Starting phenix.real_space_refine
on Wed Mar  4 01:24:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7psn_13615/03_2026/7psn_13615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7psn_13615/03_2026/7psn_13615.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/7psn_13615/03_2026/7psn_13615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7psn_13615/03_2026/7psn_13615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7psn_13615/03_2026/7psn_13615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7psn_13615/03_2026/7psn_13615.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=   0.089
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     Mg      2      5.21       5
     S      34      5.16       5
     C    6088      2.51       5
     N    1604      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  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: 9464
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4622
          Classifications: {'peptide': 585}
          Link IDs: {'PTRANS': 17, 'TRANS': 567}
    Chain: "A"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 110
          Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'LOP:plan-2': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.77, per 1000 atoms: 0.29
  Number of scatterers: 9464
  At special positions: 0
  Unit cell: (83.628, 75.348, 141.588, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      34     16.00
     P      10     15.00
     Mg      2     11.99
     O    1726      8.00
     N    1604      7.00
     C    6088      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: 0.83
  Conformation dependent library (CDL) restraints added in 275.3 milliseconds
  

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      68.7% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 93 through 100
    Processing helix  chain 'A' and resid 104 through 140
      removed outlier: 3.747A  pdb=" N   ARG A 108 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
    Processing helix  chain 'A' and resid 151 through 201
      removed outlier: 3.796A  pdb=" N   ASN A 185 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 208
    Processing helix  chain 'A' and resid 210 through 233
    Processing helix  chain 'A' and resid 236 through 253
    Processing helix  chain 'A' and resid 256 through 304
      removed outlier: 3.964A  pdb=" N   TRP A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   HIS A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   PHE A 283 " --> pdb=" O   TRP A 279 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 310
    Processing helix  chain 'A' and resid 313 through 367
      removed outlier: 3.583A  pdb=" N   LEU A 317 " --> pdb=" O   ASN A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 396
      Proline residue:  A 388  - end of helix
    Processing helix  chain 'A' and resid 399 through 414
    Processing helix  chain 'A' and resid 475 through 483
      removed outlier: 3.697A  pdb=" N   PHE A 483 " --> pdb=" O   LEU A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 503
      No H-bonds generated for 'chain 'A' and resid 501 through 503'
    Processing helix  chain 'A' and resid 504 through 509
    Processing helix  chain 'A' and resid 525 through 531
    Processing helix  chain 'A' and resid 538 through 549
      removed outlier: 3.545A  pdb=" N   VAL A 542 " --> pdb=" O   THR A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 558
    Processing helix  chain 'A' and resid 567 through 571
      removed outlier: 3.514A  pdb=" N   GLY A 570 " --> pdb=" O   GLY A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 590
      removed outlier: 3.738A  pdb=" N   LYS A 578 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 617
    Processing helix  chain 'A' and resid 632 through 636
      removed outlier: 3.593A  pdb=" N   ILE A 636 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
    Processing helix  chain 'A' and resid 665 through 676
    Processing helix  chain 'B' and resid 93 through 100
    Processing helix  chain 'B' and resid 104 through 140
      removed outlier: 3.748A  pdb=" N   ARG B 108 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 151 through 201
      removed outlier: 3.796A  pdb=" N   ASN B 185 " --> pdb=" O   LYS B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 208
    Processing helix  chain 'B' and resid 210 through 233
    Processing helix  chain 'B' and resid 236 through 253
    Processing helix  chain 'B' and resid 256 through 304
      removed outlier: 3.964A  pdb=" N   TRP B 279 " --> pdb=" O   LYS B 275 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   HIS B 282 " --> pdb=" O   ALA B 278 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   PHE B 283 " --> pdb=" O   TRP B 279 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ASN B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 310
    Processing helix  chain 'B' and resid 313 through 367
      removed outlier: 3.584A  pdb=" N   LEU B 317 " --> pdb=" O   ASN B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 396
      Proline residue:  B 388  - end of helix
    Processing helix  chain 'B' and resid 399 through 414
    Processing helix  chain 'B' and resid 475 through 483
      removed outlier: 3.696A  pdb=" N   PHE B 483 " --> pdb=" O   LEU B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 503
      No H-bonds generated for 'chain 'B' and resid 501 through 503'
    Processing helix  chain 'B' and resid 504 through 509
    Processing helix  chain 'B' and resid 525 through 531
    Processing helix  chain 'B' and resid 538 through 549
      removed outlier: 3.545A  pdb=" N   VAL B 542 " --> pdb=" O   THR B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 558
    Processing helix  chain 'B' and resid 567 through 571
      removed outlier: 3.514A  pdb=" N   GLY B 570 " --> pdb=" O   GLY B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 590
      removed outlier: 3.738A  pdb=" N   LYS B 578 " --> pdb=" O   SER B 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 617
    Processing helix  chain 'B' and resid 632 through 636
      removed outlier: 3.594A  pdb=" N   ILE B 636 " --> pdb=" O   LEU B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 661
    Processing helix  chain 'B' and resid 665 through 676
    Processing sheet with id=AA1, first strand: chain 'A' and resid 452 through 459
      removed outlier: 5.687A  pdb=" N   LYS A 453 " --> pdb=" O   PHE A 443 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   PHE A 443 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   PHE A 457 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   GLU A 439 " --> pdb=" O   PHE A 457 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 437 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   THR A 437 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL A 441 " --> pdb=" O   SER A 490 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   SER A 490 " --> pdb=" O   VAL A 441 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 515
      removed outlier: 6.528A  pdb=" N   MET A 594 " --> pdb=" O   VAL A 627 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ILE A 629 " --> pdb=" O   MET A 594 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   PHE A 596 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LYS A 641 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE A 642 " --> pdb=" O   GLU A 653 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLU A 653 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL A 644 " --> pdb=" O   ARG A 651 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 459
      removed outlier: 5.687A  pdb=" N   LYS B 453 " --> pdb=" O   PHE B 443 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   PHE B 443 " --> pdb=" O   LYS B 453 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   PHE B 457 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   GLU B 439 " --> pdb=" O   PHE B 457 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ILE B 459 " --> pdb=" O   THR B 437 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   THR B 437 " --> pdb=" O   ILE B 459 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   VAL B 441 " --> pdb=" O   SER B 490 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   SER B 490 " --> pdb=" O   VAL B 441 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 512 through 515
      removed outlier: 6.529A  pdb=" N   MET B 594 " --> pdb=" O   VAL B 627 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   ILE B 629 " --> pdb=" O   MET B 594 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE B 596 " --> pdb=" O   ILE B 629 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS B 641 " --> pdb=" O   LYS B 464 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE B 642 " --> pdb=" O   GLU B 653 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLU B 653 " --> pdb=" O   ILE B 642 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL B 644 " --> pdb=" O   ARG B 651 " (cutoff:3.500A)

    634 hydrogen bonds defined for protein.
    1878 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: 1.71

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1508
        1.31 -     1.43: 2478
        1.43 -     1.56: 5568
        1.56 -     1.68: 14
        1.68 -     1.80: 68
  Bond restraints: 9636
  Sorted by residual:
  bond pdb=" C3' ANP A 701 "
       pdb=" C4' ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.532  1.308  0.224 2.00e-02 2.50e+03 1.26e+02
  bond pdb=" C3' ANP B 701 "
       pdb=" C4' ANP B 701 "
    ideal  model  delta    sigma   weight residual
    1.532  1.308  0.224 2.00e-02 2.50e+03 1.26e+02
  bond pdb=" C4' ANP B 701 "
       pdb=" O4' ANP B 701 "
    ideal  model  delta    sigma   weight residual
    1.431  1.626 -0.195 2.00e-02 2.50e+03 9.47e+01
  bond pdb=" C4' ANP A 701 "
       pdb=" O4' ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.431  1.625 -0.194 2.00e-02 2.50e+03 9.45e+01
  bond pdb=" C6  ANP A 701 "
       pdb=" N6  ANP A 701 "
    ideal  model  delta    sigma   weight residual
    1.340  1.471 -0.131 2.00e-02 2.50e+03 4.32e+01
  ... (remaining 9631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 12846
        2.77 -     5.54: 126
        5.54 -     8.30: 28
        8.30 -    11.07: 12
       11.07 -    13.84: 8
  Bond angle restraints: 13020
  Sorted by residual:
  angle pdb=" C1' ANP B 701 "
        pdb=" N9  ANP B 701 "
        pdb=" C4  ANP B 701 "
      ideal   model   delta    sigma   weight residual
     125.38  111.54   13.84 3.00e+00 1.11e-01 2.13e+01
  angle pdb=" C1' ANP A 701 "
        pdb=" N9  ANP A 701 "
        pdb=" C4  ANP A 701 "
      ideal   model   delta    sigma   weight residual
     125.38  111.59   13.79 3.00e+00 1.11e-01 2.11e+01
  angle pdb=" O3  LOP A 704 "
        pdb=" P1  LOP A 704 "
        pdb=" O4  LOP A 704 "
      ideal   model   delta    sigma   weight residual
     120.67  109.29   11.38 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" O3  LOP B 704 "
        pdb=" P1  LOP B 704 "
        pdb=" O4  LOP B 704 "
      ideal   model   delta    sigma   weight residual
     120.67  109.32   11.35 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" O3A ANP A 701 "
        pdb=" PA  ANP A 701 "
        pdb=" O5' ANP A 701 "
      ideal   model   delta    sigma   weight residual
      98.09  109.28  -11.19 3.00e+00 1.11e-01 1.39e+01
  ... (remaining 13015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.69: 5505
       25.69 -    51.38: 293
       51.38 -    77.07: 44
       77.07 -   102.76: 8
      102.76 -   128.44: 2
  Dihedral angle restraints: 5852
    sinusoidal: 2468
      harmonic: 3384
  Sorted by residual:
  dihedral pdb=" O1A ANP B 701 "
           pdb=" O3A ANP B 701 "
           pdb=" PA  ANP B 701 "
           pdb=" PB  ANP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -45.33  128.44     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" O1A ANP A 701 "
           pdb=" O3A ANP A 701 "
           pdb=" PA  ANP A 701 "
           pdb=" PB  ANP A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -45.31  128.42     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" O2' ANP B 701 "
           pdb=" C2' ANP B 701 "
           pdb=" C3' ANP B 701 "
           pdb=" O3' ANP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.90  -36.39   84.29     1      3.00e+01 1.11e-03 9.61e+00
  ... (remaining 5849 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 954
       0.036 -    0.072: 408
       0.072 -    0.108: 114
       0.108 -    0.144: 14
       0.144 -    0.180: 6
  Chirality restraints: 1496
  Sorted by residual:
  chirality pdb=" C2' ANP A 701 "
            pdb=" C1' ANP A 701 "
            pdb=" C3' ANP A 701 "
            pdb=" O2' ANP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.54   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality pdb=" C2' ANP B 701 "
            pdb=" C1' ANP B 701 "
            pdb=" C3' ANP B 701 "
            pdb=" O2' ANP B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.55   -0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" C4  LOP A 704 "
            pdb=" C3  LOP A 704 "
            pdb=" C5  LOP A 704 "
            pdb=" O5  LOP A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.34   -2.50    0.16 2.00e-01 2.50e+01 6.10e-01
  ... (remaining 1493 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C13 LOP B 703 "    0.204 2.00e-02 2.50e+03   2.05e-01 4.21e+02
        pdb=" C14 LOP B 703 "   -0.200 2.00e-02 2.50e+03
        pdb=" C15 LOP B 703 "   -0.210 2.00e-02 2.50e+03
        pdb=" C16 LOP B 703 "    0.206 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C13 LOP A 703 "   -0.204 2.00e-02 2.50e+03   2.05e-01 4.20e+02
        pdb=" C14 LOP A 703 "    0.200 2.00e-02 2.50e+03
        pdb=" C15 LOP A 703 "    0.210 2.00e-02 2.50e+03
        pdb=" C16 LOP A 703 "   -0.206 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 387 "   -0.005 2.00e-02 2.50e+03   8.91e-03 7.93e-01
        pdb=" C   VAL A 387 "    0.015 2.00e-02 2.50e+03
        pdb=" O   VAL A 387 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   PRO A 388 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 70
        2.52 -     3.11: 7626
        3.11 -     3.71: 14350
        3.71 -     4.30: 20897
        4.30 -     4.90: 35778
  Nonbonded interactions: 78721
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 517 "
            pdb="MG    MG B 702 "
     model   vdw
     1.923 2.170
  nonbonded pdb=" OE1 GLN A 517 "
            pdb="MG    MG A 702 "
     model   vdw
     1.923 2.170
  nonbonded pdb=" O2G ANP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" O2G ANP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" O2B ANP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     2.047 2.170
  ... (remaining 78716 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.98
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:             3.230
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.590
  Find NCS groups from input model:        0.070
  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:9.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
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      :  0.009   0.224   9636  Z= 0.404
  Angle     :  0.823  13.840  13020  Z= 0.365
  Chirality :  0.042   0.180   1496
  Planarity :  0.008   0.205   1620
  Dihedral  : 15.989 128.445   3668
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.01 (0.21), residues: 1166
  helix: -1.13 (0.16), residues: 772
  sheet: -3.80 (0.43), residues: 52
  loop : -3.49 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 209 
 TYR   0.011   0.002   TYR B 161 
 PHE   0.009   0.001   PHE A 179 
 TRP   0.009   0.001   TRP A 279 
 HIS   0.002   0.001   HIS B 631 

Details of bonding type rmsd
  covalent geometry    : bond        0.00903 ( 9636)
  covalent geometry    : angle       0.82288 (13020)
  hydrogen bonds       : bond        0.11032 (  634)
  hydrogen bonds       : angle       5.29664 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  426 LEU cc_start: 0.8655 (mm) cc_final: 0.8451 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.5877
  time to fit residues: 76.4504
Evaluate side-chains
  74 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0270
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 ASN
B 304 ASN
** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.143954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.117905 restraints weight = 10409.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.16
r_work: 0.3331 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9636  Z= 0.135
  Angle     :  0.539   7.473  13020  Z= 0.275
  Chirality :  0.041   0.151   1496
  Planarity :  0.003   0.028   1620
  Dihedral  : 11.357 122.381   1470
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 10.48 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.57 (0.24), residues: 1166
  helix:  0.72 (0.18), residues: 780
  sheet: -2.62 (0.50), residues: 62
  loop : -2.59 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 424 
 TYR   0.013   0.001   TYR B 161 
 PHE   0.012   0.001   PHE A 391 
 TRP   0.009   0.001   TRP B 279 
 HIS   0.002   0.001   HIS A 631 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9636)
  covalent geometry    : angle       0.53891 (13020)
  hydrogen bonds       : bond        0.04149 (  634)
  hydrogen bonds       : angle       3.79387 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  426 LEU cc_start: 0.8303 (mm) cc_final: 0.8074 (mp)
REVERT: A  572 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8220 (mmm)
REVERT: B  572 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8217 (mmm)
  outliers start: 8
  outliers final: 0
  residues processed: 116
  average time/residue: 0.5386
  time to fit residues: 67.0836
Evaluate side-chains
  96 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain B residue  572 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN
B 618 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.139933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.112720 restraints weight = 10570.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.17
r_work: 0.3286 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9636  Z= 0.151
  Angle     :  0.540   7.390  13020  Z= 0.274
  Chirality :  0.042   0.164   1496
  Planarity :  0.003   0.032   1620
  Dihedral  :  9.976 112.144   1470
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 13.47 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.18 (0.24), residues: 1166
  helix:  1.17 (0.18), residues: 784
  sheet: -2.22 (0.56), residues: 62
  loop : -2.02 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  97 
 TYR   0.009   0.001   TYR B 161 
 PHE   0.014   0.001   PHE B 179 
 TRP   0.007   0.001   TRP A 671 
 HIS   0.003   0.001   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9636)
  covalent geometry    : angle       0.54032 (13020)
  hydrogen bonds       : bond        0.04300 (  634)
  hydrogen bonds       : angle       3.69260 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  666 LEU cc_start: 0.6693 (tm) cc_final: 0.6447 (tm)
REVERT: B  666 LEU cc_start: 0.6725 (tm) cc_final: 0.6452 (tm)
  outliers start: 14
  outliers final: 2
  residues processed: 129
  average time/residue: 0.4512
  time to fit residues: 63.0587
Evaluate side-chains
  103 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain B residue  387 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
B 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.135923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.108302 restraints weight = 11070.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.10
r_work: 0.3205 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9636  Z= 0.194
  Angle     :  0.573   6.958  13020  Z= 0.289
  Chirality :  0.043   0.153   1496
  Planarity :  0.003   0.024   1620
  Dihedral  :  9.983 112.262   1470
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.97 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.35 (0.24), residues: 1166
  helix:  1.24 (0.18), residues: 784
  sheet: -1.96 (0.57), residues: 62
  loop : -1.79 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 424 
 TYR   0.020   0.002   TYR A 161 
 PHE   0.025   0.001   PHE A 350 
 TRP   0.008   0.001   TRP B 463 
 HIS   0.004   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 9636)
  covalent geometry    : angle       0.57337 (13020)
  hydrogen bonds       : bond        0.04678 (  634)
  hydrogen bonds       : angle       3.79606 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  572 MET cc_start: 0.8585 (mmm) cc_final: 0.8256 (tpt)
REVERT: A  581 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7339 (mp)
REVERT: A  666 LEU cc_start: 0.6958 (tm) cc_final: 0.6724 (tm)
REVERT: B  581 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7332 (mp)
REVERT: B  666 LEU cc_start: 0.6937 (tm) cc_final: 0.6692 (tm)
  outliers start: 29
  outliers final: 8
  residues processed: 138
  average time/residue: 0.4599
  time to fit residues: 68.7138
Evaluate side-chains
  116 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  614 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 103 optimal weight:    0.3980
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 304 ASN
B 134 GLN
B 304 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.138405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.110874 restraints weight = 10969.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.12
r_work: 0.3209 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9636  Z= 0.135
  Angle     :  0.504   6.413  13020  Z= 0.256
  Chirality :  0.040   0.152   1496
  Planarity :  0.003   0.025   1620
  Dihedral  :  9.497 108.053   1470
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.07 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.83 (0.25), residues: 1166
  helix:  1.60 (0.18), residues: 784
  sheet: -1.87 (0.58), residues: 62
  loop : -1.60 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  97 
 TYR   0.014   0.001   TYR A 667 
 PHE   0.018   0.001   PHE B 350 
 TRP   0.008   0.001   TRP B 279 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9636)
  covalent geometry    : angle       0.50392 (13020)
  hydrogen bonds       : bond        0.04228 (  634)
  hydrogen bonds       : angle       3.59165 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6616 (mt0)
REVERT: A  421 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8308 (m-40)
REVERT: A  556 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7519 (mptt)
REVERT: A  581 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7462 (mp)
REVERT: B  134 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6624 (mt0)
REVERT: B  421 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8324 (m-40)
REVERT: B  556 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7528 (mptt)
REVERT: B  581 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7451 (mp)
  outliers start: 32
  outliers final: 8
  residues processed: 135
  average time/residue: 0.4608
  time to fit residues: 67.2869
Evaluate side-chains
  124 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  134 GLN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  421 ASN
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  652 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0970
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 304 ASN
B 134 GLN
B 304 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.137467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.110027 restraints weight = 10995.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.16
r_work: 0.3232 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9636  Z= 0.151
  Angle     :  0.522   7.178  13020  Z= 0.264
  Chirality :  0.041   0.163   1496
  Planarity :  0.003   0.025   1620
  Dihedral  :  9.422 107.299   1470
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.27 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.97 (0.25), residues: 1166
  helix:  1.68 (0.18), residues: 786
  sheet: -2.24 (0.58), residues: 52
  loop : -1.41 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  97 
 TYR   0.023   0.002   TYR B 161 
 PHE   0.015   0.001   PHE B 350 
 TRP   0.007   0.001   TRP B 279 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9636)
  covalent geometry    : angle       0.52198 (13020)
  hydrogen bonds       : bond        0.04320 (  634)
  hydrogen bonds       : angle       3.58844 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6508 (mt0)
REVERT: A  556 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7496 (mptt)
REVERT: A  572 MET cc_start: 0.8621 (mmm) cc_final: 0.8318 (tpt)
REVERT: A  581 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7430 (mp)
REVERT: A  662 MET cc_start: 0.6772 (tmm) cc_final: 0.6547 (ttt)
REVERT: B  134 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6510 (mt0)
REVERT: B  421 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8324 (m-40)
REVERT: B  556 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7505 (mptt)
REVERT: B  572 MET cc_start: 0.8625 (mmm) cc_final: 0.8350 (tpt)
REVERT: B  581 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7435 (mp)
REVERT: B  662 MET cc_start: 0.6712 (tmm) cc_final: 0.6500 (ttt)
  outliers start: 31
  outliers final: 11
  residues processed: 140
  average time/residue: 0.4666
  time to fit residues: 70.6473
Evaluate side-chains
  128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain B residue  134 GLN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  421 ASN
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  652 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 43 optimal weight:    0.3980
   chunk 54 optimal weight:    7.9990
   chunk 95 optimal weight:    2.9990
   chunk 113 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 304 ASN
B 134 GLN
B 304 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.138882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111553 restraints weight = 10863.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.15
r_work: 0.3228 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9636  Z= 0.133
  Angle     :  0.512   7.884  13020  Z= 0.260
  Chirality :  0.040   0.163   1496
  Planarity :  0.003   0.025   1620
  Dihedral  :  9.315 106.105   1470
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.17 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.13 (0.25), residues: 1166
  helix:  1.78 (0.18), residues: 786
  sheet: -2.19 (0.58), residues: 52
  loop : -1.30 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 424 
 TYR   0.032   0.001   TYR B 161 
 PHE   0.026   0.001   PHE B 254 
 TRP   0.008   0.001   TRP B 279 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9636)
  covalent geometry    : angle       0.51226 (13020)
  hydrogen bonds       : bond        0.04209 (  634)
  hydrogen bonds       : angle       3.56505 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6427 (mt0)
REVERT: A  350 PHE cc_start: 0.7240 (t80) cc_final: 0.6621 (t80)
REVERT: A  380 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7163 (mm-40)
REVERT: A  556 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7473 (mptt)
REVERT: A  572 MET cc_start: 0.8547 (mmm) cc_final: 0.8259 (tpt)
REVERT: B  134 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6405 (mt0)
REVERT: B  350 PHE cc_start: 0.7262 (t80) cc_final: 0.6665 (t80)
REVERT: B  556 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7487 (mptt)
REVERT: B  572 MET cc_start: 0.8567 (mmm) cc_final: 0.8294 (tpt)
  outliers start: 29
  outliers final: 9
  residues processed: 135
  average time/residue: 0.4581
  time to fit residues: 67.1589
Evaluate side-chains
  126 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  380 GLN
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  134 GLN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 49 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 304 ASN
A 379 ASN
B 134 GLN
B 304 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.139097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.111697 restraints weight = 10892.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.16
r_work: 0.3255 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9636  Z= 0.132
  Angle     :  0.508   7.346  13020  Z= 0.258
  Chirality :  0.040   0.175   1496
  Planarity :  0.003   0.025   1620
  Dihedral  :  9.259 105.477   1470
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.66 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.24 (0.25), residues: 1166
  helix:  1.87 (0.18), residues: 786
  sheet: -2.19 (0.57), residues: 52
  loop : -1.26 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 424 
 TYR   0.034   0.001   TYR B 161 
 PHE   0.023   0.001   PHE B 254 
 TRP   0.008   0.001   TRP B 279 
 HIS   0.004   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9636)
  covalent geometry    : angle       0.50791 (13020)
  hydrogen bonds       : bond        0.04177 (  634)
  hydrogen bonds       : angle       3.53045 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.6376 (mt0)
REVERT: A  350 PHE cc_start: 0.7119 (t80) cc_final: 0.6523 (t80)
REVERT: A  556 LYS cc_start: 0.7697 (mtmm) cc_final: 0.7382 (mptt)
REVERT: A  572 MET cc_start: 0.8428 (mmm) cc_final: 0.8143 (tpt)
REVERT: B  134 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6416 (mt0)
REVERT: B  350 PHE cc_start: 0.7127 (t80) cc_final: 0.6556 (t80)
REVERT: B  556 LYS cc_start: 0.7723 (mtmm) cc_final: 0.7403 (mptt)
REVERT: B  572 MET cc_start: 0.8428 (mmm) cc_final: 0.8152 (tpt)
  outliers start: 25
  outliers final: 10
  residues processed: 127
  average time/residue: 0.4538
  time to fit residues: 62.4299
Evaluate side-chains
  121 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  134 GLN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 107 optimal weight:    0.5980
   chunk 54 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0770
   chunk 46 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 41 optimal weight:    0.1980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 304 ASN
B 134 GLN
B 304 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.113519 restraints weight = 10913.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.15
r_work: 0.3266 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9636  Z= 0.114
  Angle     :  0.493   7.388  13020  Z= 0.250
  Chirality :  0.039   0.166   1496
  Planarity :  0.003   0.028   1620
  Dihedral  :  9.133 103.582   1470
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.66 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.46 (0.25), residues: 1166
  helix:  2.05 (0.18), residues: 782
  sheet: -2.18 (0.57), residues: 52
  loop : -1.17 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 424 
 TYR   0.031   0.001   TYR B 161 
 PHE   0.021   0.001   PHE B 254 
 TRP   0.009   0.001   TRP B 279 
 HIS   0.004   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9636)
  covalent geometry    : angle       0.49271 (13020)
  hydrogen bonds       : bond        0.03990 (  634)
  hydrogen bonds       : angle       3.45035 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6406 (mt0)
REVERT: A  350 PHE cc_start: 0.7219 (t80) cc_final: 0.6711 (t80)
REVERT: A  556 LYS cc_start: 0.7778 (mtmm) cc_final: 0.7462 (mptt)
REVERT: A  572 MET cc_start: 0.8467 (mmm) cc_final: 0.8198 (tpt)
REVERT: B  134 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6381 (mt0)
REVERT: B  350 PHE cc_start: 0.7134 (t80) cc_final: 0.6670 (t80)
REVERT: B  556 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7488 (mptt)
  outliers start: 18
  outliers final: 8
  residues processed: 123
  average time/residue: 0.4127
  time to fit residues: 55.5101
Evaluate side-chains
  117 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  134 GLN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 95 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 103 optimal weight:    0.3980
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 304 ASN
B 134 GLN
B 304 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.140103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.112870 restraints weight = 10785.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 2.15
r_work: 0.3247 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9636  Z= 0.133
  Angle     :  0.517   7.896  13020  Z= 0.261
  Chirality :  0.040   0.162   1496
  Planarity :  0.003   0.030   1620
  Dihedral  :  9.135 103.750   1470
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 19.66 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.48 (0.25), residues: 1166
  helix:  2.05 (0.18), residues: 782
  sheet: -2.10 (0.58), residues: 52
  loop : -1.14 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 424 
 TYR   0.032   0.001   TYR B 161 
 PHE   0.021   0.001   PHE B 254 
 TRP   0.009   0.001   TRP A 279 
 HIS   0.005   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9636)
  covalent geometry    : angle       0.51745 (13020)
  hydrogen bonds       : bond        0.04090 (  634)
  hydrogen bonds       : angle       3.47529 ( 1878)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6377 (mt0)
REVERT: A  350 PHE cc_start: 0.7176 (t80) cc_final: 0.6633 (t80)
REVERT: A  556 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7473 (mptt)
REVERT: A  572 MET cc_start: 0.8481 (mmm) cc_final: 0.8209 (tpt)
REVERT: B  134 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6390 (mt0)
REVERT: B  350 PHE cc_start: 0.7175 (t80) cc_final: 0.6692 (t80)
REVERT: B  556 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7492 (mptt)
REVERT: B  572 MET cc_start: 0.8466 (mmm) cc_final: 0.8218 (tpt)
  outliers start: 18
  outliers final: 8
  residues processed: 122
  average time/residue: 0.4624
  time to fit residues: 61.2306
Evaluate side-chains
  119 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 GLN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  441 VAL
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  652 GLU
Chi-restraints excluded: chain B residue  134 GLN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  441 VAL
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 99 optimal weight:    0.1980
   chunk 115 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0970
   chunk 74 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 100 optimal weight:    0.3980
   chunk 47 optimal weight:    0.0470
   chunk 44 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.3076

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 304 ASN
B 134 GLN
B 304 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.142307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.115368 restraints weight = 10741.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.13
r_work: 0.3289 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9636  Z= 0.109
  Angle     :  0.496   8.141  13020  Z= 0.251
  Chirality :  0.039   0.179   1496
  Planarity :  0.003   0.029   1620
  Dihedral  :  8.981 101.645   1470
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 20.36 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.73 (0.25), residues: 1166
  helix:  2.25 (0.18), residues: 782
  sheet: -2.09 (0.59), residues: 52
  loop : -1.04 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 424 
 TYR   0.025   0.001   TYR B 161 
 PHE   0.018   0.001   PHE B 254 
 TRP   0.010   0.001   TRP A 279 
 HIS   0.005   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9636)
  covalent geometry    : angle       0.49554 (13020)
  hydrogen bonds       : bond        0.03844 (  634)
  hydrogen bonds       : angle       3.38773 ( 1878)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2716.78 seconds
wall clock time: 47 minutes 6.64 seconds (2826.64 seconds total)