mmp)
REVERT: A  621 LEU cc_start: 0.8726 (mt) cc_final: 0.8486 (mt)
REVERT: A  793 GLN cc_start: 0.6576 (mp10) cc_final: 0.4448 (mp10)
REVERT: A  812 LYS cc_start: 0.8722 (tppt) cc_final: 0.8499 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.5265
  time to fit residues: 51.5489
Evaluate side-chains
  70 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 23 optimal weight:   20.0000
   chunk 50 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 44 optimal weight:    9.9990
   overall best weight:    6.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 882 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.144783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.100092 restraints weight = 26923.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.106083 restraints weight = 12985.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.109812 restraints weight = 8639.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6801  Z= 0.222
  Angle     :  0.725  27.091   9412  Z= 0.340
  Chirality :  0.072   1.907   1089
  Planarity :  0.005   0.058   1062
  Dihedral  : 17.596 127.834   1400
  Min Nonbonded Distance : 1.668

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  6.83 %
    Favored  : 93.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.31), residues: 728
  helix:  0.28 (0.35), residues: 221
  sheet: -2.85 (0.37), residues: 175
  loop : -2.62 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 569 
 HIS   0.010   0.001   HIS A 763 
 PHE   0.018   0.001   PHE A 340 
 TYR   0.012   0.001   TYR A 376 
 ARG   0.003   0.000   ARG A 879 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04891 (  241)
  hydrogen bonds       : angle       5.82091 (  650)
  covalent geometry    : bond        0.00515 ( 6800)
  covalent geometry    : angle       0.72540 ( 9412)
  Misc. bond           : bond        0.00188 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  621 LEU cc_start: 0.8770 (mt) cc_final: 0.8516 (mt)
REVERT: A  801 HIS cc_start: 0.8496 (t70) cc_final: 0.8217 (t-170)
REVERT: A  812 LYS cc_start: 0.8823 (tppt) cc_final: 0.8510 (tppt)
  outliers start: 1
  outliers final: 1
  residues processed: 75
  average time/residue: 0.4847
  time to fit residues: 47.4905
Evaluate side-chains
  70 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  528 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 23 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   overall best weight:    5.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** 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 = 0.3846 r_free = 0.3846 target = 0.144471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.100038 restraints weight = 26676.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.106090 restraints weight = 12758.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.109861 restraints weight = 8466.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6801  Z= 0.193
  Angle     :  0.704  27.138   9412  Z= 0.326
  Chirality :  0.072   1.910   1089
  Planarity :  0.005   0.057   1062
  Dihedral  : 17.467 125.458   1400
  Min Nonbonded Distance : 1.716

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.83 %
    Favored  : 91.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.31), residues: 728
  helix:  0.49 (0.35), residues: 222
  sheet: -2.79 (0.37), residues: 173
  loop : -2.50 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 569 
 HIS   0.006   0.001   HIS A 594 
 PHE   0.015   0.001   PHE A 340 
 TYR   0.011   0.001   TYR A 376 
 ARG   0.002   0.000   ARG A 879 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  241)
  hydrogen bonds       : angle       5.47635 (  650)
  covalent geometry    : bond        0.00449 ( 6800)
  covalent geometry    : angle       0.70360 ( 9412)
  Misc. bond           : bond        0.00082 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 MET cc_start: 0.7646 (mmp) cc_final: 0.6943 (mmp)
REVERT: A  621 LEU cc_start: 0.8801 (mt) cc_final: 0.8580 (mt)
  outliers start: 5
  outliers final: 4
  residues processed: 74
  average time/residue: 0.4712
  time to fit residues: 45.0793
Evaluate side-chains
  73 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  830 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 21 optimal weight:   40.0000
   chunk 50 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 20 optimal weight:   20.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.144254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.099536 restraints weight = 26620.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.105515 restraints weight = 12856.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.109216 restraints weight = 8537.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6801  Z= 0.195
  Angle     :  0.695  27.057   9412  Z= 0.321
  Chirality :  0.072   1.916   1089
  Planarity :  0.004   0.048   1062
  Dihedral  : 17.464 129.463   1400
  Min Nonbonded Distance : 1.712

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.83 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.32), residues: 728
  helix:  0.65 (0.35), residues: 222
  sheet: -2.66 (0.37), residues: 175
  loop : -2.46 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 569 
 HIS   0.005   0.001   HIS A 594 
 PHE   0.016   0.001   PHE A 340 
 TYR   0.011   0.001   TYR A 376 
 ARG   0.005   0.000   ARG A 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04064 (  241)
  hydrogen bonds       : angle       5.29891 (  650)
  covalent geometry    : bond        0.00456 ( 6800)
  covalent geometry    : angle       0.69515 ( 9412)
  Misc. bond           : bond        0.00084 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  73 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 MET cc_start: 0.7573 (mmp) cc_final: 0.6905 (mmp)
REVERT: A  621 LEU cc_start: 0.8814 (mt) cc_final: 0.8591 (mt)
REVERT: A  801 HIS cc_start: 0.8429 (t70) cc_final: 0.8208 (t-170)
  outliers start: 5
  outliers final: 4
  residues processed: 71
  average time/residue: 0.4934
  time to fit residues: 45.2595
Evaluate side-chains
  71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  564 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 5 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 65 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 69 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.146638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.101804 restraints weight = 26685.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.107981 restraints weight = 12699.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.111853 restraints weight = 8379.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6801  Z= 0.117
  Angle     :  0.666  26.820   9412  Z= 0.304
  Chirality :  0.071   1.939   1089
  Planarity :  0.004   0.044   1062
  Dihedral  : 17.355 130.118   1400
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  9.83 %
    Favored  : 89.50 %
  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: -2.02 (0.32), residues: 728
  helix:  0.83 (0.36), residues: 230
  sheet: -2.34 (0.39), residues: 174
  loop : -2.35 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 569 
 HIS   0.006   0.001   HIS A 594 
 PHE   0.011   0.001   PHE A 340 
 TYR   0.010   0.001   TYR A 376 
 ARG   0.002   0.000   ARG A 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  241)
  hydrogen bonds       : angle       5.04808 (  650)
  covalent geometry    : bond        0.00273 ( 6800)
  covalent geometry    : angle       0.66632 ( 9412)
  Misc. bond           : bond        0.00023 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  80 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 MET cc_start: 0.7532 (mmp) cc_final: 0.6900 (mmp)
REVERT: A  621 LEU cc_start: 0.8826 (mt) cc_final: 0.8614 (mt)
REVERT: A  801 HIS cc_start: 0.8393 (t70) cc_final: 0.8191 (t-170)
  outliers start: 4
  outliers final: 4
  residues processed: 77
  average time/residue: 0.5062
  time to fit residues: 49.7727
Evaluate side-chains
  74 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  564 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:   20.0000
   chunk 36 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 3 optimal weight:    0.2980
   chunk 60 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 22 optimal weight:   30.0000
   chunk 21 optimal weight:    7.9990
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** 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 = 0.3870 r_free = 0.3870 target = 0.146867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.102144 restraints weight = 26436.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.108374 restraints weight = 12674.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.112223 restraints weight = 8336.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6801  Z= 0.109
  Angle     :  0.656  26.755   9412  Z= 0.297
  Chirality :  0.072   1.953   1089
  Planarity :  0.004   0.040   1062
  Dihedral  : 17.275 132.684   1400
  Min Nonbonded Distance : 1.775

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 11.00 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.33), residues: 728
  helix:  1.04 (0.36), residues: 230
  sheet: -2.22 (0.39), residues: 174
  loop : -2.22 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 569 
 HIS   0.004   0.001   HIS A 594 
 PHE   0.011   0.001   PHE A 340 
 TYR   0.010   0.001   TYR A 357 
 ARG   0.003   0.000   ARG A 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03541 (  241)
  hydrogen bonds       : angle       4.90026 (  650)
  covalent geometry    : bond        0.00256 ( 6800)
  covalent geometry    : angle       0.65648 ( 9412)
  Misc. bond           : bond        0.00031 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 MET cc_start: 0.7418 (mmp) cc_final: 0.6737 (mmp)
REVERT: A  621 LEU cc_start: 0.8906 (mt) cc_final: 0.8698 (mt)
  outliers start: 4
  outliers final: 4
  residues processed: 72
  average time/residue: 0.5522
  time to fit residues: 52.0402
Evaluate side-chains
  73 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  564 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 64 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 4 optimal weight:   20.0000
   chunk 23 optimal weight:   30.0000
   chunk 69 optimal weight:    5.9990
   overall best weight:    4.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.145439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.100600 restraints weight = 26648.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.106647 restraints weight = 12812.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.110435 restraints weight = 8507.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6801  Z= 0.163
  Angle     :  0.665  26.967   9412  Z= 0.303
  Chirality :  0.072   1.944   1089
  Planarity :  0.004   0.039   1062
  Dihedral  : 17.258 135.527   1400
  Min Nonbonded Distance : 1.757

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.67 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.33), residues: 728
  helix:  1.03 (0.36), residues: 231
  sheet: -2.25 (0.39), residues: 174
  loop : -2.21 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 569 
 HIS   0.009   0.001   HIS A 801 
 PHE   0.014   0.001   PHE A 340 
 TYR   0.011   0.001   TYR A 357 
 ARG   0.003   0.000   ARG A 871 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  241)
  hydrogen bonds       : angle       4.89674 (  650)
  covalent geometry    : bond        0.00388 ( 6800)
  covalent geometry    : angle       0.66473 ( 9412)
  Misc. bond           : bond        0.00045 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  74 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 MET cc_start: 0.7446 (mmp) cc_final: 0.6775 (mmp)
REVERT: A  621 LEU cc_start: 0.8901 (mt) cc_final: 0.8699 (mt)
  outliers start: 6
  outliers final: 5
  residues processed: 71
  average time/residue: 0.4895
  time to fit residues: 44.6846
Evaluate side-chains
  72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 ARG
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  564 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 2 optimal weight:   20.0000
   chunk 74 optimal weight:   30.0000
   chunk 16 optimal weight:    8.9990
   chunk 72 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.143914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.099475 restraints weight = 26205.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.105419 restraints weight = 12631.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.109086 restraints weight = 8364.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6801  Z= 0.213
  Angle     :  0.690  27.092   9412  Z= 0.319
  Chirality :  0.072   1.929   1089
  Planarity :  0.004   0.044   1062
  Dihedral  : 17.315 138.254   1400
  Min Nonbonded Distance : 1.745

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.00 %
    Favored  : 87.83 %
  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: -1.89 (0.33), residues: 728
  helix:  0.91 (0.35), residues: 231
  sheet: -2.37 (0.39), residues: 173
  loop : -2.21 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 605 
 HIS   0.008   0.001   HIS A 801 
 PHE   0.016   0.001   PHE A 340 
 TYR   0.011   0.001   TYR A 357 
 ARG   0.004   0.000   ARG A 879 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03816 (  241)
  hydrogen bonds       : angle       4.98743 (  650)
  covalent geometry    : bond        0.00500 ( 6800)
  covalent geometry    : angle       0.69050 ( 9412)
  Misc. bond           : bond        0.00064 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A  398 MET cc_start: 0.7436 (mmp) cc_final: 0.6760 (mmp)
REVERT: A  802 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6269 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 68
  average time/residue: 0.4536
  time to fit residues: 40.0408
Evaluate side-chains
  69 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 ARG
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  487 HIS
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  564 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0270
   chunk 70 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    2.6046

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.145755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.101082 restraints weight = 26307.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107217 restraints weight = 12623.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.111057 restraints weight = 8341.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6801  Z= 0.119
  Angle     :  0.657  26.897   9412  Z= 0.299
  Chirality :  0.071   1.948   1089
  Planarity :  0.004   0.044   1062
  Dihedral  : 17.185 139.636   1400
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 11.33 %
    Favored  : 87.83 %
  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: -1.61 (0.33), residues: 728
  helix:  1.17 (0.36), residues: 231
  sheet: -2.12 (0.40), residues: 174
  loop : -2.12 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 569 
 HIS   0.006   0.001   HIS A 801 
 PHE   0.011   0.001   PHE A 340 
 TYR   0.010   0.001   TYR A 357 
 ARG   0.002   0.000   ARG A 396 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03469 (  241)
  hydrogen bonds       : angle       4.81375 (  650)
  covalent geometry    : bond        0.00280 ( 6800)
  covalent geometry    : angle       0.65678 ( 9412)
  Misc. bond           : bond        0.00029 (    1)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  435 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 MET cc_start: 0.7477 (mmp) cc_final: 0.6806 (mmp)
REVERT: A  584 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7724 (ttp80)
REVERT: A  802 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6310 (mt-10)
  outliers start: 5
  outliers final: 5
  residues processed: 71
  average time/residue: 0.5392
  time to fit residues: 48.9640
Evaluate side-chains
  74 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  564 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:   30.0000
   chunk 62 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 51 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 8 optimal weight:   50.0000
   chunk 12 optimal weight:    0.8980
   overall best weight:    4.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 HIS ** 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 = 0.3850 r_free = 0.3850 target = 0.144985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.100287 restraints weight = 26639.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.106360 restraints weight = 12828.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.110073 restraints weight = 8494.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6801  Z= 0.158
  Angle     :  0.667  27.007   9412  Z= 0.304
  Chirality :  0.072   1.944   1089
  Planarity :  0.004   0.041   1062
  Dihedral  : 17.190 140.498   1400
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.17 %
    Favored  : 87.50 %
  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: -1.63 (0.33), residues: 728
  helix:  1.15 (0.36), residues: 231
  sheet: -2.12 (0.40), residues: 176
  loop : -2.13 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 569 
 HIS   0.007   0.001   HIS A 801 
 PHE   0.007   0.001   PHE A 340 
 TYR   0.011   0.001   TYR A 357 
 ARG   0.003   0.000   ARG A 584 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03527 (  241)
  hydrogen bonds       : angle       4.84356 (  650)
  covalent geometry    : bond        0.00373 ( 6800)
  covalent geometry    : angle       0.66672 ( 9412)
  Misc. bond           : bond        0.00045 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4555.19 seconds
wall clock time: 79 minutes 16.07 seconds (4756.07 seconds total)