Starting phenix.real_space_refine
on Mon Apr 28 11:27:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n75_24220/04_2025/7n75_24220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n75_24220/04_2025/7n75_24220.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n75_24220/04_2025/7n75_24220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n75_24220/04_2025/7n75_24220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n75_24220/04_2025/7n75_24220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n75_24220/04_2025/7n75_24220.cif"
  }
  resolution = 2.9
  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=   0.022
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: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    4740      2.51       5
     N    1272      2.21       5
     O    1326      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7381
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1036, 7378
          Classifications: {'peptide': 1036}
          Incomplete info: {'truncation_to_alanine': 184}
          Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963}
          Chain breaks: 5
          Unresolved chain link angles: 19
          Unresolved non-hydrogen bonds: 668
          Unresolved non-hydrogen angles: 855
          Unresolved non-hydrogen dihedrals: 561
          Unresolved non-hydrogen chiralities: 62
          Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 23}
          Unresolved non-hydrogen planarities: 348
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.06, per 1000 atoms: 0.69
  Number of scatterers: 7381
  At special positions: 0
  Unit cell: (92.312, 104.9, 127.978, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1326      8.00
     N    1272      7.00
     C    4740      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 9 sheets defined
      52.1% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 58
      removed outlier: 4.228A  pdb=" N   ALA A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 68
    Processing helix  chain 'A' and resid 68 through 77
      removed outlier: 4.119A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 188 through 196
    Processing helix  chain 'A' and resid 200 through 212
    Processing helix  chain 'A' and resid 222 through 232
    Processing helix  chain 'A' and resid 233 through 249
    Processing helix  chain 'A' and resid 251 through 285
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 364 through 366
      No H-bonds generated for 'chain 'A' and resid 364 through 366'
    Processing helix  chain 'A' and resid 393 through 396
    Processing helix  chain 'A' and resid 397 through 408
    Processing helix  chain 'A' and resid 419 through 445
      removed outlier: 3.690A  pdb=" N   LEU A 430 " --> pdb=" O   ALA A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 463
      removed outlier: 3.967A  pdb=" N   VAL A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 487
      removed outlier: 3.647A  pdb=" N   THR A 476 " --> pdb=" O   MET A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 500
      removed outlier: 3.800A  pdb=" N   ASN A 497 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 3.941A  pdb=" N   ARG A 540 " --> pdb=" O   GLU A 537 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 537 through 541'
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 566 through 577
    Processing helix  chain 'A' and resid 651 through 659
    Processing helix  chain 'A' and resid 667 through 678
      removed outlier: 3.516A  pdb=" N   ALA A 678 " --> pdb=" O   SER A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 701
      removed outlier: 3.722A  pdb=" N   GLN A 701 " --> pdb=" O   GLU A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 709
    Processing helix  chain 'A' and resid 726 through 737
    Processing helix  chain 'A' and resid 748 through 759
    Processing helix  chain 'A' and resid 821 through 832
    Processing helix  chain 'A' and resid 835 through 842
    Processing helix  chain 'A' and resid 850 through 863
    Processing helix  chain 'A' and resid 877 through 884
    Processing helix  chain 'A' and resid 909 through 949
      removed outlier: 3.672A  pdb=" N   ILE A 949 " --> pdb=" O   ILE A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 964
    Processing helix  chain 'A' and resid 965 through 974
      removed outlier: 4.104A  pdb=" N   SER A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1020
      removed outlier: 3.900A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1061
      removed outlier: 3.834A  pdb=" N   LEU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A1061 " --> pdb=" O   ALA A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1072
    Processing helix  chain 'A' and resid 1073 through 1093
    Processing helix  chain 'A' and resid 1109 through 1145
      Proline residue:  A1138  - end of helix
    Processing helix  chain 'A' and resid 1152 through 1164
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37
    Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41
      removed outlier: 3.930A  pdb=" N   ARG A  78 " --> pdb=" O   CYS A  41 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109
      removed outlier: 5.316A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 292
    Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315
      removed outlier: 4.735A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A 387 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ASP A 325 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.643A  pdb=" N   GLU A 332 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ALA A 378 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   MET A 334 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490
      removed outlier: 5.795A  pdb=" N   GLY A 887 " --> pdb=" O   PHE A 901 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   SER A 903 " --> pdb=" O   GLY A 887 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   SER A 889 " --> pdb=" O   SER A 903 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   THR A 844 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   THR A 844 " --> pdb=" O   ARG A 816 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   LEU A 818 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   PHE A 846 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LEU A 820 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   LEU A 768 " --> pdb=" O   MET A 789 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 519 through 525
      removed outlier: 5.355A  pdb=" N   VAL A 520 " --> pdb=" O   ARG A 720 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ARG A 720 " --> pdb=" O   VAL A 520 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY A 522 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   LEU A 713 " --> pdb=" O   SER A 687 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   SER A 687 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   ARG A 631 " --> pdb=" O   PHE A 625 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   PHE A 625 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ALA A 637 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   VAL A 619 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   SER A 588 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 579 " --> pdb=" O   GLY A 591 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559
      removed outlier: 3.972A  pdb=" N   SER A 557 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL A 564 " --> pdb=" O   SER A 557 " (cutoff:3.500A)

    461 hydrogen bonds defined for protein.
    1323 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: 2.82

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1397
        1.33 -     1.45: 1697
        1.45 -     1.57: 4361
        1.57 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 7518
  Sorted by residual:
  bond pdb=" CB  VAL A 107 "
       pdb=" CG2 VAL A 107 "
    ideal  model  delta    sigma   weight residual
    1.521  1.334  0.187 3.30e-02 9.18e+02 3.22e+01
  bond pdb=" CB  TYR A 935 "
       pdb=" CG  TYR A 935 "
    ideal  model  delta    sigma   weight residual
    1.512  1.410  0.102 2.20e-02 2.07e+03 2.15e+01
  bond pdb=" CB  VAL A 105 "
       pdb=" CG1 VAL A 105 "
    ideal  model  delta    sigma   weight residual
    1.521  1.400  0.121 3.30e-02 9.18e+02 1.34e+01
  bond pdb=" CE1 TYR A 935 "
       pdb=" CZ  TYR A 935 "
    ideal  model  delta    sigma   weight residual
    1.378  1.303  0.075 2.40e-02 1.74e+03 9.67e+00
  bond pdb=" C   TYR A 935 "
       pdb=" O   TYR A 935 "
    ideal  model  delta    sigma   weight residual
    1.236  1.205  0.031 1.21e-02 6.83e+03 6.44e+00
  ... (remaining 7513 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 10135
        2.36 -     4.73: 134
        4.73 -     7.09: 11
        7.09 -     9.45: 2
        9.45 -    11.82: 1
  Bond angle restraints: 10283
  Sorted by residual:
  angle pdb=" CG1 VAL A 107 "
        pdb=" CB  VAL A 107 "
        pdb=" CG2 VAL A 107 "
      ideal   model   delta    sigma   weight residual
     110.80   98.98   11.82 2.20e+00 2.07e-01 2.89e+01
  angle pdb=" N   VAL A 897 "
        pdb=" CA  VAL A 897 "
        pdb=" C   VAL A 897 "
      ideal   model   delta    sigma   weight residual
     113.20  108.75    4.45 9.60e-01 1.09e+00 2.15e+01
  angle pdb=" C   TYR A 935 "
        pdb=" N   SER A 936 "
        pdb=" CA  SER A 936 "
      ideal   model   delta    sigma   weight residual
     120.44  124.73   -4.29 1.30e+00 5.92e-01 1.09e+01
  angle pdb=" N   PHE A 103 "
        pdb=" CA  PHE A 103 "
        pdb=" C   PHE A 103 "
      ideal   model   delta    sigma   weight residual
     109.50  105.20    4.30 1.58e+00 4.01e-01 7.39e+00
  angle pdb=" CA  VAL A 107 "
        pdb=" CB  VAL A 107 "
        pdb=" CG2 VAL A 107 "
      ideal   model   delta    sigma   weight residual
     110.40  105.90    4.50 1.70e+00 3.46e-01 7.01e+00
  ... (remaining 10278 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4155
       17.88 -    35.77: 284
       35.77 -    53.65: 35
       53.65 -    71.53: 9
       71.53 -    89.42: 7
  Dihedral angle restraints: 4490
    sinusoidal: 1497
      harmonic: 2993
  Sorted by residual:
  dihedral pdb=" CA  SER A 889 "
           pdb=" C   SER A 889 "
           pdb=" N   LEU A 890 "
           pdb=" CA  LEU A 890 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.71  -17.29     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  CYS A1136 "
           pdb=" C   CYS A1136 "
           pdb=" N   LEU A1137 "
           pdb=" CA  LEU A1137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.90  -17.10     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  GLN A 865 "
           pdb=" C   GLN A 865 "
           pdb=" N   TYR A 866 "
           pdb=" CA  TYR A 866 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.02   16.98     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 4487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1160
       0.083 -    0.166: 103
       0.166 -    0.249: 2
       0.249 -    0.332: 0
       0.332 -    0.415: 1
  Chirality restraints: 1266
  Sorted by residual:
  chirality pdb=" CG  LEU A 158 "
            pdb=" CB  LEU A 158 "
            pdb=" CD1 LEU A 158 "
            pdb=" CD2 LEU A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.17   -0.41 2.00e-01 2.50e+01 4.30e+00
  chirality pdb=" CB  VAL A 969 "
            pdb=" CA  VAL A 969 "
            pdb=" CG1 VAL A 969 "
            pdb=" CG2 VAL A 969 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  ILE A 441 "
            pdb=" CA  ILE A 441 "
            pdb=" CG1 ILE A 441 "
            pdb=" CG2 ILE A 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.05e-01
  ... (remaining 1263 not shown)

  Planarity restraints: 1314
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 935 "    0.066 2.00e-02 2.50e+03   3.55e-02 2.52e+01
        pdb=" CG  TYR A 935 "   -0.062 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 935 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 935 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 935 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 935 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 935 "    0.024 2.00e-02 2.50e+03
        pdb=" OH  TYR A 935 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 955 "   -0.015 2.00e-02 2.50e+03   3.14e-02 9.83e+00
        pdb=" CG  ASP A 955 "    0.054 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 955 "   -0.020 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 955 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 934 "   -0.015 2.00e-02 2.50e+03   3.08e-02 9.48e+00
        pdb=" C   LEU A 934 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LEU A 934 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 935 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1311 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 184
        2.71 -     3.25: 7513
        3.25 -     3.80: 12082
        3.80 -     4.35: 14712
        4.35 -     4.90: 25727
  Nonbonded interactions: 60218
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 235 "
            pdb=" O   PRO A 465 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OH  TYR A 359 "
            pdb=" OG1 THR A 368 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER A 889 "
            pdb=" OG  SER A 899 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   ASP A 325 "
            pdb=" OG1 THR A 391 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OE2 GLU A 860 "
            pdb=" NZ  LYS A 863 "
     model   vdw
     2.273 3.120
  ... (remaining 60213 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=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:             1.490
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.870
  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:14.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
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      :  0.007   0.187   7518  Z= 0.274
  Angle     :  0.689  11.817  10283  Z= 0.376
  Chirality :  0.047   0.415   1266
  Planarity :  0.005   0.058   1314
  Dihedral  : 12.885  89.418   2556
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  0.75 (0.26), residues: 1024
  helix:  1.13 (0.23), residues: 496
  sheet:  0.16 (0.39), residues: 161
  loop : -0.04 (0.35), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 100 
 HIS   0.002   0.001   HIS A 367 
 PHE   0.041   0.002   PHE A 958 
 TYR   0.066   0.003   TYR A 935 
 ARG   0.006   0.001   ARG A1153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15624 (  461)
  hydrogen bonds       : angle       6.44583 ( 1323)
  covalent geometry    : bond        0.00659 ( 7518)
  covalent geometry    : angle       0.68928 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.864 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 1.0675
  time to fit residues: 58.7727
Evaluate side-chains
  36 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:   50.0000
   chunk 41 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:   40.0000
   chunk 60 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 957 GLN
A1042 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.094490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.064268 restraints weight = 19528.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 3.04
r_work: 0.2945 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7518  Z= 0.141
  Angle     :  0.560   7.309  10283  Z= 0.284
  Chirality :  0.041   0.142   1266
  Planarity :  0.005   0.054   1314
  Dihedral  :  4.219  16.078   1097
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  5.55 %
    Favored  : 93.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.42 (0.27), residues: 1024
  helix:  1.74 (0.23), residues: 508
  sheet:  0.41 (0.42), residues: 160
  loop :  0.15 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A 408 
 PHE   0.022   0.001   PHE A 958 
 TYR   0.018   0.001   TYR A 935 
 ARG   0.010   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  461)
  hydrogen bonds       : angle       4.73944 ( 1323)
  covalent geometry    : bond        0.00328 ( 7518)
  covalent geometry    : angle       0.56008 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.9015 (tppp) cc_final: 0.8749 (tppt)
  outliers start: 6
  outliers final: 3
  residues processed: 43
  average time/residue: 1.2173
  time to fit residues: 56.2427
Evaluate side-chains
  40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue  981 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 55 optimal weight:   40.0000
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3783 r_free = 0.3783 target = 0.093853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.063531 restraints weight = 19988.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 3.09
r_work: 0.2937 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7518  Z= 0.149
  Angle     :  0.535   6.616  10283  Z= 0.266
  Chirality :  0.041   0.152   1266
  Planarity :  0.004   0.046   1314
  Dihedral  :  3.982  15.726   1097
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  8.25 %
    Favored  : 90.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.74 (0.27), residues: 1024
  helix:  2.06 (0.23), residues: 510
  sheet:  0.47 (0.42), residues: 161
  loop :  0.26 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A 408 
 PHE   0.016   0.001   PHE A 958 
 TYR   0.015   0.001   TYR A 935 
 ARG   0.008   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  461)
  hydrogen bonds       : angle       4.42338 ( 1323)
  covalent geometry    : bond        0.00350 ( 7518)
  covalent geometry    : angle       0.53532 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A  379 ARG cc_start: 0.8186 (mmm160) cc_final: 0.7963 (mmm160)
  outliers start: 7
  outliers final: 1
  residues processed: 44
  average time/residue: 0.9965
  time to fit residues: 47.6676
Evaluate side-chains
  36 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  981 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 61 optimal weight:    0.1980
   chunk 48 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 2 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.094350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.064540 restraints weight = 19797.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 3.07
r_work: 0.2959 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7518  Z= 0.114
  Angle     :  0.518   7.113  10283  Z= 0.253
  Chirality :  0.040   0.129   1266
  Planarity :  0.004   0.047   1314
  Dihedral  :  3.837  17.000   1097
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  9.67 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  1.96 (0.27), residues: 1024
  helix:  2.27 (0.23), residues: 511
  sheet:  0.42 (0.41), residues: 162
  loop :  0.38 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 775 
 PHE   0.014   0.001   PHE A 940 
 TYR   0.014   0.001   TYR A 935 
 ARG   0.004   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  461)
  hydrogen bonds       : angle       4.23720 ( 1323)
  covalent geometry    : bond        0.00266 ( 7518)
  covalent geometry    : angle       0.51778 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.759 
Fit side-chains
REVERT: A  381 TYR cc_start: 0.8193 (m-80) cc_final: 0.7798 (m-80)
  outliers start: 6
  outliers final: 1
  residues processed: 42
  average time/residue: 1.1124
  time to fit residues: 50.6055
Evaluate side-chains
  39 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 77 optimal weight:    0.8980
   chunk 47 optimal weight:   30.0000
   chunk 67 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 90 optimal weight:    7.9990
   chunk 92 optimal weight:    0.5980
   chunk 49 optimal weight:   40.0000
   chunk 101 optimal weight:    8.9990
   chunk 62 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.094004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.064289 restraints weight = 19781.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 3.07
r_work: 0.2955 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7518  Z= 0.117
  Angle     :  0.507   7.277  10283  Z= 0.247
  Chirality :  0.040   0.132   1266
  Planarity :  0.004   0.046   1314
  Dihedral  :  3.735  15.951   1097
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.52 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.15 (0.27), residues: 1024
  helix:  2.47 (0.23), residues: 510
  sheet:  0.44 (0.42), residues: 151
  loop :  0.45 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 775 
 PHE   0.013   0.001   PHE A 940 
 TYR   0.014   0.001   TYR A 935 
 ARG   0.012   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  461)
  hydrogen bonds       : angle       4.12514 ( 1323)
  covalent geometry    : bond        0.00272 ( 7518)
  covalent geometry    : angle       0.50672 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  379 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7893 (mmm160)
REVERT: A  381 TYR cc_start: 0.8247 (m-80) cc_final: 0.7809 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 40
  average time/residue: 1.0410
  time to fit residues: 45.3637
Evaluate side-chains
  38 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue  973 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 90 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 98 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.093029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.063022 restraints weight = 19884.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 3.09
r_work: 0.2916 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7518  Z= 0.168
  Angle     :  0.545   7.361  10283  Z= 0.264
  Chirality :  0.041   0.138   1266
  Planarity :  0.004   0.044   1314
  Dihedral  :  3.776  16.091   1097
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.80 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.10 (0.27), residues: 1024
  helix:  2.46 (0.22), residues: 511
  sheet:  0.11 (0.40), residues: 162
  loop :  0.52 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1166 
 HIS   0.002   0.000   HIS A 817 
 PHE   0.014   0.001   PHE A1154 
 TYR   0.011   0.001   TYR A 935 
 ARG   0.006   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03438 (  461)
  hydrogen bonds       : angle       4.15641 ( 1323)
  covalent geometry    : bond        0.00397 ( 7518)
  covalent geometry    : angle       0.54510 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.8946 (tppp) cc_final: 0.8721 (tmmt)
REVERT: A  379 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7928 (mmm160)
  outliers start: 8
  outliers final: 5
  residues processed: 39
  average time/residue: 1.0226
  time to fit residues: 43.3448
Evaluate side-chains
  41 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  973 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 49 optimal weight:   40.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.093243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.063408 restraints weight = 19882.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 3.07
r_work: 0.2934 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7518  Z= 0.143
  Angle     :  0.515   8.050  10283  Z= 0.250
  Chirality :  0.040   0.137   1266
  Planarity :  0.004   0.044   1314
  Dihedral  :  3.723  15.866   1097
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.52 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.19 (0.27), residues: 1024
  helix:  2.56 (0.22), residues: 511
  sheet:  0.19 (0.41), residues: 150
  loop :  0.50 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 367 
 PHE   0.013   0.001   PHE A 940 
 TYR   0.012   0.001   TYR A 935 
 ARG   0.005   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03253 (  461)
  hydrogen bonds       : angle       4.07517 ( 1323)
  covalent geometry    : bond        0.00338 ( 7518)
  covalent geometry    : angle       0.51512 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.8927 (tppp) cc_final: 0.8679 (tmmt)
REVERT: A  379 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7984 (mmm160)
  outliers start: 11
  outliers final: 4
  residues processed: 44
  average time/residue: 0.9998
  time to fit residues: 47.9827
Evaluate side-chains
  40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  973 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 48 optimal weight:   20.0000
   chunk 29 optimal weight:    6.9990
   chunk 87 optimal weight:    0.6980
   chunk 58 optimal weight:   50.0000
   chunk 73 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 44 optimal weight:   50.0000
   chunk 66 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 64 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 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.093480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.063739 restraints weight = 19948.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 3.09
r_work: 0.2937 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7518  Z= 0.122
  Angle     :  0.526   8.983  10283  Z= 0.252
  Chirality :  0.040   0.138   1266
  Planarity :  0.004   0.044   1314
  Dihedral  :  3.655  15.899   1097
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.52 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.26 (0.27), residues: 1024
  helix:  2.63 (0.22), residues: 511
  sheet:  0.19 (0.41), residues: 152
  loop :  0.52 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 367 
 PHE   0.013   0.001   PHE A 940 
 TYR   0.013   0.001   TYR A 935 
 ARG   0.003   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  461)
  hydrogen bonds       : angle       4.02137 ( 1323)
  covalent geometry    : bond        0.00291 ( 7518)
  covalent geometry    : angle       0.52596 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.8898 (tppp) cc_final: 0.8676 (tmmt)
REVERT: A  719 MET cc_start: 0.8153 (mtm) cc_final: 0.7594 (mtp)
  outliers start: 11
  outliers final: 4
  residues processed: 44
  average time/residue: 1.0050
  time to fit residues: 48.2187
Evaluate side-chains
  40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  722 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 47 optimal weight:   30.0000
   chunk 83 optimal weight:    0.3980
   chunk 28 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 53 optimal weight:   50.0000
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 59 optimal weight:   30.0000
   chunk 40 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.5982

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.092520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.062671 restraints weight = 20109.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.10
r_work: 0.2912 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7518  Z= 0.188
  Angle     :  0.562   9.363  10283  Z= 0.271
  Chirality :  0.041   0.139   1266
  Planarity :  0.004   0.051   1314
  Dihedral  :  3.752  15.794   1097
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.37 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.16 (0.27), residues: 1024
  helix:  2.45 (0.22), residues: 518
  sheet:  0.09 (0.41), residues: 156
  loop :  0.66 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 246 
 HIS   0.002   0.000   HIS A 817 
 PHE   0.015   0.001   PHE A 940 
 TYR   0.015   0.001   TYR A 935 
 ARG   0.012   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  461)
  hydrogen bonds       : angle       4.09980 ( 1323)
  covalent geometry    : bond        0.00447 ( 7518)
  covalent geometry    : angle       0.56191 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.8888 (tppp) cc_final: 0.8637 (tmmt)
REVERT: A  379 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8555 (mmt-90)
REVERT: A  381 TYR cc_start: 0.8370 (m-80) cc_final: 0.7792 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 41
  average time/residue: 1.0607
  time to fit residues: 47.3033
Evaluate side-chains
  41 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  722 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 101 optimal weight:    0.0170
   chunk 40 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.093358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.063853 restraints weight = 20032.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 3.10
r_work: 0.2944 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7518  Z= 0.117
  Angle     :  0.530   9.825  10283  Z= 0.255
  Chirality :  0.040   0.137   1266
  Planarity :  0.004   0.056   1314
  Dihedral  :  3.645  15.800   1097
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.66 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.27), residues: 1024
  helix:  2.60 (0.23), residues: 517
  sheet:  0.36 (0.42), residues: 144
  loop :  0.60 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 367 
 PHE   0.013   0.001   PHE A 940 
 TYR   0.022   0.001   TYR A 935 
 ARG   0.014   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03130 (  461)
  hydrogen bonds       : angle       3.99597 ( 1323)
  covalent geometry    : bond        0.00275 ( 7518)
  covalent geometry    : angle       0.52951 (10283)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  379 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8547 (mmt-90)
REVERT: A  381 TYR cc_start: 0.8373 (m-80) cc_final: 0.7781 (m-80)
REVERT: A  719 MET cc_start: 0.8156 (mtm) cc_final: 0.7561 (mtp)
  outliers start: 6
  outliers final: 3
  residues processed: 41
  average time/residue: 0.9853
  time to fit residues: 43.9358
Evaluate side-chains
  39 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  722 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 71 optimal weight:    0.1980
   chunk 42 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 58 optimal weight:   50.0000
   chunk 26 optimal weight:    6.9990
   chunk 55 optimal weight:   50.0000
   chunk 5 optimal weight:    0.0980
   chunk 7 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.093900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.064586 restraints weight = 19839.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 3.10
r_work: 0.2960 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7518  Z= 0.107
  Angle     :  0.538   9.675  10283  Z= 0.256
  Chirality :  0.040   0.136   1266
  Planarity :  0.004   0.053   1314
  Dihedral  :  3.558  15.918   1097
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.80 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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:  2.38 (0.27), residues: 1024
  helix:  2.65 (0.23), residues: 518
  sheet:  0.38 (0.41), residues: 149
  loop :  0.60 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 775 
 PHE   0.013   0.001   PHE A 940 
 TYR   0.022   0.001   TYR A 935 
 ARG   0.013   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03028 (  461)
  hydrogen bonds       : angle       3.93599 ( 1323)
  covalent geometry    : bond        0.00253 ( 7518)
  covalent geometry    : angle       0.53841 (10283)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4797.89 seconds
wall clock time: 82 minutes 39.92 seconds (4959.92 seconds total)