Starting phenix.real_space_refine
on Tue Mar  3 17:13:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n75_24220/03_2026/7n75_24220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n75_24220/03_2026/7n75_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_24220/03_2026/7n75_24220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n75_24220/03_2026/7n75_24220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n75_24220/03_2026/7n75_24220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n75_24220/03_2026/7n75_24220.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 23, 'TRP:plan': 5, 'TYR:plan': 2, 'HIS:plan': 4, 'PHE:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 13, 'GLN:plan1': 9, 'ASP:plan': 8}
          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: 1.63, per 1000 atoms: 0.22
  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: 0.74
  Conformation dependent library (CDL) restraints added in 323.8 milliseconds
  

  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: 0.32
  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: 1.53

  Time building geometry restraints manager: 0.93 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:             2.670
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.090
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:6.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.250
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.001   ARG A1153 
 TYR   0.066   0.003   TYR A 935 
 PHE   0.041   0.002   PHE A 958 
 TRP   0.013   0.002   TRP A 100 
 HIS   0.002   0.001   HIS A 367 

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

*********************** 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  : 0.288 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.4953
  time to fit residues: 27.0944
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  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:   40.0000
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:   30.0000
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0020
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.095029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.064805 restraints weight = 19785.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 3.06
r_work: 0.2961 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7518  Z= 0.124
  Angle     :  0.551   7.328  10283  Z= 0.279
  Chirality :  0.041   0.133   1266
  Planarity :  0.005   0.052   1314
  Dihedral  :  4.185  15.976   1097
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  5.55 %
    Favored  : 93.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.26), residues: 1024
  helix:  1.77 (0.23), residues: 508
  sheet:  0.44 (0.42), residues: 160
  loop :  0.15 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 379 
 TYR   0.018   0.001   TYR A 935 
 PHE   0.021   0.001   PHE A 958 
 TRP   0.016   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7518)
  covalent geometry    : angle       0.55086 (10283)
  hydrogen bonds       : bond        0.03798 (  461)
  hydrogen bonds       : angle       4.70140 ( 1323)

*********************** 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
  48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.9014 (tppp) cc_final: 0.8771 (tptp)
  outliers start: 5
  outliers final: 1
  residues processed: 44
  average time/residue: 0.5386
  time to fit residues: 25.3500
Evaluate side-chains
  37 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  905 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 55 optimal weight:   40.0000
   chunk 43 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 58 optimal weight:   50.0000
   chunk 14 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.093859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.063742 restraints weight = 19751.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 3.07
r_work: 0.2939 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7518  Z= 0.150
  Angle     :  0.542   6.684  10283  Z= 0.267
  Chirality :  0.041   0.154   1266
  Planarity :  0.004   0.047   1314
  Dihedral  :  3.967  16.374   1097
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.53 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.27), residues: 1024
  helix:  2.08 (0.23), residues: 510
  sheet:  0.44 (0.41), residues: 161
  loop :  0.27 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 379 
 TYR   0.014   0.001   TYR A 935 
 PHE   0.017   0.001   PHE A 958 
 TRP   0.004   0.001   TRP A 301 
 HIS   0.002   0.000   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7518)
  covalent geometry    : angle       0.54211 (10283)
  hydrogen bonds       : bond        0.03643 (  461)
  hydrogen bonds       : angle       4.40024 ( 1323)

*********************** 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: 8
    poor density    : 38
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A  381 TYR cc_start: 0.8220 (m-80) cc_final: 0.7822 (m-80)
  outliers start: 8
  outliers final: 2
  residues processed: 43
  average time/residue: 0.4963
  time to fit residues: 22.9027
Evaluate side-chains
  37 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 LEU
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 2 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0070
   chunk 79 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   chunk 45 optimal weight:   40.0000
   chunk 36 optimal weight:    0.0470
   chunk 4 optimal weight:    8.9990
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.094819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.064988 restraints weight = 20107.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 3.09
r_work: 0.2972 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7518  Z= 0.105
  Angle     :  0.514   7.613  10283  Z= 0.251
  Chirality :  0.040   0.129   1266
  Planarity :  0.004   0.048   1314
  Dihedral  :  3.811  16.863   1097
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.67 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.27), residues: 1024
  helix:  2.32 (0.23), residues: 511
  sheet:  0.51 (0.41), residues: 161
  loop :  0.37 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 379 
 TYR   0.014   0.001   TYR A 935 
 PHE   0.013   0.001   PHE A 940 
 TRP   0.008   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 775 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7518)
  covalent geometry    : angle       0.51389 (10283)
  hydrogen bonds       : bond        0.03198 (  461)
  hydrogen bonds       : angle       4.22378 ( 1323)

*********************** 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
  48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  270 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8101 (mm)
REVERT: A  381 TYR cc_start: 0.8233 (m-80) cc_final: 0.7818 (m-80)
  outliers start: 7
  outliers final: 1
  residues processed: 45
  average time/residue: 0.4477
  time to fit residues: 21.8227
Evaluate side-chains
  38 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
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 82 optimal weight:    0.8980
   chunk 49 optimal weight:   50.0000
   chunk 32 optimal weight:    0.0870
   chunk 28 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 79 optimal weight:    0.5980
   chunk 25 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.9162

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.093869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.064038 restraints weight = 19979.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 3.08
r_work: 0.2943 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7518  Z= 0.129
  Angle     :  0.517   7.175  10283  Z= 0.253
  Chirality :  0.040   0.134   1266
  Planarity :  0.004   0.049   1314
  Dihedral  :  3.724  15.777   1097
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.95 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.27), residues: 1024
  helix:  2.51 (0.22), residues: 510
  sheet:  0.46 (0.42), residues: 151
  loop :  0.48 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 379 
 TYR   0.012   0.001   TYR A 935 
 PHE   0.014   0.001   PHE A 940 
 TRP   0.004   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7518)
  covalent geometry    : angle       0.51655 (10283)
  hydrogen bonds       : bond        0.03246 (  461)
  hydrogen bonds       : angle       4.13115 ( 1323)

*********************** 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
  40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  381 TYR cc_start: 0.8227 (m-80) cc_final: 0.7799 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 37
  average time/residue: 0.5164
  time to fit residues: 20.7370
Evaluate side-chains
  37 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  432 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 74 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 12 optimal weight:    0.2980
   chunk 29 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.094442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.064560 restraints weight = 19808.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 3.11
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: 0.7896
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7518  Z= 0.105
  Angle     :  0.508   7.639  10283  Z= 0.245
  Chirality :  0.040   0.135   1266
  Planarity :  0.004   0.060   1314
  Dihedral  :  3.644  16.297   1097
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.09 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.27), residues: 1024
  helix:  2.63 (0.22), residues: 511
  sheet:  0.33 (0.42), residues: 149
  loop :  0.48 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 379 
 TYR   0.013   0.001   TYR A 935 
 PHE   0.013   0.001   PHE A 940 
 TRP   0.007   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 775 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7518)
  covalent geometry    : angle       0.50759 (10283)
  hydrogen bonds       : bond        0.03026 (  461)
  hydrogen bonds       : angle       4.02639 ( 1323)

*********************** 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
  47 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.8932 (tppp) cc_final: 0.8711 (tmmt)
REVERT: A  719 MET cc_start: 0.8027 (mtm) cc_final: 0.7501 (mtp)
REVERT: A 1160 GLU cc_start: 0.8883 (tt0) cc_final: 0.8194 (tm-30)
  outliers start: 9
  outliers final: 3
  residues processed: 43
  average time/residue: 0.4781
  time to fit residues: 22.1851
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  : 0.294 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.093983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.064218 restraints weight = 19957.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 3.10
r_work: 0.2957 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7518  Z= 0.120
  Angle     :  0.522   8.370  10283  Z= 0.250
  Chirality :  0.040   0.135   1266
  Planarity :  0.004   0.065   1314
  Dihedral  :  3.602  15.756   1097
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.80 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.27), residues: 1024
  helix:  2.71 (0.22), residues: 511
  sheet:  0.16 (0.40), residues: 162
  loop :  0.60 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 379 
 TYR   0.012   0.001   TYR A 935 
 PHE   0.013   0.001   PHE A 940 
 TRP   0.004   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7518)
  covalent geometry    : angle       0.52207 (10283)
  hydrogen bonds       : bond        0.03113 (  461)
  hydrogen bonds       : angle       3.98563 ( 1323)

*********************** 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
  45 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.8878 (tppp) cc_final: 0.8659 (tmmt)
REVERT: A  379 ARG cc_start: 0.8314 (mmm160) cc_final: 0.8070 (mmm160)
REVERT: A  381 TYR cc_start: 0.8221 (m-80) cc_final: 0.7753 (m-80)
  outliers start: 7
  outliers final: 2
  residues processed: 41
  average time/residue: 0.4781
  time to fit residues: 21.1689
Evaluate side-chains
  38 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  432 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 53 optimal weight:   50.0000
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 52 optimal weight:   50.0000
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.093838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.064108 restraints weight = 20115.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 3.11
r_work: 0.2951 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7518  Z= 0.122
  Angle     :  0.531   9.158  10283  Z= 0.253
  Chirality :  0.040   0.136   1266
  Planarity :  0.004   0.051   1314
  Dihedral  :  3.575  15.725   1097
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.66 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.35 (0.27), residues: 1024
  helix:  2.64 (0.23), residues: 517
  sheet:  0.14 (0.40), residues: 164
  loop :  0.70 (0.36), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 379 
 TYR   0.010   0.001   TYR A 935 
 PHE   0.013   0.001   PHE A 940 
 TRP   0.004   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7518)
  covalent geometry    : angle       0.53054 (10283)
  hydrogen bonds       : bond        0.03096 (  461)
  hydrogen bonds       : angle       3.96065 ( 1323)

*********************** 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
  45 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  285 LYS cc_start: 0.8886 (tppp) cc_final: 0.8652 (tmmt)
REVERT: A  421 MET cc_start: 0.7989 (mmm) cc_final: 0.7213 (tmm)
REVERT: A  719 MET cc_start: 0.7988 (mtm) cc_final: 0.7441 (mtp)
  outliers start: 9
  outliers final: 3
  residues processed: 40
  average time/residue: 0.5145
  time to fit residues: 22.1919
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  : 0.245 
-------------------------------------------------------------------------------
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  432 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 50 optimal weight:   50.0000
   chunk 48 optimal weight:   20.0000
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:    0.3980
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.094131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.064526 restraints weight = 19738.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 3.08
r_work: 0.2962 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2274

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= 0.112
  Angle     :  0.537   9.315  10283  Z= 0.254
  Chirality :  0.040   0.136   1266
  Planarity :  0.004   0.071   1314
  Dihedral  :  3.549  15.721   1097
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.37 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.27), residues: 1024
  helix:  2.68 (0.23), residues: 517
  sheet:  0.25 (0.40), residues: 156
  loop :  0.68 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG A 379 
 TYR   0.011   0.001   TYR A 935 
 PHE   0.013   0.001   PHE A 940 
 TRP   0.005   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 775 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7518)
  covalent geometry    : angle       0.53688 (10283)
  hydrogen bonds       : bond        0.03034 (  461)
  hydrogen bonds       : angle       3.93147 ( 1323)

*********************** 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: 6
    poor density    : 37
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8037 (mmm) cc_final: 0.7251 (tmm)
REVERT: A  719 MET cc_start: 0.8027 (mtm) cc_final: 0.7469 (mtp)
  outliers start: 6
  outliers final: 3
  residues processed: 41
  average time/residue: 0.5070
  time to fit residues: 22.3503
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  : 0.300 
-------------------------------------------------------------------------------
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  432 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 50 optimal weight:   50.0000
   chunk 56 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0670
   chunk 73 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.5296

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.094520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.064653 restraints weight = 19688.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 3.10
r_work: 0.2979 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7518  Z= 0.104
  Angle     :  0.545   9.863  10283  Z= 0.257
  Chirality :  0.040   0.135   1266
  Planarity :  0.004   0.075   1314
  Dihedral  :  3.495  15.766   1097
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 13.66 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.27), residues: 1024
  helix:  2.78 (0.23), residues: 515
  sheet:  0.30 (0.41), residues: 155
  loop :  0.61 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A 379 
 TYR   0.013   0.001   TYR A 935 
 PHE   0.012   0.001   PHE A 940 
 TRP   0.006   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 775 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7518)
  covalent geometry    : angle       0.54459 (10283)
  hydrogen bonds       : bond        0.02965 (  461)
  hydrogen bonds       : angle       3.88017 ( 1323)

********************** 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
  43 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  285 LYS cc_start: 0.8874 (tppp) cc_final: 0.8606 (tppt)
REVERT: A  421 MET cc_start: 0.8016 (mmm) cc_final: 0.7246 (tmm)
REVERT: A  719 MET cc_start: 0.7877 (mtm) cc_final: 0.7353 (mtp)
REVERT: A 1160 GLU cc_start: 0.8845 (tt0) cc_final: 0.8176 (tm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 42
  average time/residue: 0.5561
  time to fit residues: 24.9085
Evaluate side-chains
  39 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  386 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.093251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.063033 restraints weight = 19865.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 3.10
r_work: 0.2929 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7518  Z= 0.164
  Angle     :  0.576   9.900  10283  Z= 0.272
  Chirality :  0.041   0.136   1266
  Planarity :  0.004   0.072   1314
  Dihedral  :  3.601  15.561   1097
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.27), residues: 1024
  helix:  2.74 (0.22), residues: 512
  sheet:  0.23 (0.40), residues: 156
  loop :  0.65 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A 379 
 TYR   0.013   0.001   TYR A 935 
 PHE   0.014   0.001   PHE A 940 
 TRP   0.004   0.001   TRP A 246 
 HIS   0.002   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 7518)
  covalent geometry    : angle       0.57594 (10283)
  hydrogen bonds       : bond        0.03283 (  461)
  hydrogen bonds       : angle       3.96618 ( 1323)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2296.22 seconds
wall clock time: 39 minutes 50.08 seconds (2390.08 seconds total)