Starting phenix.real_space_refine
on Wed Jun 11 07:06:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jl0_22368/06_2025/7jl0_22368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jl0_22368/06_2025/7jl0_22368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jl0_22368/06_2025/7jl0_22368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jl0_22368/06_2025/7jl0_22368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jl0_22368/06_2025/7jl0_22368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jl0_22368/06_2025/7jl0_22368.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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 5893 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: 9
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     Al      1      5.89       5
     P      30      5.49       5
     Mg      1      5.21       5
     S      42      5.16       5
     C    4554      2.51       5
     N    1283      2.21       5
     O    1438      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7354
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "X"
      Number of atoms: 300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 300
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 6}
          Link IDs: {'rna3p': 13}
    Chain: "Y"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 295
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 13}
    Chain: "A"
      Number of atoms: 5311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 662, 5311
          Classifications: {'peptide': 662}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 21, 'TRANS': 640}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 33
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 1414
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 180, 1404
          Classifications: {'peptide': 180}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 43
      Conformer: "B"
        Number of residues, atoms: 180, 1404
          Classifications: {'peptide': 180}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 43
          bond proxies already assigned to first conformer: 1438
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5098  SG  CYS A 907      86.171  20.420  28.789  1.00 67.24           S
  ATOM   5121  SG  CYS A 910      86.717  17.188  28.952  1.00 79.54           S
  ATOM   5454  SG  CYS A 962      86.167  18.607  25.327  1.00 82.04           S
  ATOM   5469  SG  CYS A 964      83.656  17.332  28.245  1.00 96.45           S

  Time building chain proxies: 5.44, per 1000 atoms: 0.74
  Number of scatterers: 7354
  At special positions: 0
  Unit cell: (114.989, 102.558, 71.4799, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     Zn      1     29.99
     S      42     16.00
     P      30     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1438      8.00
     N    1283      7.00
     C    4554      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 917.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 910 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 907 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 964 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 962 "
      Number of angles added : 6


  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1602

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      43.0% alpha, 15.1% beta
      10 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 2.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 309 through 317
    Processing helix  chain 'A' and resid 318 through 321
      removed outlier: 3.667A  pdb=" N   GLU A 321 " --> pdb=" O   PRO A 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 318 through 321'
    Processing helix  chain 'A' and resid 334 through 353
      removed outlier: 3.672A  pdb=" N   ALA A 353 " --> pdb=" O   LYS A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 375
      removed outlier: 3.584A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU A 370 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 381
      removed outlier: 3.718A  pdb=" N   PHE A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 407
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 445 through 448
    Processing helix  chain 'A' and resid 452 through 472
      removed outlier: 3.668A  pdb=" N   ASN A 456 " --> pdb=" O   ALA A 452 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ILE A 457 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 524 through 532
    Processing helix  chain 'A' and resid 548 through 566
      removed outlier: 4.626A  pdb=" N   GLU A 552 " --> pdb=" O   ASP A 548 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   CYS A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 593
      removed outlier: 3.725A  pdb=" N   GLU A 579 " --> pdb=" O   THR A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 617
    Processing helix  chain 'A' and resid 618 through 640
      removed outlier: 3.812A  pdb=" N   ALA A 622 " --> pdb=" O   ARG A 618 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLU A 632 " --> pdb=" O   THR A 628 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 639 " --> pdb=" O   ASP A 635 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   VAL A 640 " --> pdb=" O   LYS A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 692
      removed outlier: 4.114A  pdb=" N   MET A 677 " --> pdb=" O   ASP A 673 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   LEU A 679 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   GLU A 682 " --> pdb=" O   THR A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 716
      removed outlier: 3.687A  pdb=" N   LYS A 703 " --> pdb=" O   GLU A 699 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU A 716 " --> pdb=" O   TYR A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 741
      removed outlier: 4.069A  pdb=" N   ASN A 741 " --> pdb=" O   TRP A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 747
      removed outlier: 3.881A  pdb=" N   GLU A 746 " --> pdb=" O   GLU A 742 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL A 747 " --> pdb=" O   LYS A 743 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 742 through 747'
    Processing helix  chain 'A' and resid 767 through 781
      removed outlier: 3.861A  pdb=" N   THR A 780 " --> pdb=" O   SER A 776 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY A 781 " --> pdb=" O   LYS A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 793
    Processing helix  chain 'A' and resid 813 through 822
      removed outlier: 4.360A  pdb=" N   ALA A 819 " --> pdb=" O   ALA A 815 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG A 820 " --> pdb=" O   MET A 816 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 821 " --> pdb=" O   VAL A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 862
    Processing helix  chain 'A' and resid 865 through 895
      removed outlier: 3.617A  pdb=" N   ILE A 881 " --> pdb=" O   GLN A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 939
      removed outlier: 4.151A  pdb=" N   TYR A 939 " --> pdb=" O   PHE A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 985
      No H-bonds generated for 'chain 'A' and resid 983 through 985'
    Processing helix  chain 'B' and resid 322 through 327
    Processing helix  chain 'B' and resid 328 through 330
      No H-bonds generated for 'chain 'B' and resid 328 through 330'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328
      removed outlier: 7.083A  pdb=" N   ILE A 325 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   THR A 488 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE A 327 " --> pdb=" O   THR A 488 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ILE A 440 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   LEU A 487 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ILE A 442 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 541
      removed outlier: 3.656A  pdb=" N   ALA A 834 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   GLY A 721 " --> pdb=" O   LEU A 786 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ALA A 788 " --> pdb=" O   GLY A 721 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   ILE A 723 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   HIS A 752 " --> pdb=" O   LEU A 785 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 913 through 916
      removed outlier: 6.903A  pdb=" N   LEU A 913 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   CYS A 907 " --> pdb=" O   LEU A 913 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   CYS A 915 " --> pdb=" O   PHE A 905 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 923
    Processing sheet with id=AA5, first strand: chain 'A' and resid 940 through 942
      removed outlier: 4.532A  pdb=" N   GLY A 969 " --> pdb=" O   ILE A 960 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU A 979 " --> pdb=" O   MET A 972 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 347
      removed outlier: 3.934A  pdb=" N   TYR B 475 " --> pdb=" O   PHE B 464 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   SER B 466 " --> pdb=" O   PRO B 473 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 374

    309 hydrogen bonds defined for protein.
    886 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: 2.33

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1806
        1.33 -     1.45: 1678
        1.45 -     1.58: 3941
        1.58 -     1.70: 58
        1.70 -     1.82: 69
  Bond restraints: 7552
  Sorted by residual:
  bond pdb=" CA  LYS A 782 "
       pdb=" C   LYS A 782 "
    ideal  model  delta    sigma   weight residual
    1.521  1.601 -0.079 1.29e-02 6.01e+03 3.79e+01
  bond pdb=" F1  ALF A1103 "
       pdb="AL   ALF A1103 "
    ideal  model  delta    sigma   weight residual
    1.684  1.780 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" F3  ALF A1103 "
       pdb="AL   ALF A1103 "
    ideal  model  delta    sigma   weight residual
    1.685  1.780 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" F4  ALF A1103 "
       pdb="AL   ALF A1103 "
    ideal  model  delta    sigma   weight residual
    1.686  1.780 -0.094 2.00e-02 2.50e+03 2.21e+01
  bond pdb=" F2  ALF A1103 "
       pdb="AL   ALF A1103 "
    ideal  model  delta    sigma   weight residual
    1.685  1.778 -0.093 2.00e-02 2.50e+03 2.17e+01
  ... (remaining 7547 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.82: 10321
       13.82 -    27.64: 5
       27.64 -    41.46: 0
       41.46 -    55.29: 0
       55.29 -    69.11: 2
  Bond angle restraints: 10328
  Sorted by residual:
  angle pdb=" F3  ALF A1103 "
        pdb="AL   ALF A1103 "
        pdb=" F4  ALF A1103 "
      ideal   model   delta    sigma   weight residual
     109.63  178.74  -69.11 3.00e+00 1.11e-01 5.31e+02
  angle pdb=" F1  ALF A1103 "
        pdb="AL   ALF A1103 "
        pdb=" F2  ALF A1103 "
      ideal   model   delta    sigma   weight residual
     108.68  177.20  -68.52 3.00e+00 1.11e-01 5.22e+02
  angle pdb=" N   ILE A 783 "
        pdb=" CA  ILE A 783 "
        pdb=" CB  ILE A 783 "
      ideal   model   delta    sigma   weight residual
     111.41  123.55  -12.14 1.38e+00 5.25e-01 7.74e+01
  angle pdb=" F2  ALF A1103 "
        pdb="AL   ALF A1103 "
        pdb=" F3  ALF A1103 "
      ideal   model   delta    sigma   weight residual
     109.59   88.39   21.20 3.00e+00 1.11e-01 4.99e+01
  angle pdb=" F1  ALF A1103 "
        pdb="AL   ALF A1103 "
        pdb=" F4  ALF A1103 "
      ideal   model   delta    sigma   weight residual
     109.02   88.09   20.93 3.00e+00 1.11e-01 4.87e+01
  ... (remaining 10323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.18: 4479
       33.18 -    66.37: 127
       66.37 -    99.55: 16
       99.55 -   132.73: 2
      132.73 -   165.91: 1
  Dihedral angle restraints: 4625
    sinusoidal: 2162
      harmonic: 2463
  Sorted by residual:
  dihedral pdb=" C5' ADP A1102 "
           pdb=" O5' ADP A1102 "
           pdb=" PA  ADP A1102 "
           pdb=" O2A ADP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  105.92 -165.91     1      2.00e+01 2.50e-03 4.73e+01
  dihedral pdb=" O2A ADP A1102 "
           pdb=" O3A ADP A1102 "
           pdb=" PA  ADP A1102 "
           pdb=" PB  ADP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   55.39 -115.39     1      2.00e+01 2.50e-03 3.43e+01
  dihedral pdb=" O1B ADP A1102 "
           pdb=" O3A ADP A1102 "
           pdb=" PB  ADP A1102 "
           pdb=" PA  ADP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   41.70 -101.71     1      2.00e+01 2.50e-03 2.89e+01
  ... (remaining 4622 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 900
       0.056 -    0.113: 240
       0.113 -    0.169: 32
       0.169 -    0.225: 2
       0.225 -    0.281: 3
  Chirality restraints: 1177
  Sorted by residual:
  chirality pdb=" CA  LYS A 782 "
            pdb=" N   LYS A 782 "
            pdb=" C   LYS A 782 "
            pdb=" CB  LYS A 782 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CB  ILE A 479 "
            pdb=" CA  ILE A 479 "
            pdb=" CG1 ILE A 479 "
            pdb=" CG2 ILE A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  ILE A 783 "
            pdb=" N   ILE A 783 "
            pdb=" C   ILE A 783 "
            pdb=" CB  ILE A 783 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.17    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 1174 not shown)

  Planarity restraints: 1210
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 711 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" CD  GLN A 711 "   -0.055 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 711 "    0.021 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 711 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 377 "    0.021 2.00e-02 2.50e+03   1.79e-02 5.61e+00
        pdb=" CG  PHE A 377 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 377 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 377 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 377 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 377 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 377 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 763 "   -0.003 2.00e-02 2.50e+03   1.67e-02 4.87e+00
        pdb=" CG  PHE A 763 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 763 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 763 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 763 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 763 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 763 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1207 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 39
        2.47 -     3.08: 5085
        3.08 -     3.68: 10739
        3.68 -     4.29: 15233
        4.29 -     4.90: 24550
  Nonbonded interactions: 55646
  Sorted by model distance:
  nonbonded pdb=" F4  ALF A1103 "
            pdb="MG    MG A1104 "
     model   vdw
     1.860 2.120
  nonbonded pdb=" O1B ADP A1102 "
            pdb=" F1  ALF A1103 "
     model   vdw
     2.119 2.990
  nonbonded pdb=" F1  ALF A1103 "
            pdb="MG    MG A1104 "
     model   vdw
     2.148 2.120
  nonbonded pdb=" NH2 ARG A 822 "
            pdb=" F3  ALF A1103 "
     model   vdw
     2.155 3.070
  nonbonded pdb=" O2B ADP A1102 "
            pdb=" F3  ALF A1103 "
     model   vdw
     2.166 2.990
  ... (remaining 55641 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.480
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
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      :  0.008   0.096   7556  Z= 0.375
  Angle     :  1.445  69.108  10334  Z= 0.631
  Chirality :  0.051   0.281   1177
  Planarity :  0.005   0.053   1210
  Dihedral  : 15.704 165.915   3023
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.55 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.27), residues: 822
  helix: -0.02 (0.27), residues: 307
  sheet: -0.96 (0.37), residues: 164
  loop : -1.88 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 423 
 HIS   0.011   0.002   HIS A 835 
 PHE   0.042   0.003   PHE A 377 
 TYR   0.019   0.003   TYR A 311 
 ARG   0.011   0.001   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13591 (  334)
  hydrogen bonds       : angle       6.23491 (  936)
  metal coordination   : bond        0.01580 (    4)
  metal coordination   : angle      14.33987 (    6)
  covalent geometry    : bond        0.00806 ( 7552)
  covalent geometry    : angle       1.40343 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 1.034 
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: A  333 SER cc_start: 0.8185 (p) cc_final: 0.7858 (t)
REVERT: A  391 SER cc_start: 0.8429 (p) cc_final: 0.8174 (p)
REVERT: A  529 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8401 (tmtt)
REVERT: A  783 ILE cc_start: 0.9457 (mt) cc_final: 0.9171 (mm)
REVERT: A  853 MET cc_start: 0.8725 (ttm) cc_final: 0.8211 (ttm)
REVERT: A  875 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7199 (tp30)
REVERT: A  942 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.7977 (ptt90)
REVERT: B  331 ARG cc_start: 0.4894 (mmt-90) cc_final: 0.4661 (mmt90)
REVERT: B  387 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7385 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2790
  time to fit residues: 64.3320
Evaluate side-chains
  96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 67 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    9.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS
A 562 GLN
A 784 ASN
B 343 HIS
B 436 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.100533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.080024 restraints weight = 45788.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.083961 restraints weight = 29975.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084346 restraints weight = 15762.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7556  Z= 0.144
  Angle     :  0.965  30.538  10334  Z= 0.405
  Chirality :  0.043   0.155   1177
  Planarity :  0.004   0.051   1210
  Dihedral  : 14.219 156.318   1337
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.37 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.28), residues: 822
  helix:  1.01 (0.28), residues: 321
  sheet: -0.64 (0.38), residues: 172
  loop : -1.44 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 327 
 HIS   0.006   0.001   HIS A 505 
 PHE   0.027   0.002   PHE B 335 
 TYR   0.017   0.002   TYR A 732 
 ARG   0.004   0.001   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05030 (  334)
  hydrogen bonds       : angle       4.66188 (  936)
  metal coordination   : bond        0.01355 (    4)
  metal coordination   : angle      11.66981 (    6)
  covalent geometry    : bond        0.00307 ( 7552)
  covalent geometry    : angle       0.92361 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 SER cc_start: 0.8591 (p) cc_final: 0.8290 (p)
REVERT: A  584 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7901 (pm20)
REVERT: A  686 MET cc_start: 0.7945 (tpp) cc_final: 0.7687 (tpp)
REVERT: A  853 MET cc_start: 0.8677 (ttm) cc_final: 0.8033 (ttm)
REVERT: A  854 MET cc_start: 0.8518 (tmm) cc_final: 0.8133 (tmm)
REVERT: A  875 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7174 (tp30)
REVERT: A  926 MET cc_start: 0.8260 (mtp) cc_final: 0.8015 (mtp)
REVERT: A  942 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.7726 (tmm-80)
REVERT: B  348 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7264 (ttm110)
REVERT: B  387 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6763 (mm-30)
REVERT: B  465 TYR cc_start: 0.7261 (m-10) cc_final: 0.6886 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2848
  time to fit residues: 44.8469
Evaluate side-chains
  81 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    0.0040
   chunk 66 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.8998

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

Flipped N/Q/H residues before XYZ refinement:
A 524 ASN
A 711 GLN
** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 470 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.094670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.073410 restraints weight = 32303.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.075130 restraints weight = 20774.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.075806 restraints weight = 13596.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7556  Z= 0.203
  Angle     :  0.990  31.067  10334  Z= 0.423
  Chirality :  0.045   0.175   1177
  Planarity :  0.005   0.047   1210
  Dihedral  : 14.244 172.485   1337
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.32 (0.29), residues: 822
  helix:  1.14 (0.28), residues: 322
  sheet: -0.40 (0.40), residues: 158
  loop : -1.42 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 327 
 HIS   0.005   0.002   HIS A 974 
 PHE   0.019   0.002   PHE B 335 
 TYR   0.017   0.002   TYR A 732 
 ARG   0.005   0.001   ARG A 689 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05796 (  334)
  hydrogen bonds       : angle       4.88271 (  936)
  metal coordination   : bond        0.00891 (    4)
  metal coordination   : angle      10.30834 (    6)
  covalent geometry    : bond        0.00456 ( 7552)
  covalent geometry    : angle       0.95816 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8835 (m) cc_final: 0.8358 (p)
REVERT: A  686 MET cc_start: 0.7932 (tpp) cc_final: 0.7639 (tpp)
REVERT: A  853 MET cc_start: 0.8669 (ttm) cc_final: 0.7971 (ttm)
REVERT: A  875 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7225 (tp30)
REVERT: A  942 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.7938 (tmm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2950
  time to fit residues: 43.7420
Evaluate side-chains
  81 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 18 optimal weight:    0.2980
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 818 GLN
A 877 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.098310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.078174 restraints weight = 38046.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.080257 restraints weight = 24852.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.080902 restraints weight = 16801.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7556  Z= 0.115
  Angle     :  0.907  30.022  10334  Z= 0.373
  Chirality :  0.041   0.170   1177
  Planarity :  0.004   0.040   1210
  Dihedral  : 13.715 147.694   1337
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.21 (0.30), residues: 822
  helix:  1.52 (0.29), residues: 326
  sheet: -0.06 (0.40), residues: 172
  loop : -1.16 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 386 
 HIS   0.005   0.001   HIS B 355 
 PHE   0.013   0.001   PHE B 477 
 TYR   0.018   0.001   TYR B 475 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  334)
  hydrogen bonds       : angle       4.51382 (  936)
  metal coordination   : bond        0.00705 (    4)
  metal coordination   : angle       8.27898 (    6)
  covalent geometry    : bond        0.00244 ( 7552)
  covalent geometry    : angle       0.88537 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8736 (m) cc_final: 0.8240 (p)
REVERT: A  600 CYS cc_start: 0.7858 (m) cc_final: 0.6529 (t)
REVERT: A  686 MET cc_start: 0.7937 (tpp) cc_final: 0.7670 (tpp)
REVERT: A  793 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7153 (mt-10)
REVERT: A  853 MET cc_start: 0.8667 (ttm) cc_final: 0.7972 (ttm)
REVERT: A  854 MET cc_start: 0.8660 (tmm) cc_final: 0.8221 (tmm)
REVERT: A  875 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7312 (tp30)
REVERT: A  942 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.8000 (tmm-80)
REVERT: B  470 GLN cc_start: 0.8175 (mm110) cc_final: 0.7578 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.2514
  time to fit residues: 36.5557
Evaluate side-chains
  83 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0570
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.1502

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

Flipped N/Q/H residues before XYZ refinement:
A 928 HIS
** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.096006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.076012 restraints weight = 51064.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.078946 restraints weight = 35768.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.080135 restraints weight = 18111.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.5095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7556  Z= 0.140
  Angle     :  0.910  30.336  10334  Z= 0.376
  Chirality :  0.042   0.157   1177
  Planarity :  0.004   0.037   1210
  Dihedral  : 13.769 154.375   1337
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.60 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.30 (0.30), residues: 822
  helix:  1.61 (0.29), residues: 326
  sheet: -0.00 (0.41), residues: 169
  loop : -1.13 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 386 
 HIS   0.007   0.001   HIS B 355 
 PHE   0.010   0.001   PHE B 477 
 TYR   0.014   0.001   TYR A 732 
 ARG   0.012   0.001   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04650 (  334)
  hydrogen bonds       : angle       4.46350 (  936)
  metal coordination   : bond        0.00713 (    4)
  metal coordination   : angle       8.23858 (    6)
  covalent geometry    : bond        0.00308 ( 7552)
  covalent geometry    : angle       0.88873 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8798 (m) cc_final: 0.8346 (p)
REVERT: A  584 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7728 (pm20)
REVERT: A  686 MET cc_start: 0.7905 (tpp) cc_final: 0.7643 (tpp)
REVERT: A  853 MET cc_start: 0.8729 (ttm) cc_final: 0.8105 (ttm)
REVERT: A  875 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7498 (tp30)
REVERT: A  942 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7970 (tmm-80)
REVERT: B  389 ARG cc_start: 0.7067 (ttm170) cc_final: 0.6697 (ttm170)
REVERT: B  470 GLN cc_start: 0.8210 (mm110) cc_final: 0.7612 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2445
  time to fit residues: 35.5818
Evaluate side-chains
  88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 82 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 531 GLN
A 771 GLN
A 999 GLN
** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.098184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.076350 restraints weight = 32702.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.078862 restraints weight = 19503.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.080244 restraints weight = 10980.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.5476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7556  Z= 0.111
  Angle     :  0.894  29.957  10334  Z= 0.365
  Chirality :  0.041   0.164   1177
  Planarity :  0.004   0.040   1210
  Dihedral  : 13.565 141.550   1337
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.45 (0.30), residues: 822
  helix:  1.66 (0.29), residues: 333
  sheet:  0.04 (0.40), residues: 173
  loop : -1.00 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 327 
 HIS   0.004   0.001   HIS A 895 
 PHE   0.011   0.001   PHE B 477 
 TYR   0.013   0.001   TYR A 732 
 ARG   0.007   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  334)
  hydrogen bonds       : angle       4.36916 (  936)
  metal coordination   : bond        0.00591 (    4)
  metal coordination   : angle       7.36343 (    6)
  covalent geometry    : bond        0.00233 ( 7552)
  covalent geometry    : angle       0.87648 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8678 (m) cc_final: 0.8225 (p)
REVERT: A  391 SER cc_start: 0.8612 (p) cc_final: 0.8323 (t)
REVERT: A  686 MET cc_start: 0.7865 (tpp) cc_final: 0.7619 (tpp)
REVERT: A  696 TYR cc_start: 0.7384 (m-10) cc_final: 0.7153 (m-80)
REVERT: A  853 MET cc_start: 0.8703 (ttm) cc_final: 0.8110 (ttm)
REVERT: A  875 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7427 (tp30)
REVERT: A  942 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.7952 (tmm-80)
REVERT: B  335 PHE cc_start: 0.6941 (m-10) cc_final: 0.6664 (m-10)
REVERT: B  377 GLN cc_start: 0.4247 (mp10) cc_final: 0.3277 (mm-40)
REVERT: B  389 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6917 (ttm170)
REVERT: B  470 GLN cc_start: 0.8247 (mm110) cc_final: 0.7570 (pp30)
REVERT: B  496 THR cc_start: 0.9050 (m) cc_final: 0.8681 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1942
  time to fit residues: 31.4843
Evaluate side-chains
  88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 78 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 71 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 895 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 = 0.3391 r_free = 0.3391 target = 0.097234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.077403 restraints weight = 50970.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.081512 restraints weight = 32295.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.082406 restraints weight = 13662.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.5680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7556  Z= 0.119
  Angle     :  0.905  30.041  10334  Z= 0.368
  Chirality :  0.041   0.143   1177
  Planarity :  0.004   0.038   1210
  Dihedral  : 13.584 141.162   1337
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.45 (0.30), residues: 822
  helix:  1.72 (0.29), residues: 327
  sheet:  0.09 (0.40), residues: 174
  loop : -1.07 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 386 
 HIS   0.007   0.001   HIS A 895 
 PHE   0.016   0.001   PHE B 489 
 TYR   0.012   0.001   TYR A 732 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (  334)
  hydrogen bonds       : angle       4.37224 (  936)
  metal coordination   : bond        0.01076 (    4)
  metal coordination   : angle       8.64762 (    6)
  covalent geometry    : bond        0.00257 ( 7552)
  covalent geometry    : angle       0.88124 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8751 (m) cc_final: 0.8340 (p)
REVERT: A  793 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7625 (mt-10)
REVERT: A  853 MET cc_start: 0.8779 (ttm) cc_final: 0.8167 (ttm)
REVERT: A  854 MET cc_start: 0.8682 (tmm) cc_final: 0.8227 (tmm)
REVERT: A  875 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7382 (tp30)
REVERT: A  942 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.8028 (tmm-80)
REVERT: B  377 GLN cc_start: 0.4239 (mp10) cc_final: 0.3141 (mm-40)
REVERT: B  470 GLN cc_start: 0.8212 (mm110) cc_final: 0.7605 (pp30)
REVERT: B  496 THR cc_start: 0.9029 (m) cc_final: 0.8658 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1741
  time to fit residues: 25.7917
Evaluate side-chains
  84 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 74 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B 384 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 = 0.3389 r_free = 0.3389 target = 0.097043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.077178 restraints weight = 42866.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.080521 restraints weight = 26468.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.080646 restraints weight = 15663.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.5816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7556  Z= 0.123
  Angle     :  0.905  30.071  10334  Z= 0.370
  Chirality :  0.041   0.140   1177
  Planarity :  0.004   0.042   1210
  Dihedral  : 13.581 141.403   1337
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.49 (0.30), residues: 822
  helix:  1.63 (0.29), residues: 333
  sheet:  0.12 (0.40), residues: 175
  loop : -0.96 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 386 
 HIS   0.007   0.001   HIS B 355 
 PHE   0.017   0.001   PHE B 489 
 TYR   0.012   0.001   TYR A 732 
 ARG   0.005   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  334)
  hydrogen bonds       : angle       4.40966 (  936)
  metal coordination   : bond        0.00737 (    4)
  metal coordination   : angle       7.98058 (    6)
  covalent geometry    : bond        0.00269 ( 7552)
  covalent geometry    : angle       0.88502 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8762 (m) cc_final: 0.8349 (p)
REVERT: A  391 SER cc_start: 0.8699 (p) cc_final: 0.8414 (t)
REVERT: A  853 MET cc_start: 0.8699 (ttm) cc_final: 0.8079 (ttm)
REVERT: A  854 MET cc_start: 0.8668 (tmm) cc_final: 0.8252 (tmm)
REVERT: A  875 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7358 (tp30)
REVERT: A  942 ARG cc_start: 0.8317 (ttp-110) cc_final: 0.8035 (tmm-80)
REVERT: B  377 GLN cc_start: 0.4142 (mp10) cc_final: 0.3065 (mm-40)
REVERT: B  470 GLN cc_start: 0.7987 (mm110) cc_final: 0.7493 (pp30)
REVERT: B  496 THR cc_start: 0.9007 (m) cc_final: 0.8619 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.2231
  time to fit residues: 33.7999
Evaluate side-chains
  89 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0370
   chunk 26 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 75 optimal weight:    9.9990
   chunk 82 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3396 r_free = 0.3396 target = 0.097585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.077525 restraints weight = 43056.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.080834 restraints weight = 26469.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.081001 restraints weight = 16113.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.5990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7556  Z= 0.111
  Angle     :  0.889  30.009  10334  Z= 0.361
  Chirality :  0.040   0.135   1177
  Planarity :  0.004   0.041   1210
  Dihedral  : 13.489 133.968   1337
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.60 (0.30), residues: 822
  helix:  1.71 (0.29), residues: 333
  sheet:  0.24 (0.40), residues: 175
  loop : -0.93 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 327 
 HIS   0.004   0.001   HIS A 603 
 PHE   0.013   0.001   PHE B 489 
 TYR   0.012   0.001   TYR A 732 
 ARG   0.005   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  334)
  hydrogen bonds       : angle       4.30560 (  936)
  metal coordination   : bond        0.00676 (    4)
  metal coordination   : angle       8.12481 (    6)
  covalent geometry    : bond        0.00237 ( 7552)
  covalent geometry    : angle       0.86774 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8740 (m) cc_final: 0.8344 (p)
REVERT: A  490 SER cc_start: 0.9244 (p) cc_final: 0.8618 (m)
REVERT: A  793 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: A  853 MET cc_start: 0.8769 (ttm) cc_final: 0.8224 (ttm)
REVERT: A  854 MET cc_start: 0.8713 (tmm) cc_final: 0.8312 (tmm)
REVERT: A  942 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.8010 (tmm-80)
REVERT: B  331 ARG cc_start: 0.7508 (mpt180) cc_final: 0.5067 (mtm-85)
REVERT: B  345 TYR cc_start: 0.5911 (m-80) cc_final: 0.5692 (m-80)
REVERT: B  377 GLN cc_start: 0.4149 (mp10) cc_final: 0.3112 (mm-40)
REVERT: B  453 MET cc_start: 0.5723 (mmt) cc_final: 0.5359 (mmp)
REVERT: B  470 GLN cc_start: 0.8054 (mm110) cc_final: 0.7385 (pp30)
REVERT: B  496 THR cc_start: 0.8975 (m) cc_final: 0.8641 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2811
  time to fit residues: 43.6546
Evaluate side-chains
  91 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 2.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0980
   chunk 11 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.098441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.078457 restraints weight = 41117.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.080630 restraints weight = 27806.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.081286 restraints weight = 18552.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.6126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7556  Z= 0.109
  Angle     :  0.895  30.039  10334  Z= 0.364
  Chirality :  0.040   0.175   1177
  Planarity :  0.004   0.042   1210
  Dihedral  : 13.468 129.964   1337
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.30), residues: 822
  helix:  1.76 (0.29), residues: 333
  sheet:  0.35 (0.41), residues: 174
  loop : -0.90 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 386 
 HIS   0.007   0.001   HIS B 355 
 PHE   0.015   0.001   PHE B 477 
 TYR   0.012   0.001   TYR A 939 
 ARG   0.005   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03825 (  334)
  hydrogen bonds       : angle       4.25400 (  936)
  metal coordination   : bond        0.00668 (    4)
  metal coordination   : angle       7.61142 (    6)
  covalent geometry    : bond        0.00233 ( 7552)
  covalent geometry    : angle       0.87607 (10328)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8756 (m) cc_final: 0.8342 (p)
REVERT: A  391 SER cc_start: 0.8739 (p) cc_final: 0.8427 (t)
REVERT: A  490 SER cc_start: 0.9206 (p) cc_final: 0.8543 (m)
REVERT: A  793 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7641 (mt-10)
REVERT: A  853 MET cc_start: 0.8781 (ttm) cc_final: 0.8248 (ttm)
REVERT: A  942 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.8084 (tmm-80)
REVERT: B  345 TYR cc_start: 0.5976 (m-80) cc_final: 0.5754 (m-80)
REVERT: B  377 GLN cc_start: 0.4144 (mp10) cc_final: 0.3099 (mm-40)
REVERT: B  470 GLN cc_start: 0.7896 (mm110) cc_final: 0.7368 (pp30)
REVERT: B  496 THR cc_start: 0.9006 (m) cc_final: 0.8649 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2020
  time to fit residues: 30.2476
Evaluate side-chains
  95 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    0.0670
   chunk 41 optimal weight:    0.2980
   chunk 2 optimal weight:    0.0030
   chunk 19 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.4128

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

Flipped N/Q/H residues before XYZ refinement:
A 455 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.099210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.079028 restraints weight = 42944.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.083305 restraints weight = 25767.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.083002 restraints weight = 15014.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.6218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7556  Z= 0.103
  Angle     :  0.891  30.046  10334  Z= 0.360
  Chirality :  0.040   0.176   1177
  Planarity :  0.004   0.041   1210
  Dihedral  : 13.392 124.085   1337
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.00 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.69 (0.30), residues: 822
  helix:  1.77 (0.29), residues: 340
  sheet:  0.30 (0.40), residues: 174
  loop : -0.91 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 386 
 HIS   0.009   0.001   HIS B 355 
 PHE   0.016   0.001   PHE B 477 
 TYR   0.013   0.001   TYR A 732 
 ARG   0.005   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03663 (  334)
  hydrogen bonds       : angle       4.16793 (  936)
  metal coordination   : bond        0.00580 (    4)
  metal coordination   : angle       7.20662 (    6)
  covalent geometry    : bond        0.00218 ( 7552)
  covalent geometry    : angle       0.87429 (10328)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2740.04 seconds
wall clock time: 49 minutes 56.67 seconds (2996.67 seconds total)