Starting phenix.real_space_refine
on Thu Mar 13 19:13:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpi_24615/03_2025/7rpi_24615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpi_24615/03_2025/7rpi_24615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpi_24615/03_2025/7rpi_24615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpi_24615/03_2025/7rpi_24615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpi_24615/03_2025/7rpi_24615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpi_24615/03_2025/7rpi_24615.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.579
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     Na      2      4.78       5
     C    5741      2.51       5
     N    1184      2.21       5
     O    1534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 8526
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7363
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 926, 7358
          Classifications: {'peptide': 926}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 926, 7358
          Classifications: {'peptide': 926}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 7550
    Chain: "A"
      Number of atoms: 1163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1163
          Unusual residues: {' NA': 2, 'AV0': 2, 'NAG': 5, 'Y01': 26}
          Classifications: {'undetermined': 35, 'water': 43}
          Link IDs: {None: 77}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 9.01, per 1000 atoms: 1.06
  Number of scatterers: 8526
  At special positions: 0
  Unit cell: (86.005, 87.675, 127.755, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     Na      2     11.00
     O    1534      8.00
     N    1184      7.00
     C    5741      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 292 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 366 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 347 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS A 417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 397 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 829 " - pdb=" SG  CYS A 849 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 863 " - pdb=" SG  CYS A 872 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 871 " - pdb=" SG  CYS A 887 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A2129 " - " ASN A 915 "
      " NAG A2130 " - " ASN A 834 "
      " NAG A2131 " - " ASN A 475 "
      " NAG A2132 " - " ASN A 390 "
      " NAG A2133 " - " ASN A 362 "
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1766

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 2 sheets defined
      66.1% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 187
    Processing helix  chain 'A' and resid 187 through 209
      removed outlier: 3.552A  pdb=" N   VAL A 191 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 242
    Processing helix  chain 'A' and resid 253 through 262
      removed outlier: 3.827A  pdb=" N   GLU A 259 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 329
      removed outlier: 3.564A  pdb=" N   CYS A 322 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 3.630A  pdb=" N   LEU A 338 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 361
    Processing helix  chain 'A' and resid 365 through 369
    Processing helix  chain 'A' and resid 370 through 390
      removed outlier: 5.239A  pdb=" N   LYS A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   HIS A 387 " --> pdb=" O   THR A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 430
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 463 through 471
    Processing helix  chain 'A' and resid 490 through 502
      removed outlier: 3.827A  pdb=" N   GLN A 496 " --> pdb=" O   HIS A 492 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ASP A 497 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 522
    Processing helix  chain 'A' and resid 523 through 548
      removed outlier: 3.653A  pdb=" N   THR A 527 " --> pdb=" O   SER A 523 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 538 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 559
    Processing helix  chain 'A' and resid 560 through 569
    Processing helix  chain 'A' and resid 570 through 587
      removed outlier: 3.642A  pdb=" N   VAL A 575 " --> pdb=" O   ASP A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 620
      removed outlier: 5.557A  pdb=" N   LEU A 605 " --> pdb=" O   GLN A 601 " (cutoff:3.500A)
      removed outlier: 5.253A  pdb=" N   SER A 606 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR A 614 " --> pdb=" O   THR A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 624
    Processing helix  chain 'A' and resid 626 through 648
    Processing helix  chain 'A' and resid 649 through 661
    Processing helix  chain 'A' and resid 661 through 666
    Processing helix  chain 'A' and resid 682 through 706
      removed outlier: 4.586A  pdb=" N   GLN A 687 " --> pdb=" O   ALA A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 715
      removed outlier: 3.720A  pdb=" N   CYS A 710 " --> pdb=" O   LYS A 706 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE A 715 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 736
    Processing helix  chain 'A' and resid 746 through 750
    Processing helix  chain 'A' and resid 757 through 765
      removed outlier: 3.689A  pdb=" N   ASP A 763 " --> pdb=" O   PHE A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 769
    Processing helix  chain 'A' and resid 770 through 775
    Processing helix  chain 'A' and resid 818 through 833
    Processing helix  chain 'A' and resid 849 through 859
      removed outlier: 3.608A  pdb=" N   THR A 853 " --> pdb=" O   CYS A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 869
    Processing helix  chain 'A' and resid 880 through 899
      removed outlier: 3.978A  pdb=" N   LYS A 889 " --> pdb=" O   GLU A 885 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ASP A 896 " --> pdb=" O   ILE A 892 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ARG A 897 " --> pdb=" O   MET A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 954
    Processing helix  chain 'A' and resid 969 through 1002
    Processing helix  chain 'A' and resid 1003 through 1028
    Processing helix  chain 'A' and resid 1035 through 1061
      removed outlier: 3.590A  pdb=" N   ILE A1040 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   SER A1041 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   VAL A1044 " --> pdb=" O   ILE A1040 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   ASP A1049 " --> pdb=" O   GLY A1045 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   PHE A1050 " --> pdb=" O   LEU A1046 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   ALA A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1094
      removed outlier: 5.434A  pdb=" N   SER A1079 " --> pdb=" O   SER A1075 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   ALA A1080 " --> pdb=" O   ARG A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1100 through 1123
    Processing helix  chain 'A' and resid 1123 through 1133
    Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458
      removed outlier: 4.013A  pdb=" N   SER A 300 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA A 305 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   VAL A 483 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912
      removed outlier: 3.577A  pdb=" N   ALA A 920 " --> pdb=" O   ARG A 911 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   LEU A 923 " --> pdb=" O   TRP A 789 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   TRP A 789 " --> pdb=" O   LEU A 923 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   PHE A 925 " --> pdb=" O   VAL A 787 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   VAL A 787 " --> pdb=" O   PHE A 925 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   SER A 927 " --> pdb=" O   ILE A 785 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   ILE A 785 " --> pdb=" O   SER A 927 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   PHE A 929 " --> pdb=" O   MET A 783 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.54

  Time building geometry restraints manager: 2.55 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1340
        1.32 -     1.45: 2192
        1.45 -     1.58: 5065
        1.58 -     1.70: 69
        1.70 -     1.83: 98
  Bond restraints: 8764
  Sorted by residual:
  bond pdb=" N   MET A 557 "
       pdb=" CA BMET A 557 "
    ideal  model  delta    sigma   weight residual
    1.458  1.357  0.102 1.27e-02 6.20e+03 6.43e+01
  bond pdb=" N   GLU A1031 "
       pdb=" CA  GLU A1031 "
    ideal  model  delta    sigma   weight residual
    1.454  1.400  0.053 1.23e-02 6.61e+03 1.86e+01
  bond pdb=" C   ASP A 578 "
       pdb=" O   ASP A 578 "
    ideal  model  delta    sigma   weight residual
    1.236  1.189  0.047 1.15e-02 7.56e+03 1.66e+01
  bond pdb=" CA  GLU A1031 "
       pdb=" CB  GLU A1031 "
    ideal  model  delta    sigma   weight residual
    1.535  1.462  0.073 1.93e-02 2.68e+03 1.42e+01
  bond pdb=" CB  THR A1122 "
       pdb=" OG1 THR A1122 "
    ideal  model  delta    sigma   weight residual
    1.433  1.373  0.060 1.60e-02 3.91e+03 1.42e+01
  ... (remaining 8759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 10331
        2.65 -     5.31: 1646
        5.31 -     7.96: 76
        7.96 -    10.61: 8
       10.61 -    13.26: 1
  Bond angle restraints: 12062
  Sorted by residual:
  angle pdb=" N   ARG A 341 "
        pdb=" CA  ARG A 341 "
        pdb=" C   ARG A 341 "
      ideal   model   delta    sigma   weight residual
     108.76  122.02  -13.26 1.69e+00 3.50e-01 6.16e+01
  angle pdb=" N   MET A 557 "
        pdb=" CA BMET A 557 "
        pdb=" C   MET A 557 "
      ideal   model   delta    sigma   weight residual
     111.75  120.36   -8.61 1.28e+00 6.10e-01 4.52e+01
  angle pdb=" CA  PHE A 759 "
        pdb=" CB  PHE A 759 "
        pdb=" CG  PHE A 759 "
      ideal   model   delta    sigma   weight residual
     113.80  120.40   -6.60 1.00e+00 1.00e+00 4.36e+01
  angle pdb=" CA  PHE A 549 "
        pdb=" CB  PHE A 549 "
        pdb=" CG  PHE A 549 "
      ideal   model   delta    sigma   weight residual
     113.80  120.17   -6.37 1.00e+00 1.00e+00 4.06e+01
  angle pdb=" CA  ASP A 293 "
        pdb=" CB  ASP A 293 "
        pdb=" CG  ASP A 293 "
      ideal   model   delta    sigma   weight residual
     112.60  118.82   -6.22 1.00e+00 1.00e+00 3.87e+01
  ... (remaining 12057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.89: 6362
       26.89 -    53.79: 229
       53.79 -    80.68: 41
       80.68 -   107.57: 21
      107.57 -   134.47: 6
  Dihedral angle restraints: 6659
    sinusoidal: 3931
      harmonic: 2728
  Sorted by residual:
  dihedral pdb=" CA  VAL A1048 "
           pdb=" C   VAL A1048 "
           pdb=" N   ASP A1049 "
           pdb=" CA  ASP A1049 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.68  -29.32     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  TYR A 420 "
           pdb=" C   TYR A 420 "
           pdb=" N   ASN A 421 "
           pdb=" CA  ASN A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.68  -26.32     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  TYR A 443 "
           pdb=" C   TYR A 443 "
           pdb=" N   ALA A 444 "
           pdb=" CA  ALA A 444 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.33  -24.67     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 6656 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 922
       0.095 -    0.191: 432
       0.191 -    0.286: 69
       0.286 -    0.381: 15
       0.381 -    0.477: 3
  Chirality restraints: 1441
  Sorted by residual:
  chirality pdb=" CA  GLU A1031 "
            pdb=" N   GLU A1031 "
            pdb=" C   GLU A1031 "
            pdb=" CB  GLU A1031 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CA BMET A 557 "
            pdb=" N   MET A 557 "
            pdb=" C   MET A 557 "
            pdb=" CB BMET A 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.08e+00
  chirality pdb=" CA  ASP A 916 "
            pdb=" N   ASP A 916 "
            pdb=" C   ASP A 916 "
            pdb=" CB  ASP A 916 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.86e+00
  ... (remaining 1438 not shown)

  Planarity restraints: 1344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 834 "   -0.102 2.00e-02 2.50e+03   1.05e-01 1.37e+02
        pdb=" CG  ASN A 834 "    0.066 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 834 "    0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 834 "    0.157 2.00e-02 2.50e+03
        pdb=" C1  NAG A2130 "   -0.125 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 313 "    0.145 2.00e-02 2.50e+03   7.20e-02 1.30e+02
        pdb=" CG  TRP A 313 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 313 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 313 "   -0.051 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 313 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 313 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 313 "   -0.090 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 313 "    0.084 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 313 "   -0.043 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 313 "    0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 915 "   -0.091 2.00e-02 2.50e+03   1.01e-01 1.28e+02
        pdb=" CG  ASN A 915 "    0.045 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 915 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 915 "    0.164 2.00e-02 2.50e+03
        pdb=" C1  NAG A2129 "   -0.119 2.00e-02 2.50e+03
  ... (remaining 1341 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 140
        2.72 -     3.26: 8270
        3.26 -     3.81: 12726
        3.81 -     4.35: 18480
        4.35 -     4.90: 29510
  Nonbonded interactions: 69126
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A1049 "
            pdb="NA    NA A2134 "
     model   vdw
     2.170 2.470
  nonbonded pdb=" O   GLY A1045 "
            pdb="NA    NA A2134 "
     model   vdw
     2.205 2.470
  nonbonded pdb=" OD1 ASP A 572 "
            pdb="NA    NA A2135 "
     model   vdw
     2.213 2.470
  nonbonded pdb=" OD2 ASP A 572 "
            pdb="NA    NA A2135 "
     model   vdw
     2.245 2.470
  nonbonded pdb="NA    NA A2135 "
            pdb=" O   HOH A2231 "
     model   vdw
     2.261 2.470
  ... (remaining 69121 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.50 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:             1.930
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.950
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.060
  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:13.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
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      :  0.016   0.102   8764  Z= 0.968
  Angle     :  1.818  13.262  12062  Z= 1.185
  Chirality :  0.106   0.477   1441
  Planarity :  0.014   0.100   1339
  Dihedral  : 14.731 134.467   4869
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.72 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.25), residues: 919
  helix: -0.43 (0.19), residues: 558
  sheet:  0.48 (0.94), residues: 29
  loop : -0.29 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.145   0.028   TRP A 313 
 HIS   0.008   0.003   HIS A 332 
 PHE   0.063   0.014   PHE A1109 
 TYR   0.114   0.021   TYR A 635 
 ARG   0.007   0.001   ARG A 301 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TRP cc_start: 0.7100 (m-10) cc_final: 0.6769 (m-10)
REVERT: A  194 MET cc_start: 0.5966 (mtp) cc_final: 0.5583 (mmp)
REVERT: A  647 MET cc_start: 0.7973 (mmp) cc_final: 0.7606 (mmt)
REVERT: A  698 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6555 (mm-30)
REVERT: A  700 SER cc_start: 0.7653 (t) cc_final: 0.7056 (m)
REVERT: A  701 ARG cc_start: 0.7019 (mmt90) cc_final: 0.6546 (tpm170)
REVERT: A  702 ILE cc_start: 0.6853 (mm) cc_final: 0.6584 (mm)
REVERT: A  860 ASN cc_start: 0.7009 (m-40) cc_final: 0.6679 (t0)
REVERT: A  937 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7445 (mtmm)
REVERT: A  943 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6813 (mmmt)
REVERT: A  997 MET cc_start: 0.7552 (mtm) cc_final: 0.7263 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 1.3958
  time to fit residues: 192.2684
Evaluate side-chains
  87 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 284 ASN
A 340 GLN
A 421 ASN
A 465 ASN
A 470 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.188529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.132659 restraints weight = 8621.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.07
r_work: 0.3400 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8764  Z= 0.187
  Angle     :  0.698   9.686  12062  Z= 0.334
  Chirality :  0.043   0.226   1441
  Planarity :  0.004   0.034   1339
  Dihedral  : 11.630 166.974   3198
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  6.39 %
    Favored  : 92.26 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.60 (0.28), residues: 919
  helix:  1.56 (0.21), residues: 568
  sheet:  0.71 (0.90), residues: 29
  loop :  0.35 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 474 
 HIS   0.007   0.001   HIS A 827 
 PHE   0.016   0.002   PHE A 608 
 TYR   0.015   0.002   TYR A 619 
 ARG   0.003   0.001   ARG A 363 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7479 (mtp) cc_final: 0.6739 (mmp)
REVERT: A  223 GLU cc_start: 0.8284 (tt0) cc_final: 0.7435 (pm20)
REVERT: A  340 GLN cc_start: 0.7319 (tt0) cc_final: 0.7048 (mt0)
REVERT: A  363 ARG cc_start: 0.7160 (mpt90) cc_final: 0.6940 (mpt90)
REVERT: A  515 LEU cc_start: 0.7991 (mt) cc_final: 0.7702 (tp)
REVERT: A  698 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6554 (mm-30)
REVERT: A  700 SER cc_start: 0.7986 (t) cc_final: 0.7479 (m)
REVERT: A  701 ARG cc_start: 0.7479 (mmt90) cc_final: 0.6882 (tpm170)
REVERT: A  746 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7237 (mm-30)
REVERT: A  771 MET cc_start: 0.7692 (mpp) cc_final: 0.7442 (mmp)
REVERT: A  887 CYS cc_start: 0.7638 (m) cc_final: 0.7217 (m)
REVERT: A  962 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6986 (mtm110)
  outliers start: 11
  outliers final: 5
  residues processed: 107
  average time/residue: 1.3668
  time to fit residues: 156.0474
Evaluate side-chains
  89 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  962 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0870
   chunk 79 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0050
   chunk 73 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.5172

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.188802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.135482 restraints weight = 8814.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 1.89
r_work: 0.3420 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3281
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3281
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8764  Z= 0.152
  Angle     :  0.616   7.832  12062  Z= 0.287
  Chirality :  0.041   0.365   1441
  Planarity :  0.004   0.043   1339
  Dihedral  : 10.881 179.309   3198
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.58 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.28), residues: 919
  helix:  2.03 (0.22), residues: 571
  sheet:  0.87 (0.94), residues: 29
  loop :  0.34 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 650 
 HIS   0.004   0.001   HIS A 827 
 PHE   0.014   0.001   PHE A 608 
 TYR   0.012   0.001   TYR A 545 
 ARG   0.005   0.000   ARG A 341 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7464 (mtp) cc_final: 0.6715 (mmp)
REVERT: A  223 GLU cc_start: 0.8172 (tt0) cc_final: 0.7430 (pm20)
REVERT: A  256 TYR cc_start: 0.5557 (t80) cc_final: 0.5330 (t80)
REVERT: A  339 CYS cc_start: 0.7567 (p) cc_final: 0.7310 (p)
REVERT: A  340 GLN cc_start: 0.7251 (tt0) cc_final: 0.7032 (tt0)
REVERT: A  515 LEU cc_start: 0.7921 (mt) cc_final: 0.7687 (tt)
REVERT: A  700 SER cc_start: 0.8038 (t) cc_final: 0.7520 (m)
REVERT: A  701 ARG cc_start: 0.7532 (mmt90) cc_final: 0.6926 (tpm170)
REVERT: A  771 MET cc_start: 0.7707 (mpp) cc_final: 0.7460 (mmp)
REVERT: A  887 CYS cc_start: 0.7635 (m) cc_final: 0.7206 (m)
  outliers start: 9
  outliers final: 3
  residues processed: 105
  average time/residue: 1.2215
  time to fit residues: 137.2988
Evaluate side-chains
  92 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain A residue  851 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 89 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 73 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.182940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126799 restraints weight = 14506.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.59
r_work: 0.3268 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3272
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3272
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8764  Z= 0.300
  Angle     :  0.717   8.327  12062  Z= 0.339
  Chirality :  0.047   0.404   1441
  Planarity :  0.004   0.045   1339
  Dihedral  : 11.143 173.997   3198
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  9.83 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.70 (0.28), residues: 919
  helix:  1.87 (0.22), residues: 566
  sheet:  0.87 (0.90), residues: 29
  loop : -0.12 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 650 
 HIS   0.004   0.001   HIS A 602 
 PHE   0.023   0.002   PHE A 608 
 TYR   0.020   0.002   TYR A 619 
 ARG   0.005   0.001   ARG A 774 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7282 (mtp) cc_final: 0.6502 (mmp)
REVERT: A  223 GLU cc_start: 0.8280 (tt0) cc_final: 0.7617 (pm20)
REVERT: A  340 GLN cc_start: 0.7472 (tt0) cc_final: 0.7077 (tt0)
REVERT: A  515 LEU cc_start: 0.8035 (mt) cc_final: 0.7669 (tt)
REVERT: A  659 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7063 (tt0)
REVERT: A  700 SER cc_start: 0.7983 (t) cc_final: 0.7458 (m)
REVERT: A  701 ARG cc_start: 0.7333 (mmt90) cc_final: 0.6777 (tpm170)
REVERT: A  771 MET cc_start: 0.7618 (mpp) cc_final: 0.7414 (mmp)
REVERT: A  887 CYS cc_start: 0.7435 (m) cc_final: 0.7044 (m)
REVERT: A  943 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7904 (mtpp)
  outliers start: 22
  outliers final: 9
  residues processed: 105
  average time/residue: 1.1740
  time to fit residues: 132.0950
Evaluate side-chains
  97 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain A residue  659 GLU
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  809 THR
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  943 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.190226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.138122 restraints weight = 12751.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.12
r_work: 0.3499 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8764  Z= 0.179
  Angle     :  0.611   7.758  12062  Z= 0.289
  Chirality :  0.042   0.375   1441
  Planarity :  0.004   0.043   1339
  Dihedral  : 10.630 171.655   3198
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.92 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.93 (0.28), residues: 919
  helix:  2.08 (0.22), residues: 566
  sheet:  0.87 (0.91), residues: 29
  loop : -0.06 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 650 
 HIS   0.002   0.000   HIS A 602 
 PHE   0.017   0.001   PHE A 608 
 TYR   0.012   0.001   TYR A 619 
 ARG   0.004   0.000   ARG A 962 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7382 (mtp) cc_final: 0.6646 (mmp)
REVERT: A  223 GLU cc_start: 0.8318 (tt0) cc_final: 0.7578 (pm20)
REVERT: A  340 GLN cc_start: 0.7472 (tt0) cc_final: 0.7079 (tt0)
REVERT: A  515 LEU cc_start: 0.7903 (mt) cc_final: 0.7630 (tt)
REVERT: A  700 SER cc_start: 0.8020 (t) cc_final: 0.7497 (m)
REVERT: A  701 ARG cc_start: 0.7337 (mmt90) cc_final: 0.6782 (tpm170)
REVERT: A  746 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6922 (pt0)
REVERT: A  771 MET cc_start: 0.7723 (mpp) cc_final: 0.7357 (mmp)
REVERT: A  887 CYS cc_start: 0.7538 (m) cc_final: 0.7106 (m)
REVERT: A  937 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7346 (mmpt)
REVERT: A  943 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7585 (tptt)
  outliers start: 14
  outliers final: 4
  residues processed: 101
  average time/residue: 1.1823
  time to fit residues: 128.0729
Evaluate side-chains
  92 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 81 optimal weight:    0.2980
   chunk 79 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.191026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.137314 restraints weight = 19600.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.75
r_work: 0.3467 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8764  Z= 0.166
  Angle     :  0.590   7.636  12062  Z= 0.280
  Chirality :  0.041   0.346   1441
  Planarity :  0.004   0.043   1339
  Dihedral  : 10.269 164.904   3198
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.79 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.28), residues: 919
  helix:  2.20 (0.22), residues: 566
  sheet:  0.83 (0.91), residues: 29
  loop : -0.10 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 650 
 HIS   0.002   0.000   HIS A 428 
 PHE   0.016   0.001   PHE A 608 
 TYR   0.011   0.001   TYR A 545 
 ARG   0.005   0.000   ARG A 363 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7220 (mtp) cc_final: 0.6523 (mmp)
REVERT: A  223 GLU cc_start: 0.8128 (tt0) cc_final: 0.7575 (pm20)
REVERT: A  363 ARG cc_start: 0.7228 (mtt-85) cc_final: 0.6950 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7803 (mt) cc_final: 0.7587 (tt)
REVERT: A  700 SER cc_start: 0.8003 (t) cc_final: 0.7503 (m)
REVERT: A  701 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6788 (tpm170)
REVERT: A  771 MET cc_start: 0.7676 (mpp) cc_final: 0.7476 (mmp)
REVERT: A  887 CYS cc_start: 0.7419 (m) cc_final: 0.7004 (m)
REVERT: A  937 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7343 (mmpt)
REVERT: A  943 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7630 (tptt)
  outliers start: 14
  outliers final: 6
  residues processed: 100
  average time/residue: 1.1914
  time to fit residues: 127.8145
Evaluate side-chains
  95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Chi-restraints excluded: chain A residue 1008 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0870
   chunk 77 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   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 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.191987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.141937 restraints weight = 11312.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.92
r_work: 0.3553 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3386
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8764  Z= 0.157
  Angle     :  0.578   9.039  12062  Z= 0.273
  Chirality :  0.040   0.327   1441
  Planarity :  0.004   0.043   1339
  Dihedral  : 10.106 163.088   3198
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.16 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.29), residues: 919
  helix:  2.25 (0.22), residues: 566
  sheet:  0.83 (0.91), residues: 29
  loop : -0.13 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 650 
 HIS   0.002   0.000   HIS A 428 
 PHE   0.021   0.001   PHE A 585 
 TYR   0.011   0.001   TYR A 545 
 ARG   0.004   0.000   ARG A 363 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7363 (mtp) cc_final: 0.6649 (mmp)
REVERT: A  223 GLU cc_start: 0.8203 (tt0) cc_final: 0.7558 (pm20)
REVERT: A  515 LEU cc_start: 0.7849 (mt) cc_final: 0.7629 (tt)
REVERT: A  700 SER cc_start: 0.8016 (t) cc_final: 0.7510 (m)
REVERT: A  701 ARG cc_start: 0.7387 (mmt90) cc_final: 0.6806 (tpm170)
REVERT: A  771 MET cc_start: 0.7665 (mpp) cc_final: 0.7326 (mmp)
REVERT: A  887 CYS cc_start: 0.7503 (m) cc_final: 0.7109 (m)
REVERT: A  937 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7306 (mmpt)
REVERT: A  943 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7653 (tptt)
  outliers start: 11
  outliers final: 5
  residues processed: 93
  average time/residue: 1.1555
  time to fit residues: 115.2942
Evaluate side-chains
  92 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Chi-restraints excluded: chain A residue  947 SER
Chi-restraints excluded: chain A residue 1008 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0010
   chunk 81 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.192013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.141383 restraints weight = 10980.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.02
r_work: 0.3538 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3375
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3375
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8764  Z= 0.157
  Angle     :  0.578   9.097  12062  Z= 0.272
  Chirality :  0.040   0.333   1441
  Planarity :  0.004   0.044   1339
  Dihedral  :  9.917 161.904   3198
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.79 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.29), residues: 919
  helix:  2.28 (0.22), residues: 566
  sheet:  0.81 (0.91), residues: 29
  loop : -0.21 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 650 
 HIS   0.002   0.000   HIS A 428 
 PHE   0.014   0.001   PHE A 608 
 TYR   0.011   0.001   TYR A 545 
 ARG   0.005   0.000   ARG A 363 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7343 (mtp) cc_final: 0.6616 (mmp)
REVERT: A  223 GLU cc_start: 0.8230 (tt0) cc_final: 0.7538 (pm20)
REVERT: A  515 LEU cc_start: 0.7818 (mt) cc_final: 0.7586 (tt)
REVERT: A  700 SER cc_start: 0.7872 (t) cc_final: 0.7348 (m)
REVERT: A  701 ARG cc_start: 0.7299 (mmt90) cc_final: 0.6725 (tpm170)
REVERT: A  771 MET cc_start: 0.7654 (mpp) cc_final: 0.7281 (mmp)
REVERT: A  887 CYS cc_start: 0.7535 (m) cc_final: 0.7145 (m)
REVERT: A  937 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7281 (mmpt)
REVERT: A  943 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7615 (tptt)
  outliers start: 13
  outliers final: 6
  residues processed: 94
  average time/residue: 1.3441
  time to fit residues: 136.6246
Evaluate side-chains
  95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Chi-restraints excluded: chain A residue  947 SER
Chi-restraints excluded: chain A residue 1008 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.190198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.138634 restraints weight = 11317.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.06
r_work: 0.3507 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8764  Z= 0.183
  Angle     :  0.602   9.140  12062  Z= 0.285
  Chirality :  0.041   0.333   1441
  Planarity :  0.004   0.044   1339
  Dihedral  :  9.972 159.528   3198
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 12.53 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.95 (0.29), residues: 919
  helix:  2.19 (0.22), residues: 568
  sheet:  0.84 (0.89), residues: 29
  loop : -0.27 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 650 
 HIS   0.002   0.000   HIS A 428 
 PHE   0.022   0.002   PHE A 585 
 TYR   0.012   0.001   TYR A 644 
 ARG   0.007   0.001   ARG A 363 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 1.824 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7373 (mtp) cc_final: 0.6622 (mmp)
REVERT: A  223 GLU cc_start: 0.8215 (tt0) cc_final: 0.7567 (pm20)
REVERT: A  363 ARG cc_start: 0.7323 (mtt-85) cc_final: 0.7038 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7911 (mt) cc_final: 0.7646 (tt)
REVERT: A  700 SER cc_start: 0.8015 (t) cc_final: 0.7500 (m)
REVERT: A  701 ARG cc_start: 0.7348 (mmt90) cc_final: 0.6757 (tpm170)
REVERT: A  887 CYS cc_start: 0.7484 (m) cc_final: 0.7131 (m)
REVERT: A  937 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7353 (mmpt)
REVERT: A  943 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7604 (tptt)
  outliers start: 7
  outliers final: 4
  residues processed: 91
  average time/residue: 1.7539
  time to fit residues: 174.4448
Evaluate side-chains
  92 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0470
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 21 optimal weight:    6.9990
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.190940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.140427 restraints weight = 11248.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.04
r_work: 0.3523 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8764  Z= 0.170
  Angle     :  0.597   9.368  12062  Z= 0.281
  Chirality :  0.041   0.329   1441
  Planarity :  0.004   0.044   1339
  Dihedral  :  9.920 159.951   3198
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 12.65 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.29), residues: 919
  helix:  2.24 (0.22), residues: 566
  sheet:  0.96 (0.90), residues: 29
  loop : -0.26 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 650 
 HIS   0.001   0.000   HIS A 602 
 PHE   0.015   0.001   PHE A 608 
 TYR   0.011   0.001   TYR A 644 
 ARG   0.007   0.000   ARG A 363 

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7351 (mtp) cc_final: 0.6611 (mmp)
REVERT: A  223 GLU cc_start: 0.8237 (tt0) cc_final: 0.7533 (pm20)
REVERT: A  363 ARG cc_start: 0.7254 (mtt-85) cc_final: 0.6959 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7857 (mt) cc_final: 0.7597 (tt)
REVERT: A  700 SER cc_start: 0.7972 (t) cc_final: 0.7448 (m)
REVERT: A  701 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6705 (tpm170)
REVERT: A  746 GLU cc_start: 0.7735 (pt0) cc_final: 0.6967 (pm20)
REVERT: A  887 CYS cc_start: 0.7486 (m) cc_final: 0.7091 (m)
REVERT: A  937 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7287 (mmpt)
REVERT: A  943 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7615 (tptt)
  outliers start: 8
  outliers final: 3
  residues processed: 94
  average time/residue: 1.0767
  time to fit residues: 109.4456
Evaluate side-chains
  95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0570
   chunk 52 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 58 optimal weight:    0.3980
   chunk 27 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.191673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.140912 restraints weight = 10933.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.95
r_work: 0.3542 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3378
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3378
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8764  Z= 0.162
  Angle     :  0.589  10.286  12062  Z= 0.276
  Chirality :  0.040   0.328   1441
  Planarity :  0.004   0.044   1339
  Dihedral  :  9.837 158.466   3198
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 12.90 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.29), residues: 919
  helix:  2.28 (0.22), residues: 566
  sheet:  0.96 (0.90), residues: 29
  loop : -0.24 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 650 
 HIS   0.001   0.000   HIS A 428 
 PHE   0.014   0.001   PHE A 608 
 TYR   0.011   0.001   TYR A 545 
 ARG   0.007   0.000   ARG A 363 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8847.49 seconds
wall clock time: 156 minutes 11.66 seconds (9371.66 seconds total)