Starting phenix.real_space_refine
on Tue Mar  3 17:19:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y48_33603/03_2026/7y48_33603_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y48_33603/03_2026/7y48_33603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y48_33603/03_2026/7y48_33603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y48_33603/03_2026/7y48_33603.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y48_33603/03_2026/7y48_33603_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y48_33603/03_2026/7y48_33603_neut_trim.cif"
  }
  resolution = 2.85
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3638 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2776      2.51       5
     N     744      2.21       5
     O     788      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 4324
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 567, 4253
          Classifications: {'peptide': 567}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 20, 'TRANS': 546}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "B"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 71
          Unusual residues: {'CLR': 1, 'IE5': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.05, per 1000 atoms: 0.24
  Number of scatterers: 4324
  At special positions: 0
  Unit cell: (64.6, 89.25, 147.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     788      8.00
     N     744      7.00
     C    2776      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: 0.39
  Conformation dependent library (CDL) restraints added in 281.1 milliseconds
  

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1040

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 3 sheets defined
      69.5% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 155 through 165
    Processing helix  chain 'B' and resid 167 through 201
      removed outlier: 4.042A  pdb=" N   ALA B 173 " --> pdb=" O   ARG B 169 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET B 180 " --> pdb=" O   GLY B 176 " (cutoff:3.500A)
      Proline residue:  B 189  - end of helix
    Processing helix  chain 'B' and resid 207 through 256
      removed outlier: 3.546A  pdb=" N   LEU B 223 " --> pdb=" O   SER B 219 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   CYS B 224 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY B 240 " --> pdb=" O   MET B 236 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLN B 241 " --> pdb=" O   GLN B 237 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG B 246 " --> pdb=" O   ARG B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 266
      removed outlier: 3.794A  pdb=" N   PHE B 263 " --> pdb=" O   GLU B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 277
      removed outlier: 3.675A  pdb=" N   LEU B 271 " --> pdb=" O   ARG B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 288
      removed outlier: 3.817A  pdb=" N   VAL B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR B 287 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 311
      removed outlier: 3.596A  pdb=" N   VAL B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   GLY B 303 " --> pdb=" O   GLN B 299 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ILE B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 320
      removed outlier: 3.515A  pdb=" N   THR B 316 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE B 317 " --> pdb=" O   ASN B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 360
      removed outlier: 3.531A  pdb=" N   VAL B 325 " --> pdb=" O   VAL B 321 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASN B 360 " --> pdb=" O   GLU B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 367
    Processing helix  chain 'B' and resid 370 through 419
      removed outlier: 4.083A  pdb=" N   ILE B 374 " --> pdb=" O   GLU B 370 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LYS B 390 " --> pdb=" O   GLN B 386 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLU B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLY B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LEU B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL B 410 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B 411 " --> pdb=" O   ASN B 407 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B 419 " --> pdb=" O   TYR B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 425
      removed outlier: 4.279A  pdb=" N   ALA B 424 " --> pdb=" O   MET B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 466
      removed outlier: 3.828A  pdb=" N   GLY B 446 " --> pdb=" O   GLY B 442 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER B 450 " --> pdb=" O   GLY B 446 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE B 451 " --> pdb=" O   GLY B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 541
      removed outlier: 3.980A  pdb=" N   SER B 538 " --> pdb=" O   SER B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 569
      removed outlier: 3.555A  pdb=" N   SER B 568 " --> pdb=" O   VAL B 564 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LYS B 569 " --> pdb=" O   TRP B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 592
      removed outlier: 4.209A  pdb=" N   ALA B 589 " --> pdb=" O   GLU B 586 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   TYR B 590 " --> pdb=" O   ASN B 587 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLY B 591 " --> pdb=" O   ILE B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 598
    Processing helix  chain 'B' and resid 599 through 610
      removed outlier: 3.643A  pdb=" N   ILE B 603 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA B 607 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU B 608 " --> pdb=" O   GLN B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 618
      removed outlier: 3.892A  pdb=" N   ARG B 617 " --> pdb=" O   VAL B 613 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASN B 618 " --> pdb=" O   ALA B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 624
    Processing helix  chain 'B' and resid 635 through 651
      removed outlier: 3.501A  pdb=" N   ARG B 641 " --> pdb=" O   GLY B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 680
      removed outlier: 4.013A  pdb=" N   GLN B 673 " --> pdb=" O   GLU B 669 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ARG B 678 " --> pdb=" O   GLU B 674 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU B 679 " --> pdb=" O   ALA B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 720
      removed outlier: 3.589A  pdb=" N   LEU B 718 " --> pdb=" O   LYS B 714 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU B 719 " --> pdb=" O   HIS B 715 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 517
      removed outlier: 7.066A  pdb=" N   GLN B 511 " --> pdb=" O   HIS B 498 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   HIS B 498 " --> pdb=" O   GLN B 511 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   PHE B 513 " --> pdb=" O   ASN B 496 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 570 through 573
      removed outlier: 6.685A  pdb=" N   THR B 523 " --> pdb=" O   VAL B 687 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   VAL B 522 " --> pdb=" O   MET B 700 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ALA B 702 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ALA B 524 " --> pdb=" O   ALA B 702 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   LEU B 704 " --> pdb=" O   ALA B 524 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   VAL B 526 " --> pdb=" O   LEU B 704 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLU B 711 " --> pdb=" O   VAL B 703 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 582 through 583

    278 hydrogen bonds defined for protein.
    807 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: 0.56

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 698
        1.31 -     1.43: 1123
        1.43 -     1.56: 2549
        1.56 -     1.68: 4
        1.68 -     1.81: 29
  Bond restraints: 4403
  Sorted by residual:
  bond pdb=" C13 IE5 B 802 "
       pdb=" C14 IE5 B 802 "
    ideal  model  delta    sigma   weight residual
    1.357  1.612 -0.255 2.00e-02 2.50e+03 1.63e+02
  bond pdb=" C1' IE5 B 802 "
       pdb=" CAC IE5 B 802 "
    ideal  model  delta    sigma   weight residual
    1.353  1.594 -0.241 2.00e-02 2.50e+03 1.45e+02
  bond pdb=" C2  IE5 B 802 "
       pdb=" N3  IE5 B 802 "
    ideal  model  delta    sigma   weight residual
    1.321  1.499 -0.178 2.00e-02 2.50e+03 7.91e+01
  bond pdb=" C15 IE5 B 802 "
       pdb=" C2  IE5 B 802 "
    ideal  model  delta    sigma   weight residual
    1.450  1.610 -0.160 2.00e-02 2.50e+03 6.42e+01
  bond pdb=" C15 IE5 B 802 "
       pdb=" C17 IE5 B 802 "
    ideal  model  delta    sigma   weight residual
    1.363  1.521 -0.158 2.00e-02 2.50e+03 6.23e+01
  ... (remaining 4398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 5847
        2.44 -     4.89: 95
        4.89 -     7.33: 27
        7.33 -     9.78: 7
        9.78 -    12.22: 2
  Bond angle restraints: 5978
  Sorted by residual:
  angle pdb=" N   MET B 186 "
        pdb=" CA  MET B 186 "
        pdb=" C   MET B 186 "
      ideal   model   delta    sigma   weight residual
     113.97  104.97    9.00 1.28e+00 6.10e-01 4.94e+01
  angle pdb=" N   GLY B 480 "
        pdb=" CA  GLY B 480 "
        pdb=" C   GLY B 480 "
      ideal   model   delta    sigma   weight residual
     110.38  115.60   -5.22 1.28e+00 6.10e-01 1.66e+01
  angle pdb=" C1' IE5 B 802 "
        pdb=" C27 IE5 B 802 "
        pdb=" N4  IE5 B 802 "
      ideal   model   delta    sigma   weight residual
     106.14  118.36  -12.22 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" N   VAL B 687 "
        pdb=" CA  VAL B 687 "
        pdb=" C   VAL B 687 "
      ideal   model   delta    sigma   weight residual
     107.80  113.25   -5.45 1.45e+00 4.76e-01 1.41e+01
  angle pdb=" C13 IE5 B 802 "
        pdb=" C12 IE5 B 802 "
        pdb=" NAA IE5 B 802 "
      ideal   model   delta    sigma   weight residual
     105.60  116.36  -10.76 3.00e+00 1.11e-01 1.29e+01
  ... (remaining 5973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 2446
       17.83 -    35.66: 210
       35.66 -    53.48: 30
       53.48 -    71.31: 9
       71.31 -    89.14: 3
  Dihedral angle restraints: 2698
    sinusoidal: 1078
      harmonic: 1620
  Sorted by residual:
  dihedral pdb=" CA  ILE B 199 "
           pdb=" C   ILE B 199 "
           pdb=" N   TYR B 200 "
           pdb=" CA  TYR B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.18  -17.82     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  ASP B 681 "
           pdb=" CB  ASP B 681 "
           pdb=" CG  ASP B 681 "
           pdb=" OD1 ASP B 681 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.38   59.38     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CA  ASN B 478 "
           pdb=" CB  ASN B 478 "
           pdb=" CG  ASN B 478 "
           pdb=" OD1 ASN B 478 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -176.79  -63.21     2      2.00e+01 2.50e-03 9.56e+00
  ... (remaining 2695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 496
       0.036 -    0.072: 153
       0.072 -    0.109: 38
       0.109 -    0.145: 10
       0.145 -    0.181: 4
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" C9  CLR B 801 "
            pdb=" C10 CLR B 801 "
            pdb=" C11 CLR B 801 "
            pdb=" C8  CLR B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.63    0.18 2.00e-01 2.50e+01 8.19e-01
  chirality pdb=" C10 CLR B 801 "
            pdb=" C1  CLR B 801 "
            pdb=" C5  CLR B 801 "
            pdb=" C9  CLR B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.68   -0.17 2.00e-01 2.50e+01 6.93e-01
  chirality pdb=" CA  PHE B 499 "
            pdb=" N   PHE B 499 "
            pdb=" C   PHE B 499 "
            pdb=" CB  PHE B 499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.02e-01
  ... (remaining 698 not shown)

  Planarity restraints: 756
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' IE5 B 802 "   -0.046 2.00e-02 2.50e+03   1.70e-01 7.24e+02
        pdb=" C27 IE5 B 802 "    0.025 2.00e-02 2.50e+03
        pdb=" C31 IE5 B 802 "    0.025 2.00e-02 2.50e+03
        pdb=" C33 IE5 B 802 "   -0.175 2.00e-02 2.50e+03
        pdb=" C8  IE5 B 802 "    0.130 2.00e-02 2.50e+03
        pdb=" CAA IE5 B 802 "   -0.387 2.00e-02 2.50e+03
        pdb=" CAB IE5 B 802 "    0.263 2.00e-02 2.50e+03
        pdb=" CAC IE5 B 802 "    0.040 2.00e-02 2.50e+03
        pdb=" N4  IE5 B 802 "    0.135 2.00e-02 2.50e+03
        pdb=" O2' IE5 B 802 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 IE5 B 802 "   -0.209 2.00e-02 2.50e+03   1.49e-01 5.56e+02
        pdb=" C11 IE5 B 802 "   -0.126 2.00e-02 2.50e+03
        pdb=" C12 IE5 B 802 "   -0.034 2.00e-02 2.50e+03
        pdb=" C13 IE5 B 802 "    0.031 2.00e-02 2.50e+03
        pdb=" C14 IE5 B 802 "   -0.034 2.00e-02 2.50e+03
        pdb=" C2  IE5 B 802 "    0.342 2.00e-02 2.50e+03
        pdb=" C28 IE5 B 802 "   -0.002 2.00e-02 2.50e+03
        pdb=" C29 IE5 B 802 "    0.164 2.00e-02 2.50e+03
        pdb=" NAA IE5 B 802 "   -0.126 2.00e-02 2.50e+03
        pdb=" OP3 IE5 B 802 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C17 IE5 B 802 "   -0.022 2.00e-02 2.50e+03   2.31e-02 6.65e+00
        pdb=" C4  IE5 B 802 "    0.005 2.00e-02 2.50e+03
        pdb=" C5  IE5 B 802 "    0.036 2.00e-02 2.50e+03
        pdb=" C6  IE5 B 802 "   -0.028 2.00e-02 2.50e+03
        pdb=" N3  IE5 B 802 "    0.008 2.00e-02 2.50e+03
  ... (remaining 753 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1049
        2.80 -     3.32: 4296
        3.32 -     3.85: 6634
        3.85 -     4.37: 7439
        4.37 -     4.90: 13064
  Nonbonded interactions: 32482
  Sorted by model distance:
  nonbonded pdb=" O   GLN B 489 "
            pdb=" OG  SER B 519 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   ALA B 378 "
            pdb=" OD1 ASP B 382 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" N   GLU B 373 "
            pdb=" OE1 GLU B 373 "
     model   vdw
     2.371 3.120
  nonbonded pdb=" OE1 GLU B 356 "
            pdb=" NH1 ARG B 357 "
     model   vdw
     2.403 3.120
  nonbonded pdb=" OE1 GLU B 259 "
            pdb=" N   LYS B 474 "
     model   vdw
     2.409 3.120
  ... (remaining 32477 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.880
  Find NCS groups from input model:        0.010
  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:8.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
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      :  0.010   0.255   4403  Z= 0.525
  Angle     :  0.839  12.224   5978  Z= 0.446
  Chirality :  0.039   0.181    701
  Planarity :  0.009   0.170    756
  Dihedral  : 13.515  89.138   1658
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  2.03 %
    Favored  : 97.07 %
  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 (0.36), residues: 563
  helix:  1.91 (0.28), residues: 352
  sheet: -1.68 (0.81), residues: 35
  loop : -1.13 (0.41), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 248 
 TYR   0.005   0.001   TYR B 332 
 PHE   0.009   0.001   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.003   0.001   HIS B 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00958 ( 4403)
  covalent geometry    : angle       0.83907 ( 5978)
  hydrogen bonds       : bond        0.20111 (  278)
  hydrogen bonds       : angle       6.00166 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.163 
Fit side-chains
REVERT: B  185 SER cc_start: 0.7948 (t) cc_final: 0.7729 (m)
REVERT: B  687 VAL cc_start: 0.6728 (OUTLIER) cc_final: 0.6507 (m)
  outliers start: 4
  outliers final: 1
  residues processed: 87
  average time/residue: 0.5960
  time to fit residues: 53.4861
Evaluate side-chains
  85 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  569 LYS
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
B 313 ASN
B 478 ASN
B 699 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.153641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.126696 restraints weight = 5627.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.00
r_work: 0.3513 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4403  Z= 0.183
  Angle     :  0.549   5.399   5978  Z= 0.285
  Chirality :  0.040   0.140    701
  Planarity :  0.005   0.048    756
  Dihedral  :  6.892  61.676    719
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  9.23 %
    Favored  : 88.51 %
  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:  1.38 (0.35), residues: 563
  helix:  2.11 (0.28), residues: 360
  sheet: -1.39 (0.82), residues: 35
  loop : -1.26 (0.40), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 257 
 TYR   0.008   0.001   TYR B 207 
 PHE   0.015   0.002   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.006   0.002   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 4403)
  covalent geometry    : angle       0.54922 ( 5978)
  hydrogen bonds       : bond        0.08334 (  278)
  hydrogen bonds       : angle       4.46409 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.147 
Fit side-chains
REVERT: B  472 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7482 (tp30)
REVERT: B  687 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7152 (m)
  outliers start: 10
  outliers final: 3
  residues processed: 95
  average time/residue: 0.6086
  time to fit residues: 59.5520
Evaluate side-chains
  95 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  391 GLU
Chi-restraints excluded: chain B residue  472 GLU
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 46 optimal weight:    0.0980
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0470
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
B 313 ASN
B 699 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.153244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.126609 restraints weight = 5608.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 1.94
r_work: 0.3513 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3366 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4403  Z= 0.166
  Angle     :  0.503   5.306   5978  Z= 0.261
  Chirality :  0.039   0.137    701
  Planarity :  0.004   0.046    756
  Dihedral  :  5.905  59.172    715
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 11.04 %
    Favored  : 86.71 %
  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:  1.40 (0.35), residues: 563
  helix:  2.12 (0.28), residues: 361
  sheet: -1.42 (0.80), residues: 35
  loop : -1.24 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 257 
 TYR   0.008   0.001   TYR B 452 
 PHE   0.013   0.001   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.005   0.002   HIS B 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4403)
  covalent geometry    : angle       0.50276 ( 5978)
  hydrogen bonds       : bond        0.08172 (  278)
  hydrogen bonds       : angle       4.22932 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.168 
Fit side-chains
REVERT: B  472 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7495 (tp30)
REVERT: B  687 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7069 (m)
  outliers start: 10
  outliers final: 4
  residues processed: 96
  average time/residue: 0.6211
  time to fit residues: 61.4309
Evaluate side-chains
  94 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  391 GLU
Chi-restraints excluded: chain B residue  472 GLU
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  560 GLN
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0980
   chunk 27 optimal weight:    0.2980
   chunk 26 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0970
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
B 313 ASN
B 699 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.154589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.127784 restraints weight = 5607.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.00
r_work: 0.3525 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4403  Z= 0.146
  Angle     :  0.476   7.627   5978  Z= 0.247
  Chirality :  0.038   0.135    701
  Planarity :  0.004   0.040    756
  Dihedral  :  5.423  57.665    715
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.84 %
    Favored  : 85.59 %
  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:  1.54 (0.35), residues: 563
  helix:  2.24 (0.28), residues: 361
  sheet: -1.31 (0.79), residues: 35
  loop : -1.22 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 395 
 TYR   0.009   0.001   TYR B 452 
 PHE   0.011   0.001   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.004   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4403)
  covalent geometry    : angle       0.47591 ( 5978)
  hydrogen bonds       : bond        0.07545 (  278)
  hydrogen bonds       : angle       4.01411 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.182 
Fit side-chains
REVERT: B  185 SER cc_start: 0.8208 (p) cc_final: 0.7995 (m)
REVERT: B  265 LYS cc_start: 0.7394 (ptpp) cc_final: 0.6917 (ptpp)
REVERT: B  687 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.7018 (m)
  outliers start: 7
  outliers final: 4
  residues processed: 92
  average time/residue: 0.6420
  time to fit residues: 60.8115
Evaluate side-chains
  92 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  391 GLU
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  560 GLN
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0070
   chunk 18 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0970
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
B 313 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.153537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.126613 restraints weight = 5569.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.00
r_work: 0.3508 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4403  Z= 0.160
  Angle     :  0.483   5.330   5978  Z= 0.252
  Chirality :  0.038   0.135    701
  Planarity :  0.004   0.041    756
  Dihedral  :  5.297  57.059    715
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.41 %
    Favored  : 83.56 %
  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:  1.51 (0.35), residues: 563
  helix:  2.20 (0.27), residues: 361
  sheet: -1.30 (0.79), residues: 35
  loop : -1.22 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.007   0.001   TYR B 452 
 PHE   0.012   0.001   PHE B 190 
 TRP   0.002   0.001   TRP B 440 
 HIS   0.005   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4403)
  covalent geometry    : angle       0.48334 ( 5978)
  hydrogen bonds       : bond        0.07886 (  278)
  hydrogen bonds       : angle       4.00737 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.124 
Fit side-chains
REVERT: B  355 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: B  687 VAL cc_start: 0.7417 (OUTLIER) cc_final: 0.6978 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 90
  average time/residue: 0.6311
  time to fit residues: 58.5494
Evaluate side-chains
  92 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  560 GLN
Chi-restraints excluded: chain B residue  685 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0870
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
B 313 ASN
B 699 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.151105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.123927 restraints weight = 5627.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.00
r_work: 0.3468 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4403  Z= 0.214
  Angle     :  0.559   7.801   5978  Z= 0.288
  Chirality :  0.041   0.137    701
  Planarity :  0.004   0.045    756
  Dihedral  :  5.520  55.508    715
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.19 %
    Favored  : 83.33 %
  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:  1.22 (0.35), residues: 563
  helix:  1.96 (0.27), residues: 361
  sheet: -1.37 (0.78), residues: 35
  loop : -1.31 (0.41), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 257 
 TYR   0.009   0.002   TYR B 200 
 PHE   0.014   0.002   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.006   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 4403)
  covalent geometry    : angle       0.55919 ( 5978)
  hydrogen bonds       : bond        0.09125 (  278)
  hydrogen bonds       : angle       4.16881 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.148 
Fit side-chains
REVERT: B  472 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7539 (tp30)
REVERT: B  687 VAL cc_start: 0.7433 (OUTLIER) cc_final: 0.7028 (m)
  outliers start: 11
  outliers final: 6
  residues processed: 98
  average time/residue: 0.6425
  time to fit residues: 64.7351
Evaluate side-chains
  98 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain B residue  467 GLU
Chi-restraints excluded: chain B residue  472 GLU
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  560 GLN
Chi-restraints excluded: chain B residue  685 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    0.2980
   chunk 43 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
B 313 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.151324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.124279 restraints weight = 5610.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.96
r_work: 0.3475 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4403  Z= 0.191
  Angle     :  0.526   5.724   5978  Z= 0.274
  Chirality :  0.040   0.136    701
  Planarity :  0.004   0.040    756
  Dihedral  :  5.409  55.490    715
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.54 %
    Favored  : 82.21 %
  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:  1.17 (0.35), residues: 563
  helix:  1.97 (0.27), residues: 361
  sheet: -1.17 (0.81), residues: 32
  loop : -1.49 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 395 
 TYR   0.012   0.002   TYR B 452 
 PHE   0.012   0.002   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.005   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 4403)
  covalent geometry    : angle       0.52589 ( 5978)
  hydrogen bonds       : bond        0.08867 (  278)
  hydrogen bonds       : angle       4.13692 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.157 
Fit side-chains
REVERT: B  265 LYS cc_start: 0.7348 (ptpp) cc_final: 0.6955 (ptpp)
REVERT: B  416 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8029 (mmtt)
REVERT: B  472 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7544 (tp30)
REVERT: B  687 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7033 (m)
  outliers start: 10
  outliers final: 6
  residues processed: 95
  average time/residue: 0.6553
  time to fit residues: 64.0784
Evaluate side-chains
  98 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain B residue  467 GLU
Chi-restraints excluded: chain B residue  472 GLU
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  560 GLN
Chi-restraints excluded: chain B residue  685 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 36 optimal weight:    0.2980
   chunk 8 optimal weight:    0.0980
   chunk 41 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:    0.1980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
B 313 ASN
B 699 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.153766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.126913 restraints weight = 5587.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 1.98
r_work: 0.3511 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4403  Z= 0.148
  Angle     :  0.473   5.338   5978  Z= 0.248
  Chirality :  0.038   0.128    701
  Planarity :  0.004   0.037    756
  Dihedral  :  5.047  57.599    715
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 16.22 %
    Favored  : 82.21 %
  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:  1.42 (0.35), residues: 563
  helix:  2.16 (0.27), residues: 361
  sheet: -1.12 (0.82), residues: 32
  loop : -1.37 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 395 
 TYR   0.010   0.001   TYR B 452 
 PHE   0.010   0.001   PHE B 190 
 TRP   0.003   0.001   TRP B 466 
 HIS   0.004   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4403)
  covalent geometry    : angle       0.47251 ( 5978)
  hydrogen bonds       : bond        0.07714 (  278)
  hydrogen bonds       : angle       3.94917 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.135 
Fit side-chains
REVERT: B  265 LYS cc_start: 0.7323 (ptpp) cc_final: 0.7026 (ptpp)
REVERT: B  416 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7972 (mmtt)
REVERT: B  687 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.6938 (m)
  outliers start: 7
  outliers final: 4
  residues processed: 90
  average time/residue: 0.6249
  time to fit residues: 57.9494
Evaluate side-chains
  92 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  560 GLN
Chi-restraints excluded: chain B residue  685 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 45 optimal weight:    0.2980
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0270
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
B 313 ASN
B 699 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.152736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.125677 restraints weight = 5681.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.01
r_work: 0.3492 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4403  Z= 0.169
  Angle     :  0.510   7.395   5978  Z= 0.264
  Chirality :  0.039   0.129    701
  Planarity :  0.004   0.036    756
  Dihedral  :  5.149  57.769    715
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.67 %
    Favored  : 81.53 %
  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:  1.38 (0.35), residues: 563
  helix:  2.12 (0.27), residues: 361
  sheet: -1.16 (0.81), residues: 32
  loop : -1.38 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 395 
 TYR   0.011   0.001   TYR B 452 
 PHE   0.012   0.002   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.005   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 4403)
  covalent geometry    : angle       0.51009 ( 5978)
  hydrogen bonds       : bond        0.08188 (  278)
  hydrogen bonds       : angle       4.00012 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.164 
Fit side-chains
REVERT: B  265 LYS cc_start: 0.7234 (ptpp) cc_final: 0.6910 (ptpp)
REVERT: B  416 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8006 (mmtt)
REVERT: B  472 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7539 (tp30)
REVERT: B  687 VAL cc_start: 0.7427 (OUTLIER) cc_final: 0.6963 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 92
  average time/residue: 0.6499
  time to fit residues: 61.5986
Evaluate side-chains
  96 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain B residue  472 GLU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  560 GLN
Chi-restraints excluded: chain B residue  685 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 50 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 313 ASN
B 699 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.152402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.125396 restraints weight = 5592.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 1.98
r_work: 0.3489 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4403  Z= 0.174
  Angle     :  0.516   6.166   5978  Z= 0.268
  Chirality :  0.039   0.130    701
  Planarity :  0.004   0.036    756
  Dihedral  :  5.164  57.917    715
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.89 %
    Favored  : 81.31 %
  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:  1.39 (0.35), residues: 563
  helix:  2.15 (0.27), residues: 361
  sheet: -1.26 (0.81), residues: 32
  loop : -1.40 (0.43), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 257 
 TYR   0.010   0.001   TYR B 452 
 PHE   0.012   0.002   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.005   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4403)
  covalent geometry    : angle       0.51586 ( 5978)
  hydrogen bonds       : bond        0.08351 (  278)
  hydrogen bonds       : angle       4.01235 (  807)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.153 
Fit side-chains
REVERT: B  265 LYS cc_start: 0.7232 (ptpp) cc_final: 0.6915 (ptpp)
REVERT: B  416 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8015 (mmtt)
REVERT: B  472 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7536 (tp30)
REVERT: B  687 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.6960 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 95
  average time/residue: 0.6556
  time to fit residues: 64.1291
Evaluate side-chains
  99 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain B residue  472 GLU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  560 GLN
Chi-restraints excluded: chain B residue  685 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 44 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 35 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 313 ASN
B 699 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.152167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.125492 restraints weight = 5626.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.93
r_work: 0.3494 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4403  Z= 0.175
  Angle     :  0.516   6.564   5978  Z= 0.268
  Chirality :  0.039   0.129    701
  Planarity :  0.004   0.039    756
  Dihedral  :  5.172  58.283    715
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.12 %
    Favored  : 81.08 %
  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:  1.42 (0.35), residues: 563
  helix:  2.16 (0.27), residues: 361
  sheet: -1.22 (0.81), residues: 32
  loop : -1.35 (0.43), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 257 
 TYR   0.010   0.001   TYR B 452 
 PHE   0.012   0.002   PHE B 190 
 TRP   0.003   0.001   TRP B 440 
 HIS   0.005   0.001   HIS B 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4403)
  covalent geometry    : angle       0.51592 ( 5978)
  hydrogen bonds       : bond        0.08413 (  278)
  hydrogen bonds       : angle       4.01424 (  807)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2269.86 seconds
wall clock time: 39 minutes 6.86 seconds (2346.86 seconds total)