Starting phenix.real_space_refine
on Wed Feb  4 08:10:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9la9_62922/02_2026/9la9_62922_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9la9_62922/02_2026/9la9_62922.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9la9_62922/02_2026/9la9_62922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9la9_62922/02_2026/9la9_62922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9la9_62922/02_2026/9la9_62922_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9la9_62922/02_2026/9la9_62922_trim.cif"
  }
  resolution = 4.38
  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=  -0.000 sd=   0.996
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      41      5.16       5
     C    5857      2.51       5
     N    1627      2.21       5
     O    1739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9267
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 974, 7761
          Classifications: {'peptide': 974}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 924}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "B"
      Number of atoms: 1474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1474
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 3, 'TRANS': 180}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GNP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.47, per 1000 atoms: 0.27
  Number of scatterers: 9267
  At special positions: 0
  Unit cell: (89.06, 121.18, 208.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     P       3     15.00
     O    1739      8.00
     N    1627      7.00
     C    5857      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 803 " - pdb=" SG  CYS A 862 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 536.4 milliseconds
  

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2204

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      55.0% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 62
      removed outlier: 3.617A  pdb=" N   TYR A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 90
      removed outlier: 3.933A  pdb=" N   LEU A  81 " --> pdb=" O   GLU A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
    Processing helix  chain 'A' and resid 249 through 253
      removed outlier: 3.718A  pdb=" N   ASP A 252 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 295
      removed outlier: 4.109A  pdb=" N   GLN A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 316
    Processing helix  chain 'A' and resid 328 through 337
    Processing helix  chain 'A' and resid 345 through 364
      removed outlier: 4.039A  pdb=" N   GLN A 349 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 370
    Processing helix  chain 'A' and resid 371 through 381
      removed outlier: 3.719A  pdb=" N   THR A 376 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   SER A 377 " --> pdb=" O   HIS A 373 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 378 " --> pdb=" O   PRO A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 412
      removed outlier: 3.961A  pdb=" N   GLN A 392 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLU A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   GLU A 394 " --> pdb=" O   GLU A 390 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ARG A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 436
    Processing helix  chain 'A' and resid 441 through 447
      removed outlier: 3.728A  pdb=" N   PHE A 444 " --> pdb=" O   MET A 441 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A 447 " --> pdb=" O   PHE A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 477
    Processing helix  chain 'A' and resid 483 through 508
      removed outlier: 3.614A  pdb=" N   THR A 508 " --> pdb=" O   GLN A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 515
    Processing helix  chain 'A' and resid 520 through 545
      removed outlier: 3.913A  pdb=" N   MET A 524 " --> pdb=" O   HIS A 520 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG A 536 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ASP A 539 " --> pdb=" O   LYS A 535 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY A 545 " --> pdb=" O   THR A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 569
    Processing helix  chain 'A' and resid 570 through 573
    Processing helix  chain 'A' and resid 589 through 591
      No H-bonds generated for 'chain 'A' and resid 589 through 591'
    Processing helix  chain 'A' and resid 592 through 615
      removed outlier: 3.582A  pdb=" N   TYR A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 612 " --> pdb=" O   VAL A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 648
      removed outlier: 3.756A  pdb=" N   VAL A 631 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 686
    Processing helix  chain 'A' and resid 690 through 719
      Proline residue:  A 716  - end of helix
    Processing helix  chain 'A' and resid 720 through 726
      removed outlier: 3.771A  pdb=" N   GLN A 726 " --> pdb=" O   GLU A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 735 through 741
    Processing helix  chain 'A' and resid 741 through 754
      removed outlier: 3.555A  pdb=" N   LEU A 745 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 779
      removed outlier: 3.567A  pdb=" N   LEU A 763 " --> pdb=" O   GLY A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 806
    Processing helix  chain 'A' and resid 810 through 833
    Processing helix  chain 'A' and resid 842 through 857
    Processing helix  chain 'A' and resid 871 through 883
      removed outlier: 3.686A  pdb=" N   GLN A 875 " --> pdb=" O   THR A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 905
    Processing helix  chain 'A' and resid 956 through 960
    Processing helix  chain 'A' and resid 988 through 994
      removed outlier: 3.798A  pdb=" N   CYS A 992 " --> pdb=" O   PRO A 988 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS A 994 " --> pdb=" O   GLU A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1059
    Processing helix  chain 'A' and resid 1065 through 1084
      removed outlier: 3.569A  pdb=" N   GLN A1083 " --> pdb=" O   LYS A1079 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   HIS A1084 " --> pdb=" O   GLN A1080 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 31
    Processing helix  chain 'B' and resid 78 through 82
    Processing helix  chain 'B' and resid 83 through 90
      removed outlier: 3.544A  pdb=" N   ARG B  90 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 119
      removed outlier: 4.479A  pdb=" N   ARG B 111 " --> pdb=" O   PHE B 107 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   ASN B 112 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   MET B 119 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 156
    Processing helix  chain 'B' and resid 169 through 189
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 191
      removed outlier: 3.914A  pdb=" N   PHE A 188 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ALA A 115 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   HIS A 277 " --> pdb=" O   LYS A 118 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ALA A 120 " --> pdb=" O   GLN A 275 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   GLN A 275 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191
      removed outlier: 3.914A  pdb=" N   PHE A 188 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ALA A 115 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 141
      removed outlier: 3.598A  pdb=" N   TRP A 205 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASP A 203 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLU A 141 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU A 202 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   GLY A 244 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   ASP A 206 " --> pdb=" O   PHE A 242 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   PHE A 242 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 978 through 986
      removed outlier: 6.240A  pdb=" N   LEU A 932 " --> pdb=" O   PHE A 979 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   GLU A 981 " --> pdb=" O   GLU A 930 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLU A 930 " --> pdb=" O   GLU A 981 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   PHE A 983 " --> pdb=" O   ARG A 928 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ARG A 928 " --> pdb=" O   PHE A 983 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   PHE A 985 " --> pdb=" O   LYS A 926 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   LYS A 926 " --> pdb=" O   PHE A 985 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   VAL A 929 " --> pdb=" O   SER A 919 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   SER A 919 " --> pdb=" O   VAL A 929 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   LEU A 931 " --> pdb=" O   LYS A 917 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LYS A 917 " --> pdb=" O   LEU A 931 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER A 933 " --> pdb=" O   THR A 915 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   VAL A 914 " --> pdb=" O   LEU A1042 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   LEU A1042 " --> pdb=" O   VAL A 914 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL A 916 " --> pdb=" O   THR A1040 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 966 through 967
      removed outlier: 3.868A  pdb=" N   ARG A 966 " --> pdb=" O   LEU A 952 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.532A  pdb=" N   TYR B   8 " --> pdb=" O   HIS B  69 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   GLN B  71 " --> pdb=" O   TYR B   8 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   ILE B  10 " --> pdb=" O   GLN B  71 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   TRP B  73 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   PHE B  12 " --> pdb=" O   TRP B  73 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   LEU B  96 " --> pdb=" O   LYS B  11 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B  13 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU B  98 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU B  15 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 9.533A  pdb=" N   ASP B 100 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   PHE B  95 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   CYS B 131 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   LEU B  97 " --> pdb=" O   CYS B 131 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ASN B 133 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   PHE B  99 " --> pdb=" O   ASN B 133 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1368 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: 1.50

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2895
        1.34 -     1.46: 1405
        1.46 -     1.58: 5095
        1.58 -     1.69: 5
        1.69 -     1.81: 61
  Bond restraints: 9461
  Sorted by residual:
  bond pdb=" CG  PRO A 453 "
       pdb=" CD  PRO A 453 "
    ideal  model  delta    sigma   weight residual
    1.503  1.328  0.175 3.40e-02 8.65e+02 2.64e+01
  bond pdb=" N3B GNP B 301 "
       pdb=" PG  GNP B 301 "
    ideal  model  delta    sigma   weight residual
    1.801  1.706  0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" C   ILE A 593 "
       pdb=" N   PRO A 594 "
    ideal  model  delta    sigma   weight residual
    1.335  1.386 -0.052 1.19e-02 7.06e+03 1.87e+01
  bond pdb=" O5' GNP B 301 "
       pdb=" PA  GNP B 301 "
    ideal  model  delta    sigma   weight residual
    1.660  1.574  0.086 2.00e-02 2.50e+03 1.84e+01
  bond pdb=" N   PRO A 453 "
       pdb=" CD  PRO A 453 "
    ideal  model  delta    sigma   weight residual
    1.473  1.523 -0.050 1.40e-02 5.10e+03 1.30e+01
  ... (remaining 9456 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.16: 12792
        7.16 -    14.32: 36
       14.32 -    21.48: 1
       21.48 -    28.63: 2
       28.63 -    35.79: 2
  Bond angle restraints: 12833
  Sorted by residual:
  angle pdb=" N   ALA A 886 "
        pdb=" CA  ALA A 886 "
        pdb=" CB  ALA A 886 "
      ideal   model   delta    sigma   weight residual
     110.40   76.45   33.95 1.50e+00 4.44e-01 5.12e+02
  angle pdb=" C   ALA A 885 "
        pdb=" CA  ALA A 885 "
        pdb=" CB  ALA A 885 "
      ideal   model   delta    sigma   weight residual
     109.68   73.89   35.79 1.98e+00 2.55e-01 3.27e+02
  angle pdb=" N   ALA A 885 "
        pdb=" CA  ALA A 885 "
        pdb=" C   ALA A 885 "
      ideal   model   delta    sigma   weight residual
     108.75  135.50  -26.75 1.71e+00 3.42e-01 2.45e+02
  angle pdb=" CA  PRO A 453 "
        pdb=" N   PRO A 453 "
        pdb=" CD  PRO A 453 "
      ideal   model   delta    sigma   weight residual
     112.00   94.63   17.37 1.40e+00 5.10e-01 1.54e+02
  angle pdb=" N   ALA A 886 "
        pdb=" CA  ALA A 886 "
        pdb=" C   ALA A 886 "
      ideal   model   delta    sigma   weight residual
     111.00  139.28  -28.28 2.80e+00 1.28e-01 1.02e+02
  ... (remaining 12828 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4909
       17.74 -    35.49: 631
       35.49 -    53.23: 163
       53.23 -    70.98: 32
       70.98 -    88.72: 19
  Dihedral angle restraints: 5754
    sinusoidal: 2371
      harmonic: 3383
  Sorted by residual:
  dihedral pdb=" C   ALA A 885 "
           pdb=" N   ALA A 885 "
           pdb=" CA  ALA A 885 "
           pdb=" CB  ALA A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -87.72  -34.88     0      2.50e+00 1.60e-01 1.95e+02
  dihedral pdb=" N   ALA A 886 "
           pdb=" C   ALA A 886 "
           pdb=" CA  ALA A 886 "
           pdb=" CB  ALA A 886 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90   92.41   30.49     0      2.50e+00 1.60e-01 1.49e+02
  dihedral pdb=" N   ALA A 885 "
           pdb=" C   ALA A 885 "
           pdb=" CA  ALA A 885 "
           pdb=" CB  ALA A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  103.27   19.63     0      2.50e+00 1.60e-01 6.16e+01
  ... (remaining 5751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1312
       0.085 -    0.170: 116
       0.170 -    0.255: 14
       0.255 -    0.340: 3
       0.340 -    0.425: 2
  Chirality restraints: 1447
  Sorted by residual:
  chirality pdb=" C2' GNP B 301 "
            pdb=" C1' GNP B 301 "
            pdb=" C3' GNP B 301 "
            pdb=" O2' GNP B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.97    0.43 2.00e-01 2.50e+01 4.52e+00
  chirality pdb=" CA  ALA A 886 "
            pdb=" N   ALA A 886 "
            pdb=" C   ALA A 886 "
            pdb=" CB  ALA A 886 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.08    0.41 2.00e-01 2.50e+01 4.14e+00
  chirality pdb=" CA  PRO A 453 "
            pdb=" N   PRO A 453 "
            pdb=" C   PRO A 453 "
            pdb=" CB  PRO A 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.33 2.00e-01 2.50e+01 2.68e+00
  ... (remaining 1444 not shown)

  Planarity restraints: 1660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 673 "   -0.026 2.00e-02 2.50e+03   3.30e-02 2.18e+01
        pdb=" CG  TYR A 673 "    0.080 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 673 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 673 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 673 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 673 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 673 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 673 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 452 "    0.078 5.00e-02 4.00e+02   1.05e-01 1.76e+01
        pdb=" N   PRO A 453 "   -0.181 5.00e-02 4.00e+02
        pdb=" CA  PRO A 453 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 453 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1052 "   -0.046 5.00e-02 4.00e+02   6.97e-02 7.78e+00
        pdb=" N   PRO A1053 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A1053 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A1053 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1657 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.49: 41
        2.49 -     3.09: 6030
        3.09 -     3.69: 14682
        3.69 -     4.30: 20302
        4.30 -     4.90: 33199
  Nonbonded interactions: 74254
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 100 "
            pdb=" NZ  LYS B 134 "
     model   vdw
     1.882 3.120
  nonbonded pdb=" OG1 THR B  41 "
            pdb=" O2G GNP B 301 "
     model   vdw
     1.884 3.040
  nonbonded pdb=" OD2 ASP B 100 "
            pdb=" CE  LYS B 134 "
     model   vdw
     1.932 3.440
  nonbonded pdb=" O   ALA A 885 "
            pdb=" CB  ALA A 885 "
     model   vdw
     2.189 2.768
  nonbonded pdb=" OG  SER B 163 "
            pdb=" O6  GNP B 301 "
     model   vdw
     2.219 3.040
  ... (remaining 74249 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             18.070
  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:          0.300
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.680
  Find NCS groups from input model:        0.040
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5994
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      :  0.005   0.178   9462  Z= 0.240
  Angle     :  1.164  35.793  12835  Z= 0.615
  Chirality :  0.054   0.425   1447
  Planarity :  0.007   0.105   1660
  Dihedral  : 17.671  88.724   3547
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 18.38 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.70 (0.23), residues: 1148
  helix: -0.50 (0.20), residues: 582
  sheet: -2.01 (0.43), residues: 127
  loop : -1.54 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 527 
 TYR   0.080   0.002   TYR A 673 
 PHE   0.037   0.002   PHE A 797 
 TRP   0.041   0.002   TRP A 382 
 HIS   0.012   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 9461)
  covalent geometry    : angle       1.16380 (12833)
  SS BOND              : bond        0.01189 (    1)
  SS BOND              : angle       2.49160 (    2)
  hydrogen bonds       : bond        0.15753 (  475)
  hydrogen bonds       : angle       6.79033 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  453 PRO cc_start: 0.6191 (Cg_endo) cc_final: 0.5536 (Cg_exo)
  outliers start: 2
  outliers final: 1
  residues processed: 80
  average time/residue: 0.1126
  time to fit residues: 12.4915
Evaluate side-chains
  71 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0980
   chunk 97 optimal weight:    0.5980
   chunk 113 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.0270
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    0.0970
   chunk 100 optimal weight:    0.0970
   overall best weight:    0.0832

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

Flipped N/Q/H residues before XYZ refinement:
** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 ASN
A 626 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 806 ASN
A1076 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.161928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.135285 restraints weight = 18283.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.132961 restraints weight = 34281.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.134185 restraints weight = 33304.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.135084 restraints weight = 20460.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.135164 restraints weight = 19121.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5518
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061   9462  Z= 0.120
  Angle     :  0.603  10.767  12835  Z= 0.304
  Chirality :  0.038   0.127   1447
  Planarity :  0.005   0.061   1660
  Dihedral  :  5.589  46.492   1281
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.90 (0.25), residues: 1148
  helix:  0.38 (0.21), residues: 601
  sheet: -1.88 (0.40), residues: 147
  loop : -1.45 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 527 
 TYR   0.021   0.001   TYR A  56 
 PHE   0.012   0.001   PHE A 366 
 TRP   0.029   0.002   TRP A 588 
 HIS   0.009   0.001   HIS A1076 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9461)
  covalent geometry    : angle       0.60301 (12833)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       1.94116 (    2)
  hydrogen bonds       : bond        0.04344 (  475)
  hydrogen bonds       : angle       4.84894 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A  281 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7042 (mp10)
REVERT: A  335 LEU cc_start: 0.8306 (mt) cc_final: 0.7938 (tp)
REVERT: A  453 PRO cc_start: 0.5631 (Cg_endo) cc_final: 0.5091 (Cg_exo)
REVERT: A  768 GLU cc_start: 0.7638 (tp30) cc_final: 0.7153 (tt0)
REVERT: B  180 LEU cc_start: 0.6257 (mt) cc_final: 0.5805 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1159
  time to fit residues: 17.9082
Evaluate side-chains
  70 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0170
   chunk 77 optimal weight:    0.1980
   chunk 4 optimal weight:   30.0000
   chunk 2 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 85 optimal weight:    0.2980
   overall best weight:    0.3820

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

Flipped N/Q/H residues before XYZ refinement:
** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 HIS
A 381 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 806 ASN
** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.160199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.133638 restraints weight = 18341.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.131919 restraints weight = 30720.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.132744 restraints weight = 32135.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.132529 restraints weight = 20230.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.132906 restraints weight = 20596.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5582
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9462  Z= 0.126
  Angle     :  0.589  10.639  12835  Z= 0.299
  Chirality :  0.039   0.171   1447
  Planarity :  0.005   0.071   1660
  Dihedral  :  5.475  46.120   1281
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.05 %
    Favored  : 95.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.53 (0.25), residues: 1148
  helix:  0.81 (0.21), residues: 592
  sheet: -1.95 (0.41), residues: 143
  loop : -1.37 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 527 
 TYR   0.015   0.001   TYR B  27 
 PHE   0.054   0.002   PHE A 444 
 TRP   0.015   0.001   TRP A 588 
 HIS   0.004   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9461)
  covalent geometry    : angle       0.58824 (12833)
  SS BOND              : bond        0.00294 (    1)
  SS BOND              : angle       1.80963 (    2)
  hydrogen bonds       : bond        0.03950 (  475)
  hydrogen bonds       : angle       4.48817 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  335 LEU cc_start: 0.8476 (mt) cc_final: 0.8108 (tp)
REVERT: A  347 PHE cc_start: 0.7150 (t80) cc_final: 0.6947 (t80)
REVERT: A  768 GLU cc_start: 0.7628 (tp30) cc_final: 0.7186 (tt0)
REVERT: B  180 LEU cc_start: 0.6573 (mt) cc_final: 0.6213 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0871
  time to fit residues: 12.8612
Evaluate side-chains
  73 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 89 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 114 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A 540 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.155031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.128352 restraints weight = 18573.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.127024 restraints weight = 37978.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.128314 restraints weight = 40121.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.127839 restraints weight = 24136.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.128283 restraints weight = 22738.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5707
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   9462  Z= 0.248
  Angle     :  0.725  10.287  12835  Z= 0.365
  Chirality :  0.043   0.157   1447
  Planarity :  0.005   0.060   1660
  Dihedral  :  5.920  54.306   1281
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.79 (0.25), residues: 1148
  helix:  0.51 (0.21), residues: 587
  sheet: -2.02 (0.42), residues: 137
  loop : -1.35 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 761 
 TYR   0.016   0.002   TYR B  27 
 PHE   0.038   0.002   PHE A 444 
 TRP   0.021   0.002   TRP A 649 
 HIS   0.012   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 ( 9461)
  covalent geometry    : angle       0.72494 (12833)
  SS BOND              : bond        0.02475 (    1)
  SS BOND              : angle       1.81965 (    2)
  hydrogen bonds       : bond        0.04704 (  475)
  hydrogen bonds       : angle       4.77856 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  281 GLN cc_start: 0.7466 (mm110) cc_final: 0.6781 (mm110)
REVERT: A  335 LEU cc_start: 0.8412 (mt) cc_final: 0.8040 (tp)
REVERT: A  351 MET cc_start: 0.7238 (mmt) cc_final: 0.7027 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0876
  time to fit residues: 11.3420
Evaluate side-chains
  67 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 13 optimal weight:   20.0000
   chunk 31 optimal weight:    0.5980
   chunk 82 optimal weight:   20.0000
   chunk 89 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   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 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 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 = 0.4312 r_free = 0.4312 target = 0.156085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.130401 restraints weight = 18068.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.129050 restraints weight = 36982.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.128759 restraints weight = 31471.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.127483 restraints weight = 26031.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.128143 restraints weight = 22904.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5688
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9462  Z= 0.164
  Angle     :  0.630  10.587  12835  Z= 0.317
  Chirality :  0.040   0.142   1447
  Planarity :  0.004   0.055   1660
  Dihedral  :  5.740  49.595   1281
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.54 (0.26), residues: 1148
  helix:  0.76 (0.22), residues: 590
  sheet: -2.11 (0.41), residues: 145
  loop : -1.21 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 761 
 TYR   0.017   0.002   TYR A 673 
 PHE   0.020   0.002   PHE A 444 
 TRP   0.014   0.001   TRP A 649 
 HIS   0.006   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9461)
  covalent geometry    : angle       0.62959 (12833)
  SS BOND              : bond        0.01206 (    1)
  SS BOND              : angle       2.75153 (    2)
  hydrogen bonds       : bond        0.04171 (  475)
  hydrogen bonds       : angle       4.53379 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  281 GLN cc_start: 0.7357 (mm110) cc_final: 0.6607 (mp10)
REVERT: A  311 HIS cc_start: 0.7337 (m90) cc_final: 0.7099 (m-70)
REVERT: A  335 LEU cc_start: 0.8333 (mt) cc_final: 0.8006 (tp)
REVERT: A  347 PHE cc_start: 0.7414 (t80) cc_final: 0.7102 (t80)
REVERT: A  351 MET cc_start: 0.7175 (mmt) cc_final: 0.6960 (mmt)
REVERT: A  531 TRP cc_start: 0.7050 (t60) cc_final: 0.6835 (t60)
REVERT: B  134 LYS cc_start: 0.7516 (mttt) cc_final: 0.7276 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0909
  time to fit residues: 10.7698
Evaluate side-chains
  65 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 44 optimal weight:    0.0060
   chunk 89 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 110 optimal weight:    0.5980
   chunk 14 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0770
   chunk 0 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 7 optimal weight:    9.9990
   overall best weight:    0.9356

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 HIS
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.155221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.129045 restraints weight = 18244.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.128202 restraints weight = 38651.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.127775 restraints weight = 33999.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.127312 restraints weight = 24252.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.127665 restraints weight = 23342.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5710
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9462  Z= 0.197
  Angle     :  0.657  10.279  12835  Z= 0.331
  Chirality :  0.041   0.150   1447
  Planarity :  0.004   0.059   1660
  Dihedral  :  5.781  49.847   1281
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.47 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.62 (0.26), residues: 1148
  helix:  0.70 (0.22), residues: 592
  sheet: -2.19 (0.40), residues: 145
  loop : -1.25 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 761 
 TYR   0.019   0.002   TYR B  27 
 PHE   0.018   0.002   PHE A 399 
 TRP   0.017   0.002   TRP A 649 
 HIS   0.008   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 9461)
  covalent geometry    : angle       0.65677 (12833)
  SS BOND              : bond        0.00622 (    1)
  SS BOND              : angle       2.05455 (    2)
  hydrogen bonds       : bond        0.04292 (  475)
  hydrogen bonds       : angle       4.53487 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  281 GLN cc_start: 0.7314 (mm110) cc_final: 0.6577 (mp10)
REVERT: A  335 LEU cc_start: 0.8429 (mt) cc_final: 0.8164 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0888
  time to fit residues: 10.5985
Evaluate side-chains
  60 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 82 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 HIS
A 392 GLN
A 476 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1068 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.155408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.124190 restraints weight = 18412.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.117582 restraints weight = 26507.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.118356 restraints weight = 28368.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.119374 restraints weight = 22755.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.119498 restraints weight = 18845.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6051
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9462  Z= 0.207
  Angle     :  0.684  10.208  12835  Z= 0.342
  Chirality :  0.042   0.145   1447
  Planarity :  0.005   0.057   1660
  Dihedral  :  5.869  50.442   1281
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.98 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.71 (0.25), residues: 1148
  helix:  0.62 (0.21), residues: 592
  sheet: -2.26 (0.40), residues: 145
  loop : -1.28 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 761 
 TYR   0.021   0.002   TYR A 673 
 PHE   0.027   0.002   PHE A 399 
 TRP   0.017   0.002   TRP A 649 
 HIS   0.008   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 9461)
  covalent geometry    : angle       0.68293 (12833)
  SS BOND              : bond        0.00793 (    1)
  SS BOND              : angle       3.18080 (    2)
  hydrogen bonds       : bond        0.04367 (  475)
  hydrogen bonds       : angle       4.58208 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 GLN cc_start: 0.7587 (mm110) cc_final: 0.6944 (mp10)
REVERT: A  335 LEU cc_start: 0.8506 (mt) cc_final: 0.8196 (tp)
REVERT: A  889 ARG cc_start: 0.7800 (mmt180) cc_final: 0.7499 (mmt180)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0869
  time to fit residues: 10.0433
Evaluate side-chains
  61 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0870
   chunk 64 optimal weight:    0.6980
   chunk 102 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 13 optimal weight:   20.0000
   chunk 104 optimal weight:    0.1980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  69 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.157493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.130806 restraints weight = 18237.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.129063 restraints weight = 33300.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.129992 restraints weight = 35796.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.129864 restraints weight = 20847.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.130290 restraints weight = 19026.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5667
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9462  Z= 0.141
  Angle     :  0.622  10.698  12835  Z= 0.310
  Chirality :  0.040   0.158   1447
  Planarity :  0.004   0.055   1660
  Dihedral  :  5.692  49.492   1281
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.56 (0.26), residues: 1148
  helix:  0.78 (0.22), residues: 598
  sheet: -2.27 (0.39), residues: 154
  loop : -1.23 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 527 
 TYR   0.018   0.001   TYR A 673 
 PHE   0.045   0.002   PHE A 444 
 TRP   0.012   0.001   TRP A 649 
 HIS   0.005   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9461)
  covalent geometry    : angle       0.62155 (12833)
  SS BOND              : bond        0.00615 (    1)
  SS BOND              : angle       2.41373 (    2)
  hydrogen bonds       : bond        0.04000 (  475)
  hydrogen bonds       : angle       4.38731 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 GLN cc_start: 0.7352 (mm110) cc_final: 0.6642 (mp10)
REVERT: A  335 LEU cc_start: 0.8376 (mt) cc_final: 0.8022 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0818
  time to fit residues: 9.8358
Evaluate side-chains
  59 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 83 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9980
   chunk 82 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
A 301 HIS
A 476 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.156616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.126018 restraints weight = 18046.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.122145 restraints weight = 36841.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.123682 restraints weight = 34758.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.124225 restraints weight = 23003.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.124412 restraints weight = 21215.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5833
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9462  Z= 0.167
  Angle     :  0.643  10.646  12835  Z= 0.320
  Chirality :  0.041   0.149   1447
  Planarity :  0.004   0.057   1660
  Dihedral  :  5.699  48.085   1281
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.40 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.59 (0.25), residues: 1148
  helix:  0.74 (0.22), residues: 597
  sheet: -2.21 (0.41), residues: 143
  loop : -1.28 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 527 
 TYR   0.013   0.002   TYR A 673 
 PHE   0.044   0.002   PHE A 444 
 TRP   0.020   0.002   TRP A 382 
 HIS   0.006   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9461)
  covalent geometry    : angle       0.64267 (12833)
  SS BOND              : bond        0.00429 (    1)
  SS BOND              : angle       2.04641 (    2)
  hydrogen bonds       : bond        0.04095 (  475)
  hydrogen bonds       : angle       4.43007 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  281 GLN cc_start: 0.7461 (mm110) cc_final: 0.6793 (mp10)
REVERT: A  335 LEU cc_start: 0.8298 (mt) cc_final: 0.8052 (tp)
REVERT: A  476 HIS cc_start: 0.5844 (OUTLIER) cc_final: 0.5600 (t-90)
REVERT: A  889 ARG cc_start: 0.7146 (mmt180) cc_final: 0.6927 (mmt180)
REVERT: B   27 TYR cc_start: 0.6447 (t80) cc_final: 0.6243 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0816
  time to fit residues: 9.2378
Evaluate side-chains
  61 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0070
   chunk 98 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0670
   chunk 63 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 33 optimal weight:    0.3980
   chunk 85 optimal weight:    0.0040
   chunk 79 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.2348

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

Flipped N/Q/H residues before XYZ refinement:
A 301 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.158990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.127653 restraints weight = 18122.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.124236 restraints weight = 39064.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.125635 restraints weight = 33640.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.126083 restraints weight = 22324.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.126280 restraints weight = 18986.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5767
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9462  Z= 0.113
  Angle     :  0.600  10.765  12835  Z= 0.296
  Chirality :  0.039   0.193   1447
  Planarity :  0.004   0.058   1660
  Dihedral  :  5.466  47.861   1281
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.30 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.39 (0.26), residues: 1148
  helix:  0.91 (0.22), residues: 595
  sheet: -2.15 (0.40), residues: 152
  loop : -1.15 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 527 
 TYR   0.031   0.001   TYR A 673 
 PHE   0.029   0.002   PHE A 444 
 TRP   0.020   0.001   TRP A 382 
 HIS   0.003   0.001   HIS A 754 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9461)
  covalent geometry    : angle       0.59948 (12833)
  SS BOND              : bond        0.00567 (    1)
  SS BOND              : angle       1.85178 (    2)
  hydrogen bonds       : bond        0.03732 (  475)
  hydrogen bonds       : angle       4.26691 ( 1368)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.5697 (pp20) cc_final: 0.5430 (pp20)
REVERT: A  281 GLN cc_start: 0.7449 (mm110) cc_final: 0.6781 (mp10)
REVERT: A  335 LEU cc_start: 0.8337 (mt) cc_final: 0.7963 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0893
  time to fit residues: 9.9561
Evaluate side-chains
  57 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 37 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   chunk 111 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0270
   chunk 46 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 96 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 301 HIS
A 476 HIS
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.157602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.129327 restraints weight = 18010.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.127617 restraints weight = 33899.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.128932 restraints weight = 34888.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.128432 restraints weight = 20710.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.128869 restraints weight = 20439.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5695
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9462  Z= 0.141
  Angle     :  0.618  10.593  12835  Z= 0.306
  Chirality :  0.040   0.220   1447
  Planarity :  0.004   0.057   1660
  Dihedral  :  5.495  48.352   1281
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.34 (0.26), residues: 1148
  helix:  0.95 (0.22), residues: 595
  sheet: -2.02 (0.42), residues: 141
  loop : -1.22 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 893 
 TYR   0.034   0.001   TYR A 673 
 PHE   0.025   0.002   PHE A 444 
 TRP   0.016   0.001   TRP A 382 
 HIS   0.013   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9461)
  covalent geometry    : angle       0.61811 (12833)
  SS BOND              : bond        0.00598 (    1)
  SS BOND              : angle       1.70590 (    2)
  hydrogen bonds       : bond        0.03844 (  475)
  hydrogen bonds       : angle       4.28567 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1681.12 seconds
wall clock time: 29 minutes 51.54 seconds (1791.54 seconds total)