Starting phenix.real_space_refine
on Thu Mar 13 06:42:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ywi_39634/03_2025/8ywi_39634.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ywi_39634/03_2025/8ywi_39634.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ywi_39634/03_2025/8ywi_39634.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ywi_39634/03_2025/8ywi_39634.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ywi_39634/03_2025/8ywi_39634.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ywi_39634/03_2025/8ywi_39634.cif"
  }
  resolution = 2.7
  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=   0.001 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      37      5.49       5
     Mg      1      5.21       5
     S      51      5.16       5
     C    5463      2.51       5
     N    1477      2.21       5
     O    1681      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8710
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 980, 7983
          Classifications: {'peptide': 980}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 934}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "P"
      Number of atoms: 287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 287
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "T"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 410
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "T"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'TTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.86, per 1000 atoms: 0.67
  Number of scatterers: 8710
  At special positions: 0
  Unit cell: (94.53, 106.26, 101.43, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      51     16.00
     P      37     15.00
     Mg      1     11.99
     O    1681      8.00
     N    1477      7.00
     C    5463      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: 2.62
  Conformation dependent library (CDL) restraints added in 889.5 milliseconds
  

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1872

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      49.4% alpha, 16.8% beta
      14 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 2.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 15
    Processing helix  chain 'A' and resid 15 through 29
    Processing helix  chain 'A' and resid 79 through 93
      removed outlier: 3.793A  pdb=" N   GLU A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 117
      removed outlier: 3.799A  pdb=" N   GLU A 117 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 143
      removed outlier: 3.800A  pdb=" N   ARG A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 163
    Processing helix  chain 'A' and resid 271 through 287
    Processing helix  chain 'A' and resid 299 through 312
      removed outlier: 3.742A  pdb=" N   PHE A 303 " --> pdb=" O   TYR A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 322
    Processing helix  chain 'A' and resid 328 through 335
    Processing helix  chain 'A' and resid 366 through 374
    Processing helix  chain 'A' and resid 381 through 389
      removed outlier: 3.739A  pdb=" N   CYS A 389 " --> pdb=" O   PHE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 409
    Processing helix  chain 'A' and resid 410 through 436
      removed outlier: 3.799A  pdb=" N   CYS A 428 " --> pdb=" O   ASP A 424 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
      removed outlier: 4.101A  pdb=" N   ASP A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 458
    Processing helix  chain 'A' and resid 460 through 474
      removed outlier: 3.626A  pdb=" N   HIS A 474 " --> pdb=" O   ALA A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 530
    Processing helix  chain 'A' and resid 532 through 534
      No H-bonds generated for 'chain 'A' and resid 532 through 534'
    Processing helix  chain 'A' and resid 539 through 550
    Processing helix  chain 'A' and resid 580 through 609
      removed outlier: 3.723A  pdb=" N   LYS A 584 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASN A 591 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   LYS A 592 " --> pdb=" O   ASP A 588 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ARG A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   CYS A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 646
      removed outlier: 3.835A  pdb=" N   PHE A 641 " --> pdb=" O   PHE A 637 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   TYR A 642 " --> pdb=" O   MET A 638 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLY A 646 " --> pdb=" O   TYR A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 678
      removed outlier: 3.717A  pdb=" N   ALA A 658 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 709
    Processing helix  chain 'A' and resid 713 through 748
      removed outlier: 3.701A  pdb=" N   THR A 734 " --> pdb=" O   LYS A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 814
      removed outlier: 3.601A  pdb=" N   LYS A 804 " --> pdb=" O   THR A 800 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLU A 813 " --> pdb=" O   ARG A 809 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER A 814 " --> pdb=" O   ILE A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 840
      removed outlier: 3.788A  pdb=" N   ILE A 830 " --> pdb=" O   PRO A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 845
      removed outlier: 3.977A  pdb=" N   GLN A 844 " --> pdb=" O   ASN A 841 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TRP A 845 " --> pdb=" O   MET A 842 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 841 through 845'
    Processing helix  chain 'A' and resid 864 through 883
      removed outlier: 3.687A  pdb=" N   SER A 870 " --> pdb=" O   GLN A 866 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   HIS A 882 " --> pdb=" O   GLN A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 890
      removed outlier: 3.523A  pdb=" N   PHE A 889 " --> pdb=" O   ALA A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 934
    Processing helix  chain 'A' and resid 939 through 956
      removed outlier: 3.971A  pdb=" N   TYR A 943 " --> pdb=" O   ASP A 939 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   LEU A 949 " --> pdb=" O   ASN A 945 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   GLY A 950 " --> pdb=" O   ASN A 946 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU A 951 " --> pdb=" O   TYR A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 963
      removed outlier: 3.704A  pdb=" N   PHE A 962 " --> pdb=" O   ASN A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 991
      removed outlier: 3.606A  pdb=" N   TYR A 974 " --> pdb=" O   ASN A 970 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   HIS A 991 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172
      removed outlier: 6.256A  pdb=" N   SER A  54 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS A 184 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU A  62 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 74
      removed outlier: 7.848A  pdb=" N   ALA A 481 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ARG A 106 " --> pdb=" O   ALA A 481 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268
      removed outlier: 4.144A  pdb=" N   ALA A 249 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLY A 293 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 346
      removed outlier: 5.507A  pdb=" N   LYS A 339 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   PHE A 355 " --> pdb=" O   LYS A 339 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 345 " --> pdb=" O   LYS A 349 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LYS A 349 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 508
      removed outlier: 5.324A  pdb=" N   TYR A 756 " --> pdb=" O   ASP A 517 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ASP A 517 " --> pdb=" O   TYR A 756 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLU A 758 " --> pdb=" O   GLY A 515 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLY A 515 " --> pdb=" O   GLU A 758 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER A 690 " --> pdb=" O   GLY A 686 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLY A 686 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TYR A 692 " --> pdb=" O   LYS A 684 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508
      removed outlier: 4.854A  pdb=" N   ILE A 774 " --> pdb=" O   PHE A 761 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   VAL A 763 " --> pdb=" O   TYR A 772 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   TYR A 772 " --> pdb=" O   VAL A 763 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   PHE A 765 " --> pdb=" O   LYS A 770 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   LYS A 770 " --> pdb=" O   PHE A 765 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537
    Processing sheet with id=AA8, first strand: chain 'A' and resid 852 through 855

    411 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      33 hydrogen bonds
      66 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 3.10

  Time building geometry restraints manager: 2.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2281
        1.33 -     1.45: 1784
        1.45 -     1.57: 4770
        1.57 -     1.69: 71
        1.69 -     1.81: 81
  Bond restraints: 8987
  Sorted by residual:
  bond pdb=" C5  TTP T1101 "
       pdb=" C6  TTP T1101 "
    ideal  model  delta    sigma   weight residual
    1.390  1.342  0.048 2.00e-02 2.50e+03 5.74e+00
  bond pdb=" C4  TTP T1101 "
       pdb=" N3  TTP T1101 "
    ideal  model  delta    sigma   weight residual
    1.337  1.383 -0.046 2.00e-02 2.50e+03 5.20e+00
  bond pdb=" C4  TTP T1101 "
       pdb=" C5  TTP T1101 "
    ideal  model  delta    sigma   weight residual
    1.487  1.445  0.042 2.00e-02 2.50e+03 4.50e+00
  bond pdb=" C6  TTP T1101 "
       pdb=" N1  TTP T1101 "
    ideal  model  delta    sigma   weight residual
    1.337  1.379 -0.042 2.00e-02 2.50e+03 4.40e+00
  bond pdb=" C2  TTP T1101 "
       pdb=" N3  TTP T1101 "
    ideal  model  delta    sigma   weight residual
    1.337  1.373 -0.036 2.00e-02 2.50e+03 3.18e+00
  ... (remaining 8982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 12091
        2.12 -     4.25: 171
        4.25 -     6.37: 25
        6.37 -     8.49: 7
        8.49 -    10.61: 7
  Bond angle restraints: 12301
  Sorted by residual:
  angle pdb=" C   LEU A 193 "
        pdb=" N   VAL A 194 "
        pdb=" CA  VAL A 194 "
      ideal   model   delta    sigma   weight residual
     121.97  132.58  -10.61 1.80e+00 3.09e-01 3.48e+01
  angle pdb=" C   ASP A 230 "
        pdb=" N   VAL A 231 "
        pdb=" CA  VAL A 231 "
      ideal   model   delta    sigma   weight residual
     121.97  131.44   -9.47 1.80e+00 3.09e-01 2.77e+01
  angle pdb=" N   VAL A 194 "
        pdb=" CA  VAL A 194 "
        pdb=" CB  VAL A 194 "
      ideal   model   delta    sigma   weight residual
     111.23  117.17   -5.94 1.65e+00 3.67e-01 1.29e+01
  angle pdb=" O1B TTP T1101 "
        pdb=" PB  TTP T1101 "
        pdb=" O2B TTP T1101 "
      ideal   model   delta    sigma   weight residual
     109.50  119.90  -10.40 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" C2' TTP T1101 "
        pdb=" C3' TTP T1101 "
        pdb=" C4' TTP T1101 "
      ideal   model   delta    sigma   weight residual
     111.00  101.07    9.93 3.00e+00 1.11e-01 1.10e+01
  ... (remaining 12296 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.69: 4982
       27.69 -    55.37: 338
       55.37 -    83.05: 21
       83.05 -   110.74: 3
      110.74 -   138.42: 3
  Dihedral angle restraints: 5347
    sinusoidal: 2440
      harmonic: 2907
  Sorted by residual:
  dihedral pdb=" C2  TTP T1101 "
           pdb=" C1' TTP T1101 "
           pdb=" N1  TTP T1101 "
           pdb=" O4' TTP T1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  163.26  138.42     1      2.00e+01 2.50e-03 4.20e+01
  dihedral pdb=" O3A TTP T1101 "
           pdb=" O3B TTP T1101 "
           pdb=" PB  TTP T1101 "
           pdb=" PG  TTP T1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.98  -48.45 -131.57     1      2.00e+01 2.50e-03 3.99e+01
  dihedral pdb=" O5' TTP T1101 "
           pdb=" O3A TTP T1101 "
           pdb=" PA  TTP T1101 "
           pdb=" PB  TTP T1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.02   54.77  125.25     1      2.00e+01 2.50e-03 3.79e+01
  ... (remaining 5344 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1279
       0.096 -    0.192: 51
       0.192 -    0.288: 0
       0.288 -    0.384: 1
       0.384 -    0.480: 1
  Chirality restraints: 1332
  Sorted by residual:
  chirality pdb=" CB  VAL A 231 "
            pdb=" CA  VAL A 231 "
            pdb=" CG1 VAL A 231 "
            pdb=" CG2 VAL A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.15   -0.48 2.00e-01 2.50e+01 5.75e+00
  chirality pdb=" CB  VAL A 194 "
            pdb=" CA  VAL A 194 "
            pdb=" CG1 VAL A 194 "
            pdb=" CG2 VAL A 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" CB  ILE A 792 "
            pdb=" CA  ILE A 792 "
            pdb=" CG1 ILE A 792 "
            pdb=" CG2 ILE A 792 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.15e-01
  ... (remaining 1329 not shown)

  Planarity restraints: 1449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 287 "    0.062 5.00e-02 4.00e+02   9.37e-02 1.40e+01
        pdb=" N   PRO A 288 "   -0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 164 "   -0.041 5.00e-02 4.00e+02   6.27e-02 6.28e+00
        pdb=" N   PRO A 165 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 165 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 165 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 824 "    0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO A 825 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 825 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 825 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1446 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 842
        2.75 -     3.29: 7895
        3.29 -     3.82: 13752
        3.82 -     4.36: 15611
        4.36 -     4.90: 27490
  Nonbonded interactions: 65590
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 517 "
            pdb="MG    MG A1301 "
     model   vdw
     2.209 2.170
  nonbonded pdb=" OD2 ASP A 689 "
            pdb=" O1A TTP T1101 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OE2 GLU A 644 "
            pdb=" OG  SER A 650 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG1 THR A 146 "
            pdb=" OD2 ASP A 149 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   PHE A 518 "
            pdb="MG    MG A1301 "
     model   vdw
     2.305 2.170
  ... (remaining 65585 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.420
  Find NCS groups from input model:        0.080
  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:11.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
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      :  0.003   0.048   8987  Z= 0.208
  Angle     :  0.654  10.613  12301  Z= 0.340
  Chirality :  0.042   0.480   1332
  Planarity :  0.005   0.094   1449
  Dihedral  : 16.773 138.423   3475
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  4.82 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.11 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.94 (0.28), residues: 976
  helix:  2.23 (0.25), residues: 443
  sheet:  0.30 (0.40), residues: 173
  loop : -1.33 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 325 
 HIS   0.004   0.001   HIS A 624 
 PHE   0.019   0.001   PHE A 324 
 TYR   0.010   0.001   TYR A 756 
 ARG   0.008   0.000   ARG A 744 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
REVERT: A  599 GLU cc_start: 0.7457 (tp30) cc_final: 0.7104 (tp30)
REVERT: A  601 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7938 (ttpt)
REVERT: A  744 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7666 (ttm110)
REVERT: A  882 HIS cc_start: 0.6987 (t70) cc_final: 0.6766 (t70)
  outliers start: 1
  outliers final: 1
  residues processed: 197
  average time/residue: 1.3530
  time to fit residues: 282.4768
Evaluate side-chains
  180 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  959 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A  29 ASN
A 778 ASN
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.123723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.108470 restraints weight = 12347.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.65
r_work: 0.3412 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8987  Z= 0.259
  Angle     :  0.601  10.624  12301  Z= 0.319
  Chirality :  0.043   0.463   1332
  Planarity :  0.005   0.065   1449
  Dihedral  : 16.522 136.873   1484
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.64 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.60 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.97 (0.28), residues: 976
  helix:  2.25 (0.25), residues: 445
  sheet:  0.23 (0.40), residues: 173
  loop : -1.28 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 325 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.002   PHE A  85 
 TYR   0.023   0.001   TYR A 756 
 ARG   0.005   0.000   ARG A 744 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 181
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8128 (tt)
REVERT: A  248 LEU cc_start: 0.8521 (mt) cc_final: 0.8293 (mp)
REVERT: A  598 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8013 (mt0)
REVERT: A  599 GLU cc_start: 0.8125 (tp30) cc_final: 0.7721 (tp30)
REVERT: A  601 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8230 (ttpt)
REVERT: A  728 SER cc_start: 0.8965 (m) cc_final: 0.8680 (m)
REVERT: A  744 ARG cc_start: 0.8436 (ttp80) cc_final: 0.7807 (ttm170)
REVERT: A  841 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7572 (t0)
REVERT: A  882 HIS cc_start: 0.7876 (t70) cc_final: 0.7510 (t70)
REVERT: A  974 TYR cc_start: 0.8131 (t80) cc_final: 0.7606 (t80)
REVERT: A  978 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7962 (tpp-160)
REVERT: A  988 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8070 (mt0)
  outliers start: 17
  outliers final: 11
  residues processed: 186
  average time/residue: 1.3842
  time to fit residues: 272.1073
Evaluate side-chains
  189 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 174
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  592 LYS
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  841 ASN
Chi-restraints excluded: chain A residue  919 SER
Chi-restraints excluded: chain A residue  988 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0870
   chunk 72 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 530 ASN
A 778 ASN
A 841 ASN
A 873 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.124914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.109513 restraints weight = 12385.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.67
r_work: 0.3431 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8987  Z= 0.190
  Angle     :  0.565  10.124  12301  Z= 0.300
  Chirality :  0.041   0.490   1332
  Planarity :  0.004   0.047   1449
  Dihedral  : 16.330 137.382   1482
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  4.82 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.42 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.07 (0.28), residues: 976
  helix:  2.37 (0.25), residues: 449
  sheet:  0.21 (0.39), residues: 173
  loop : -1.27 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 325 
 HIS   0.010   0.001   HIS A 873 
 PHE   0.016   0.001   PHE A  85 
 TYR   0.019   0.001   TYR A 756 
 ARG   0.008   0.000   ARG A 977 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 1.247 
Fit side-chains
REVERT: A  146 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8379 (p)
REVERT: A  182 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8126 (tt)
REVERT: A  185 ARG cc_start: 0.7738 (mmt90) cc_final: 0.7471 (mmt90)
REVERT: A  336 TYR cc_start: 0.8671 (m-80) cc_final: 0.8412 (m-80)
REVERT: A  598 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8004 (mt0)
REVERT: A  599 GLU cc_start: 0.8138 (tp30) cc_final: 0.7772 (tp30)
REVERT: A  601 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8245 (ttpt)
REVERT: A  644 GLU cc_start: 0.7880 (tp30) cc_final: 0.7643 (mm-30)
REVERT: A  728 SER cc_start: 0.8956 (m) cc_final: 0.8701 (m)
REVERT: A  744 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7829 (ttm170)
REVERT: A  882 HIS cc_start: 0.7842 (t70) cc_final: 0.7484 (t70)
REVERT: A  930 GLU cc_start: 0.8165 (tp30) cc_final: 0.7830 (tm-30)
  outliers start: 20
  outliers final: 8
  residues processed: 184
  average time/residue: 1.5831
  time to fit residues: 308.5303
Evaluate side-chains
  189 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  592 LYS
Chi-restraints excluded: chain A residue  598 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    0.0870
   chunk 83 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 96 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 778 ASN
A 841 ASN
A 873 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.124196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.108834 restraints weight = 12420.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.67
r_work: 0.3419 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8987  Z= 0.221
  Angle     :  0.574   9.678  12301  Z= 0.304
  Chirality :  0.042   0.528   1332
  Planarity :  0.004   0.045   1449
  Dihedral  : 16.256 137.033   1482
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.12 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.68 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.05 (0.28), residues: 976
  helix:  2.36 (0.25), residues: 449
  sheet:  0.19 (0.39), residues: 173
  loop : -1.29 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 241 
 HIS   0.009   0.001   HIS A 873 
 PHE   0.015   0.001   PHE A 889 
 TYR   0.019   0.001   TYR A 756 
 ARG   0.009   0.000   ARG A 977 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 1.008 
Fit side-chains
REVERT: A  182 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8126 (tt)
REVERT: A  248 LEU cc_start: 0.8537 (mp) cc_final: 0.8272 (mt)
REVERT: A  336 TYR cc_start: 0.8674 (m-80) cc_final: 0.8401 (m-80)
REVERT: A  598 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8000 (mt0)
REVERT: A  599 GLU cc_start: 0.8147 (tp30) cc_final: 0.7782 (tp30)
REVERT: A  601 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8222 (ttpt)
REVERT: A  728 SER cc_start: 0.8963 (m) cc_final: 0.8707 (m)
REVERT: A  744 ARG cc_start: 0.8445 (ttp80) cc_final: 0.7844 (ttm170)
REVERT: A  882 HIS cc_start: 0.7820 (t70) cc_final: 0.7456 (t70)
REVERT: A  930 GLU cc_start: 0.8170 (tp30) cc_final: 0.7826 (tm-30)
  outliers start: 23
  outliers final: 10
  residues processed: 188
  average time/residue: 1.4398
  time to fit residues: 286.7071
Evaluate side-chains
  188 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 176
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  592 LYS
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  632 LYS
Chi-restraints excluded: chain A residue  919 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 227 GLN
A 778 ASN
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.122989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.107661 restraints weight = 12379.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.66
r_work: 0.3401 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8987  Z= 0.261
  Angle     :  0.591   9.603  12301  Z= 0.313
  Chirality :  0.043   0.564   1332
  Planarity :  0.004   0.043   1449
  Dihedral  : 16.264 137.600   1482
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.33 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.24 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.98 (0.27), residues: 976
  helix:  2.35 (0.25), residues: 445
  sheet:  0.09 (0.39), residues: 175
  loop : -1.32 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 241 
 HIS   0.008   0.001   HIS A 873 
 PHE   0.012   0.002   PHE A 240 
 TYR   0.019   0.001   TYR A 756 
 ARG   0.004   0.000   ARG A 123 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 186
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  182 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8201 (tt)
REVERT: A  248 LEU cc_start: 0.8561 (mp) cc_final: 0.8317 (mt)
REVERT: A  598 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8027 (mt0)
REVERT: A  599 GLU cc_start: 0.8162 (tp30) cc_final: 0.7798 (tp30)
REVERT: A  601 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8241 (ttpt)
REVERT: A  644 GLU cc_start: 0.7926 (tp30) cc_final: 0.7691 (mm-30)
REVERT: A  728 SER cc_start: 0.8961 (m) cc_final: 0.8702 (m)
REVERT: A  744 ARG cc_start: 0.8471 (ttp80) cc_final: 0.7863 (ttm170)
REVERT: A  756 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7882 (t80)
REVERT: A  882 HIS cc_start: 0.7820 (t70) cc_final: 0.7463 (t70)
REVERT: A  930 GLU cc_start: 0.8172 (tp30) cc_final: 0.7829 (tm-30)
REVERT: A  974 TYR cc_start: 0.8387 (t80) cc_final: 0.8141 (t80)
REVERT: A  978 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.8014 (tpp-160)
  outliers start: 30
  outliers final: 12
  residues processed: 197
  average time/residue: 1.3293
  time to fit residues: 277.9576
Evaluate side-chains
  198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 183
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  592 LYS
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  632 LYS
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  919 SER
Chi-restraints excluded: chain A residue  988 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0980
   chunk 40 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   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  29 ASN
A 227 GLN
A 778 ASN
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.123788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.108576 restraints weight = 12275.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.65
r_work: 0.3421 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8987  Z= 0.213
  Angle     :  0.574   9.832  12301  Z= 0.303
  Chirality :  0.043   0.580   1332
  Planarity :  0.004   0.041   1449
  Dihedral  : 16.207 138.251   1482
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  4.92 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.29 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.01 (0.27), residues: 976
  helix:  2.38 (0.25), residues: 449
  sheet:  0.11 (0.39), residues: 173
  loop : -1.36 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 241 
 HIS   0.006   0.001   HIS A 873 
 PHE   0.012   0.001   PHE A  85 
 TYR   0.018   0.001   TYR A 756 
 ARG   0.004   0.000   ARG A  99 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A  182 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8180 (tt)
REVERT: A  248 LEU cc_start: 0.8555 (mp) cc_final: 0.8320 (mt)
REVERT: A  598 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8009 (mt0)
REVERT: A  599 GLU cc_start: 0.8163 (tp30) cc_final: 0.7818 (tp30)
REVERT: A  601 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8207 (ttpt)
REVERT: A  728 SER cc_start: 0.8949 (m) cc_final: 0.8724 (m)
REVERT: A  744 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7916 (ttm170)
REVERT: A  882 HIS cc_start: 0.7772 (t70) cc_final: 0.7428 (t70)
REVERT: A  930 GLU cc_start: 0.8119 (tp30) cc_final: 0.7828 (tm-30)
  outliers start: 20
  outliers final: 11
  residues processed: 192
  average time/residue: 1.5303
  time to fit residues: 310.9434
Evaluate side-chains
  195 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 182
  time to evaluate  : 1.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  592 LYS
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  632 LYS
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain A residue  919 SER
Chi-restraints excluded: chain A residue  988 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0470
   chunk 39 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 88 optimal weight:    0.0270
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 227 GLN
A 778 ASN
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.125171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.109872 restraints weight = 12397.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.68
r_work: 0.3438 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8987  Z= 0.171
  Angle     :  0.556   9.920  12301  Z= 0.292
  Chirality :  0.042   0.600   1332
  Planarity :  0.004   0.040   1449
  Dihedral  : 16.130 138.633   1482
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  4.61 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.61 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.13 (0.28), residues: 976
  helix:  2.52 (0.25), residues: 447
  sheet:  0.09 (0.38), residues: 178
  loop : -1.30 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 241 
 HIS   0.006   0.001   HIS A 873 
 PHE   0.011   0.001   PHE A  85 
 TYR   0.022   0.001   TYR A 974 
 ARG   0.005   0.000   ARG A  99 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 179
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A  126 PHE cc_start: 0.8180 (m-80) cc_final: 0.7971 (m-80)
REVERT: A  182 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8199 (tt)
REVERT: A  248 LEU cc_start: 0.8535 (mp) cc_final: 0.8286 (mt)
REVERT: A  598 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8004 (mt0)
REVERT: A  599 GLU cc_start: 0.8163 (tp30) cc_final: 0.7825 (tp30)
REVERT: A  601 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8160 (ttpt)
REVERT: A  644 GLU cc_start: 0.7694 (tp30) cc_final: 0.7476 (mm-30)
REVERT: A  728 SER cc_start: 0.8931 (m) cc_final: 0.8716 (m)
REVERT: A  882 HIS cc_start: 0.7801 (t70) cc_final: 0.7452 (t70)
REVERT: A  930 GLU cc_start: 0.8095 (tp30) cc_final: 0.7804 (tm-30)
  outliers start: 28
  outliers final: 10
  residues processed: 192
  average time/residue: 1.2922
  time to fit residues: 263.0951
Evaluate side-chains
  191 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 179
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain A residue  750 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0070
   chunk 97 optimal weight:    0.6980
   chunk 86 optimal weight:    0.2980
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.5400

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 227 GLN
A 778 ASN
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.124544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.109239 restraints weight = 12537.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 1.69
r_work: 0.3431 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8987  Z= 0.194
  Angle     :  0.574   9.737  12301  Z= 0.300
  Chirality :  0.042   0.586   1332
  Planarity :  0.004   0.040   1449
  Dihedral  : 16.134 138.532   1482
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  4.92 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.97 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.12 (0.28), residues: 976
  helix:  2.53 (0.25), residues: 447
  sheet: -0.00 (0.38), residues: 180
  loop : -1.29 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 241 
 HIS   0.008   0.001   HIS A 873 
 PHE   0.011   0.001   PHE A  85 
 TYR   0.018   0.001   TYR A 555 
 ARG   0.005   0.000   ARG A  99 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  182 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8204 (tt)
REVERT: A  248 LEU cc_start: 0.8535 (mp) cc_final: 0.8298 (mt)
REVERT: A  598 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8014 (mt0)
REVERT: A  599 GLU cc_start: 0.8174 (tp30) cc_final: 0.7833 (tp30)
REVERT: A  601 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8157 (ttpt)
REVERT: A  626 MET cc_start: 0.7270 (mmt) cc_final: 0.6754 (mmt)
REVERT: A  728 SER cc_start: 0.8941 (m) cc_final: 0.8718 (m)
REVERT: A  825 PRO cc_start: 0.8983 (Cg_endo) cc_final: 0.8746 (Cg_exo)
REVERT: A  882 HIS cc_start: 0.7802 (t70) cc_final: 0.7460 (t70)
REVERT: A  930 GLU cc_start: 0.8101 (tp30) cc_final: 0.7807 (tm-30)
  outliers start: 20
  outliers final: 10
  residues processed: 185
  average time/residue: 1.2969
  time to fit residues: 254.7519
Evaluate side-chains
  189 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 177
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  919 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0370
   chunk 15 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 227 GLN
A 778 ASN
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.123943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.108635 restraints weight = 12363.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.67
r_work: 0.3422 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8987  Z= 0.214
  Angle     :  0.577   9.449  12301  Z= 0.304
  Chirality :  0.042   0.549   1332
  Planarity :  0.004   0.039   1449
  Dihedral  : 16.171 138.887   1482
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.02 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.43 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.04 (0.27), residues: 976
  helix:  2.47 (0.25), residues: 445
  sheet:  0.00 (0.38), residues: 175
  loop : -1.33 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 568 
 HIS   0.008   0.001   HIS A 873 
 PHE   0.011   0.001   PHE A  85 
 TYR   0.019   0.001   TYR A 974 
 ARG   0.004   0.000   ARG A  99 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 182
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A  182 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8218 (tt)
REVERT: A  248 LEU cc_start: 0.8545 (mp) cc_final: 0.8315 (mt)
REVERT: A  598 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8006 (mt0)
REVERT: A  599 GLU cc_start: 0.8167 (tp30) cc_final: 0.7826 (tp30)
REVERT: A  601 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8181 (ttpt)
REVERT: A  728 SER cc_start: 0.8949 (m) cc_final: 0.8711 (m)
REVERT: A  825 PRO cc_start: 0.8997 (Cg_endo) cc_final: 0.8753 (Cg_exo)
REVERT: A  882 HIS cc_start: 0.7799 (t70) cc_final: 0.7449 (t70)
REVERT: A  930 GLU cc_start: 0.8108 (tp30) cc_final: 0.7804 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 189
  average time/residue: 1.3756
  time to fit residues: 275.7513
Evaluate side-chains
  191 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 179
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain A residue  919 SER
Chi-restraints excluded: chain A residue  988 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 92 optimal weight:    0.3980
   chunk 66 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 227 GLN
A 778 ASN
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.123293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.107940 restraints weight = 12442.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.69
r_work: 0.3410 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8987  Z= 0.242
  Angle     :  0.603   9.133  12301  Z= 0.317
  Chirality :  0.043   0.483   1332
  Planarity :  0.004   0.039   1449
  Dihedral  : 16.210 139.095   1482
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.43 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.89 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.97 (0.27), residues: 976
  helix:  2.41 (0.25), residues: 446
  sheet: -0.07 (0.38), residues: 175
  loop : -1.36 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 568 
 HIS   0.006   0.001   HIS A 873 
 PHE   0.011   0.001   PHE A  85 
 TYR   0.019   0.001   TYR A 555 
 ARG   0.004   0.000   ARG A  99 

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 179
  time to evaluate  : 1.134 
Fit side-chains
REVERT: A  182 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8212 (tt)
REVERT: A  248 LEU cc_start: 0.8562 (mp) cc_final: 0.8331 (mt)
REVERT: A  598 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8025 (mt0)
REVERT: A  599 GLU cc_start: 0.8184 (tp30) cc_final: 0.7817 (tp30)
REVERT: A  601 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8182 (ttpt)
REVERT: A  644 GLU cc_start: 0.7767 (tp30) cc_final: 0.7500 (mm-30)
REVERT: A  728 SER cc_start: 0.8947 (m) cc_final: 0.8697 (m)
REVERT: A  744 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7810 (ttm170)
REVERT: A  825 PRO cc_start: 0.8991 (Cg_endo) cc_final: 0.8749 (Cg_exo)
REVERT: A  882 HIS cc_start: 0.7807 (t70) cc_final: 0.7438 (t70)
REVERT: A  930 GLU cc_start: 0.8120 (tp30) cc_final: 0.7773 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 186
  average time/residue: 1.6314
  time to fit residues: 322.0406
Evaluate side-chains
  190 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  577 ASP
Chi-restraints excluded: chain A residue  598 GLN
Chi-restraints excluded: chain A residue  632 LYS
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain A residue  919 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0870
   chunk 4 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A 227 GLN
A 778 ASN
A 841 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.124372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.109070 restraints weight = 12494.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.69
r_work: 0.3427 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8987  Z= 0.202
  Angle     :  0.586   9.823  12301  Z= 0.307
  Chirality :  0.040   0.276   1332
  Planarity :  0.004   0.038   1449
  Dihedral  : 16.172 139.302   1482
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.23 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.80 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.96 (0.27), residues: 976
  helix:  2.43 (0.25), residues: 446
  sheet: -0.10 (0.38), residues: 175
  loop : -1.37 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 241 
 HIS   0.006   0.001   HIS A 873 
 PHE   0.011   0.001   PHE A  85 
 TYR   0.022   0.001   TYR A 974 
 ARG   0.005   0.000   ARG A  99 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8161.65 seconds
wall clock time: 143 minutes 9.36 seconds (8589.36 seconds total)