Starting phenix.real_space_refine
on Wed Jan 14 03:11:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ya1_33699/01_2026/7ya1_33699.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ya1_33699/01_2026/7ya1_33699.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ya1_33699/01_2026/7ya1_33699.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ya1_33699/01_2026/7ya1_33699.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ya1_33699/01_2026/7ya1_33699.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ya1_33699/01_2026/7ya1_33699.map"
  }
  resolution = 3.11
  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=   0.008
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 6505 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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4170      2.51       5
     N    1078      2.21       5
     O    1239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6525
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4869
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4990
    Chain: "B"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1557
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 2.56, per 1000 atoms: 0.39
  Number of scatterers: 6525
  At special positions: 0
  Unit cell: (71.28, 97.68, 117.04, 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)
     Zn      1     29.99
     S      37     16.00
     O    1239      8.00
     N    1078      7.00
     C    4170      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG I   1 " - " NAG I   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A  53 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 322 "
      " NAG A 704 " - " ASN A 432 "
      " NAG A 705 " - " ASN A 546 "
      " NAG I   1 " - " ASN B 343 "
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 385.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 706 "
        pdb="ZN    ZN A 706 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 706 " - pdb=" NE2 HIS A 374 "


  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 5 sheets defined
      52.5% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.673A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 58
      No H-bonds generated for 'chain 'A' and resid 56 through 58'
    Processing helix  chain 'A' and resid 59 through 80
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.804A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.606A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 100 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 4.069A  pdb=" N   ARG A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ASN A 117 " --> pdb=" O   SER A 113 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR A 118 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 152
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.663A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TRP A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   GLU A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.849A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 231
      removed outlier: 3.940A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR A 229 " --> pdb=" O   ASP A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 4.601A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ALA A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TYR A 252 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 305 through 311
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 3.759A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 329
      removed outlier: 3.569A  pdb=" N   GLU A 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 383
      removed outlier: 3.669A  pdb=" N   PHE A 369 " --> pdb=" O   THR A 365 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.639A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 405
      removed outlier: 3.562A  pdb=" N   VAL A 404 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 400 through 405'
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.850A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ILE A 436 " --> pdb=" O   ASN A 432 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 473 through 484
      removed outlier: 3.544A  pdb=" N   TRP A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ARG A 482 " --> pdb=" O   TRP A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.065A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN A 526 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLU A 527 " --> pdb=" O   PHE A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.737A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLN A 552 " --> pdb=" O   THR A 548 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.685A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 598
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.149A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.394A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474

    253 hydrogen bonds defined for protein.
    701 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: 0.78

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1231
        1.33 -     1.45: 1840
        1.45 -     1.57: 3579
        1.57 -     1.69: 0
        1.69 -     1.82: 58
  Bond restraints: 6708
  Sorted by residual:
  bond pdb=" N   LEU A 143 "
       pdb=" CA  LEU A 143 "
    ideal  model  delta    sigma   weight residual
    1.457  1.505 -0.047 1.29e-02 6.01e+03 1.35e+01
  bond pdb=" N   LEU A 144 "
       pdb=" CA  LEU A 144 "
    ideal  model  delta    sigma   weight residual
    1.458  1.503 -0.045 1.27e-02 6.20e+03 1.26e+01
  bond pdb=" N   GLU A 197 "
       pdb=" CA  GLU A 197 "
    ideal  model  delta    sigma   weight residual
    1.457  1.503 -0.045 1.29e-02 6.01e+03 1.23e+01
  bond pdb=" N   LEU A 424 "
       pdb=" CA  LEU A 424 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.23e-02 6.61e+03 1.09e+01
  bond pdb=" CA  LEU A 143 "
       pdb=" C   LEU A 143 "
    ideal  model  delta    sigma   weight residual
    1.523  1.553 -0.030 1.34e-02 5.57e+03 5.08e+00
  ... (remaining 6703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 9032
        2.85 -     5.70: 80
        5.70 -     8.54: 6
        8.54 -    11.39: 0
       11.39 -    14.24: 1
  Bond angle restraints: 9119
  Sorted by residual:
  angle pdb=" C   GLY A 319 "
        pdb=" N   LEU A 320 "
        pdb=" CA  LEU A 320 "
      ideal   model   delta    sigma   weight residual
     123.56  109.32   14.24 1.98e+00 2.55e-01 5.17e+01
  angle pdb=" N   VAL A  59 "
        pdb=" CA  VAL A  59 "
        pdb=" C   VAL A  59 "
      ideal   model   delta    sigma   weight residual
     113.71  107.15    6.56 9.50e-01 1.11e+00 4.76e+01
  angle pdb=" C   SER A 425 "
        pdb=" N   PRO A 426 "
        pdb=" CA  PRO A 426 "
      ideal   model   delta    sigma   weight residual
     119.87  124.95   -5.08 1.04e+00 9.25e-01 2.39e+01
  angle pdb=" C   PRO A 258 "
        pdb=" CA  PRO A 258 "
        pdb=" CB  PRO A 258 "
      ideal   model   delta    sigma   weight residual
     111.44  104.60    6.84 1.51e+00 4.39e-01 2.05e+01
  angle pdb=" CA  PRO A 492 "
        pdb=" N   PRO A 492 "
        pdb=" CD  PRO A 492 "
      ideal   model   delta    sigma   weight residual
     112.00  107.21    4.79 1.40e+00 5.10e-01 1.17e+01
  ... (remaining 9114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 3595
       16.24 -    32.48: 345
       32.48 -    48.72: 92
       48.72 -    64.96: 18
       64.96 -    81.20: 5
  Dihedral angle restraints: 4055
    sinusoidal: 1725
      harmonic: 2330
  Sorted by residual:
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.03  -47.03     1      1.00e+01 1.00e-02 3.06e+01
  dihedral pdb=" CA  GLY A 319 "
           pdb=" C   GLY A 319 "
           pdb=" N   LEU A 320 "
           pdb=" CA  LEU A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.01  -25.99     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  TRP A 478 "
           pdb=" C   TRP A 478 "
           pdb=" N   GLU A 479 "
           pdb=" CA  GLU A 479 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.97   18.03     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4052 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 770
       0.054 -    0.108: 173
       0.108 -    0.162: 28
       0.162 -    0.216: 1
       0.216 -    0.270: 2
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" CA  TYR A 196 "
            pdb=" N   TYR A 196 "
            pdb=" C   TYR A 196 "
            pdb=" CB  TYR A 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CA  ILE A 259 "
            pdb=" N   ILE A 259 "
            pdb=" C   ILE A 259 "
            pdb=" CB  ILE A 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  GLN A 300 "
            pdb=" N   GLN A 300 "
            pdb=" C   GLN A 300 "
            pdb=" CB  GLN A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.43e-01
  ... (remaining 971 not shown)

  Planarity restraints: 1179
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 491 "   -0.054 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO A 492 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 492 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 492 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 144 "    0.013 2.00e-02 2.50e+03   2.72e-02 7.39e+00
        pdb=" C   LEU A 144 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   LEU A 144 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLU A 145 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 257 "    0.010 2.00e-02 2.50e+03   2.08e-02 4.32e+00
        pdb=" C   SER A 257 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   SER A 257 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PRO A 258 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1176 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 955
        2.76 -     3.29: 5980
        3.29 -     3.83: 10306
        3.83 -     4.36: 12205
        4.36 -     4.90: 21588
  Nonbonded interactions: 51034
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OG1 THR B 500 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OE1 GLU A 227 "
            pdb=" OH  TYR A 454 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   GLN A 300 "
            pdb=" NE2 GLN A 300 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   ASP A 597 "
            pdb=" NZ  LYS A 600 "
     model   vdw
     2.276 3.120
  ... (remaining 51029 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=0.49 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:             29.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.680
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
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      :  0.004   0.065   6724  Z= 0.219
  Angle     :  0.769  14.239   9154  Z= 0.470
  Chirality :  0.046   0.270    974
  Planarity :  0.005   0.080   1173
  Dihedral  : 13.734  81.203   2538
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.97 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  0.00 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.59 (0.30), residues: 788
  helix: -0.83 (0.28), residues: 376
  sheet:  0.89 (0.84), residues: 41
  loop : -1.45 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 219 
 TYR   0.019   0.001   TYR A 196 
 PHE   0.010   0.001   PHE A 555 
 TRP   0.013   0.001   TRP A 168 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6708)
  covalent geometry    : angle       0.75639 ( 9119)
  SS BOND              : bond        0.00215 (    7)
  SS BOND              : angle       0.96994 (   14)
  hydrogen bonds       : bond        0.23544 (  253)
  hydrogen bonds       : angle       8.05664 (  701)
  metal coordination   : bond        0.00069 (    2)
  link_BETA1-4         : bond        0.00335 (    1)
  link_BETA1-4         : angle       4.38653 (    3)
  link_NAG-ASN         : bond        0.00381 (    6)
  link_NAG-ASN         : angle       2.61003 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 183
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 TYR cc_start: 0.8293 (t80) cc_final: 0.7915 (t80)
REVERT: A  465 LYS cc_start: 0.8076 (tppp) cc_final: 0.7724 (tppp)
REVERT: A  571 GLU cc_start: 0.7476 (tt0) cc_final: 0.7275 (tt0)
REVERT: B  365 TYR cc_start: 0.7416 (m-10) cc_final: 0.7214 (m-10)
REVERT: B  455 LEU cc_start: 0.8664 (tp) cc_final: 0.8427 (tp)
REVERT: B  474 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6782 (tm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 185
  average time/residue: 0.0952
  time to fit residues: 22.9004
Evaluate side-chains
  158 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 156
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  197 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0270
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    0.0010
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.3980
   chunk 74 optimal weight:    0.0980
   overall best weight:    0.2044

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
** A 374 HIS ** 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 = 0.3555 r_free = 0.3555 target = 0.120958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.106195 restraints weight = 9816.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.28
r_work: 0.3231 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
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      :  0.004   0.037   6724  Z= 0.161
  Angle     :  0.633   8.360   9154  Z= 0.327
  Chirality :  0.045   0.181    974
  Planarity :  0.005   0.050   1173
  Dihedral  :  5.663  51.219   1015
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.60 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.33 (0.30), residues: 788
  helix: -0.55 (0.27), residues: 388
  sheet:  1.02 (0.86), residues: 41
  loop : -1.41 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 219 
 TYR   0.022   0.001   TYR A 215 
 PHE   0.010   0.001   PHE A 512 
 TRP   0.018   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6708)
  covalent geometry    : angle       0.61919 ( 9119)
  SS BOND              : bond        0.00382 (    7)
  SS BOND              : angle       0.79911 (   14)
  hydrogen bonds       : bond        0.05793 (  253)
  hydrogen bonds       : angle       5.29013 (  701)
  metal coordination   : bond        0.00081 (    2)
  link_BETA1-4         : bond        0.00315 (    1)
  link_BETA1-4         : angle       3.61254 (    3)
  link_NAG-ASN         : bond        0.00402 (    6)
  link_NAG-ASN         : angle       2.57119 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 154
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6730 (mp0)
REVERT: A  166 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7237 (mm-30)
REVERT: A  189 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7537 (tp30)
REVERT: A  215 TYR cc_start: 0.8577 (m-80) cc_final: 0.8062 (m-80)
REVERT: A  227 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7814 (mp0)
REVERT: A  329 GLU cc_start: 0.8217 (pt0) cc_final: 0.8015 (pt0)
REVERT: A  560 LEU cc_start: 0.8717 (mp) cc_final: 0.8488 (mp)
REVERT: A  564 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7530 (mm-30)
REVERT: B  346 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7577 (ttm-80)
REVERT: B  474 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7407 (tm-30)
  outliers start: 8
  outliers final: 1
  residues processed: 157
  average time/residue: 0.0917
  time to fit residues: 18.7000
Evaluate side-chains
  152 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 149
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  579 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.4980
   chunk 74 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0370
   chunk 58 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0970
   chunk 32 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 22 optimal weight:    0.1980
   overall best weight:    0.1856

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

Flipped N/Q/H residues before XYZ refinement:
A  33 ASN
A  81 GLN
** A 374 HIS ** 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 = 0.3544 r_free = 0.3544 target = 0.120101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.104313 restraints weight = 12632.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.65
r_work: 0.3191 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6724  Z= 0.143
  Angle     :  0.606  12.907   9154  Z= 0.308
  Chirality :  0.044   0.159    974
  Planarity :  0.005   0.078   1173
  Dihedral  :  4.797  33.635   1010
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.76 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.14 (0.30), residues: 788
  helix: -0.31 (0.28), residues: 387
  sheet:  1.12 (0.85), residues: 41
  loop : -1.43 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 219 
 TYR   0.015   0.001   TYR A 215 
 PHE   0.008   0.001   PHE A 314 
 TRP   0.012   0.001   TRP A 566 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6708)
  covalent geometry    : angle       0.59406 ( 9119)
  SS BOND              : bond        0.00378 (    7)
  SS BOND              : angle       0.83314 (   14)
  hydrogen bonds       : bond        0.05335 (  253)
  hydrogen bonds       : angle       4.88330 (  701)
  metal coordination   : bond        0.00155 (    2)
  link_BETA1-4         : bond        0.00634 (    1)
  link_BETA1-4         : angle       3.74069 (    3)
  link_NAG-ASN         : bond        0.00365 (    6)
  link_NAG-ASN         : angle       2.30162 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6577 (mp0)
REVERT: A  182 GLU cc_start: 0.7794 (tt0) cc_final: 0.7494 (mt-10)
REVERT: A  189 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7584 (tm-30)
REVERT: A  224 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7280 (mt-10)
REVERT: A  329 GLU cc_start: 0.8060 (pt0) cc_final: 0.7853 (pt0)
REVERT: A  479 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7330 (mt-10)
REVERT: A  560 LEU cc_start: 0.8741 (mp) cc_final: 0.8502 (mp)
REVERT: A  564 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7325 (mm-30)
  outliers start: 7
  outliers final: 3
  residues processed: 154
  average time/residue: 0.0927
  time to fit residues: 18.6679
Evaluate side-chains
  149 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 145
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.0980
   chunk 60 optimal weight:    0.0980
   chunk 18 optimal weight:    0.0370
   chunk 8 optimal weight:    0.4980
   chunk 54 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 59 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 69 optimal weight:    0.1980
   chunk 42 optimal weight:    0.3980
   chunk 64 optimal weight:    0.0170
   overall best weight:    0.0896

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A 374 HIS ** 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 = 0.3565 r_free = 0.3565 target = 0.121409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.103860 restraints weight = 19884.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.42
r_work: 0.3151 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6724  Z= 0.110
  Angle     :  0.591  11.649   9154  Z= 0.292
  Chirality :  0.042   0.146    974
  Planarity :  0.005   0.067   1173
  Dihedral  :  4.498  33.339   1010
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.20 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.30), residues: 788
  helix:  0.09 (0.28), residues: 379
  sheet:  1.33 (0.84), residues: 41
  loop : -1.42 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.011   0.001   TYR A 454 
 PHE   0.007   0.001   PHE A 452 
 TRP   0.010   0.001   TRP A 566 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6708)
  covalent geometry    : angle       0.57987 ( 9119)
  SS BOND              : bond        0.00272 (    7)
  SS BOND              : angle       0.64343 (   14)
  hydrogen bonds       : bond        0.04376 (  253)
  hydrogen bonds       : angle       4.64968 (  701)
  metal coordination   : bond        0.00130 (    2)
  link_BETA1-4         : bond        0.00507 (    1)
  link_BETA1-4         : angle       3.73253 (    3)
  link_NAG-ASN         : bond        0.00313 (    6)
  link_NAG-ASN         : angle       2.08925 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 GLU cc_start: 0.7851 (tt0) cc_final: 0.7564 (mt-10)
REVERT: A  215 TYR cc_start: 0.8581 (m-80) cc_final: 0.8093 (m-80)
REVERT: A  224 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7463 (mt-10)
REVERT: A  329 GLU cc_start: 0.8166 (pt0) cc_final: 0.7944 (pt0)
REVERT: A  347 THR cc_start: 0.8590 (p) cc_final: 0.8357 (p)
REVERT: A  350 ASP cc_start: 0.7631 (t0) cc_final: 0.7267 (p0)
REVERT: A  479 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7456 (mt-10)
REVERT: A  560 LEU cc_start: 0.8758 (mp) cc_final: 0.8526 (mp)
REVERT: A  564 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7417 (mm-30)
REVERT: A  586 ASN cc_start: 0.8102 (m-40) cc_final: 0.7892 (m-40)
  outliers start: 8
  outliers final: 3
  residues processed: 156
  average time/residue: 0.0892
  time to fit residues: 18.0726
Evaluate side-chains
  152 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 149
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  368 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    0.2980
   chunk 56 optimal weight:    0.1980
   chunk 63 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    0.2980
   chunk 71 optimal weight:    0.6980
   chunk 66 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0070
   chunk 69 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.2398

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 154 ASN
** A 374 HIS ** 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 = 0.3530 r_free = 0.3530 target = 0.119120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.101506 restraints weight = 19825.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 3.45
r_work: 0.3108 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6724  Z= 0.166
  Angle     :  0.625  11.599   9154  Z= 0.314
  Chirality :  0.045   0.154    974
  Planarity :  0.005   0.063   1173
  Dihedral  :  4.631  30.650   1010
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.77 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.30), residues: 788
  helix: -0.04 (0.28), residues: 386
  sheet:  1.35 (0.84), residues: 41
  loop : -1.42 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 306 
 TYR   0.014   0.001   TYR A 183 
 PHE   0.010   0.001   PHE A 314 
 TRP   0.026   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6708)
  covalent geometry    : angle       0.61451 ( 9119)
  SS BOND              : bond        0.00340 (    7)
  SS BOND              : angle       0.65247 (   14)
  hydrogen bonds       : bond        0.05319 (  253)
  hydrogen bonds       : angle       4.63197 (  701)
  metal coordination   : bond        0.00176 (    2)
  link_BETA1-4         : bond        0.00349 (    1)
  link_BETA1-4         : angle       3.63011 (    3)
  link_NAG-ASN         : bond        0.00326 (    6)
  link_NAG-ASN         : angle       2.19600 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8177 (p) cc_final: 0.7971 (p)
REVERT: A  182 GLU cc_start: 0.7876 (tt0) cc_final: 0.7577 (mt-10)
REVERT: A  189 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7620 (tp30)
REVERT: A  215 TYR cc_start: 0.8640 (m-80) cc_final: 0.8359 (m-80)
REVERT: A  224 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7541 (mt-10)
REVERT: A  329 GLU cc_start: 0.8192 (pt0) cc_final: 0.7903 (pt0)
REVERT: A  347 THR cc_start: 0.8612 (p) cc_final: 0.8372 (p)
REVERT: A  350 ASP cc_start: 0.7647 (t0) cc_final: 0.7286 (p0)
REVERT: A  560 LEU cc_start: 0.8786 (mp) cc_final: 0.8548 (mp)
REVERT: A  564 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7389 (mm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 151
  average time/residue: 0.0901
  time to fit residues: 17.8573
Evaluate side-chains
  154 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 148
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0050
   chunk 67 optimal weight:    0.0020
   chunk 1 optimal weight:    0.3980
   chunk 56 optimal weight:    0.0770
   chunk 39 optimal weight:    0.0050
   chunk 47 optimal weight:    0.4980
   chunk 17 optimal weight:    0.5980
   chunk 29 optimal weight:    0.2980
   chunk 38 optimal weight:    0.1980
   chunk 27 optimal weight:    0.0870
   overall best weight:    0.0352

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 154 ASN
** A 374 HIS ** 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 = 0.3578 r_free = 0.3578 target = 0.122407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.106618 restraints weight = 12289.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.57
r_work: 0.3232 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6724  Z= 0.106
  Angle     :  0.578  10.340   9154  Z= 0.289
  Chirality :  0.041   0.141    974
  Planarity :  0.004   0.058   1173
  Dihedral  :  4.326  32.397   1010
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 13.34 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.30), residues: 788
  helix:  0.28 (0.29), residues: 379
  sheet:  1.45 (0.83), residues: 41
  loop : -1.45 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.010   0.001   TYR A 454 
 PHE   0.006   0.001   PHE A 452 
 TRP   0.020   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 6708)
  covalent geometry    : angle       0.56753 ( 9119)
  SS BOND              : bond        0.00350 (    7)
  SS BOND              : angle       0.58457 (   14)
  hydrogen bonds       : bond        0.03941 (  253)
  hydrogen bonds       : angle       4.47683 (  701)
  metal coordination   : bond        0.00115 (    2)
  link_BETA1-4         : bond        0.00600 (    1)
  link_BETA1-4         : angle       3.80237 (    3)
  link_NAG-ASN         : bond        0.00313 (    6)
  link_NAG-ASN         : angle       1.97720 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 155
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8116 (p) cc_final: 0.7901 (p)
REVERT: A  215 TYR cc_start: 0.8514 (m-80) cc_final: 0.8129 (m-80)
REVERT: A  224 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7376 (mt-10)
REVERT: A  329 GLU cc_start: 0.8057 (pt0) cc_final: 0.7772 (pt0)
REVERT: A  347 THR cc_start: 0.8512 (p) cc_final: 0.8231 (p)
REVERT: A  350 ASP cc_start: 0.7528 (t0) cc_final: 0.7177 (p0)
REVERT: A  560 LEU cc_start: 0.8769 (mp) cc_final: 0.8530 (mp)
REVERT: A  564 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7235 (mm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 156
  average time/residue: 0.0854
  time to fit residues: 17.7034
Evaluate side-chains
  153 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  364 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 24 optimal weight:    0.4980
   chunk 1 optimal weight:    0.4980
   chunk 72 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0370
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 71 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0870
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 195 HIS
** A 374 HIS ** 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 = 0.3517 r_free = 0.3517 target = 0.118061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.103329 restraints weight = 9819.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.25
r_work: 0.3191 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3041
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3041
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6724  Z= 0.199
  Angle     :  0.649  10.395   9154  Z= 0.329
  Chirality :  0.046   0.156    974
  Planarity :  0.005   0.060   1173
  Dihedral  :  4.649  29.210   1010
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.35 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.30), residues: 788
  helix:  0.07 (0.28), residues: 381
  sheet:  1.50 (0.80), residues: 43
  loop : -1.52 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 306 
 TYR   0.016   0.002   TYR A 183 
 PHE   0.013   0.001   PHE A 314 
 TRP   0.041   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 6708)
  covalent geometry    : angle       0.63895 ( 9119)
  SS BOND              : bond        0.00380 (    7)
  SS BOND              : angle       0.73547 (   14)
  hydrogen bonds       : bond        0.05804 (  253)
  hydrogen bonds       : angle       4.60970 (  701)
  metal coordination   : bond        0.00236 (    2)
  link_BETA1-4         : bond        0.00324 (    1)
  link_BETA1-4         : angle       3.56507 (    3)
  link_NAG-ASN         : bond        0.00335 (    6)
  link_NAG-ASN         : angle       2.19894 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8227 (p) cc_final: 0.8019 (p)
REVERT: A  124 SER cc_start: 0.8353 (t) cc_final: 0.8033 (p)
REVERT: A  189 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7648 (tp30)
REVERT: A  215 TYR cc_start: 0.8634 (m-80) cc_final: 0.8118 (m-80)
REVERT: A  224 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7709 (mt-10)
REVERT: A  329 GLU cc_start: 0.8270 (pt0) cc_final: 0.7964 (pt0)
REVERT: A  347 THR cc_start: 0.8643 (p) cc_final: 0.8325 (p)
REVERT: A  360 MET cc_start: 0.8647 (ptm) cc_final: 0.8382 (ptm)
REVERT: A  511 SER cc_start: 0.8779 (m) cc_final: 0.8467 (t)
REVERT: A  560 LEU cc_start: 0.8820 (mp) cc_final: 0.8575 (mp)
REVERT: A  564 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7445 (mm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 151
  average time/residue: 0.0872
  time to fit residues: 17.2579
Evaluate side-chains
  146 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 75 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0980
   chunk 12 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   chunk 76 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 50 optimal weight:    0.1980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 154 ASN
** A 374 HIS ** 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 = 0.3513 r_free = 0.3513 target = 0.117843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.101429 restraints weight = 14987.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.93
r_work: 0.3128 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6724  Z= 0.204
  Angle     :  0.647  11.505   9154  Z= 0.329
  Chirality :  0.047   0.168    974
  Planarity :  0.005   0.058   1173
  Dihedral  :  4.766  30.770   1010
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.92 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.02 (0.29), residues: 788
  helix: -0.14 (0.27), residues: 388
  sheet:  1.46 (0.80), residues: 43
  loop : -1.53 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 306 
 TYR   0.016   0.002   TYR A 183 
 PHE   0.011   0.001   PHE A 314 
 TRP   0.051   0.002   TRP A 168 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 6708)
  covalent geometry    : angle       0.63589 ( 9119)
  SS BOND              : bond        0.00381 (    7)
  SS BOND              : angle       0.77257 (   14)
  hydrogen bonds       : bond        0.05814 (  253)
  hydrogen bonds       : angle       4.67512 (  701)
  metal coordination   : bond        0.00215 (    2)
  link_BETA1-4         : bond        0.00484 (    1)
  link_BETA1-4         : angle       3.75781 (    3)
  link_NAG-ASN         : bond        0.00348 (    6)
  link_NAG-ASN         : angle       2.25866 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7557 (tp30)
REVERT: A  215 TYR cc_start: 0.8606 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  224 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7468 (mt-10)
REVERT: A  329 GLU cc_start: 0.8144 (pt0) cc_final: 0.7853 (pt0)
REVERT: A  347 THR cc_start: 0.8558 (p) cc_final: 0.8224 (p)
REVERT: A  360 MET cc_start: 0.8583 (ptm) cc_final: 0.8337 (ptm)
REVERT: A  560 LEU cc_start: 0.8798 (mp) cc_final: 0.8550 (mp)
REVERT: A  564 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7332 (mm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 143
  average time/residue: 0.0881
  time to fit residues: 16.5656
Evaluate side-chains
  150 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  368 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0870
   chunk 20 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 6 optimal weight:    0.1980
   chunk 46 optimal weight:    0.3980
   chunk 18 optimal weight:    0.2980
   chunk 22 optimal weight:    0.3980
   chunk 29 optimal weight:    0.2980
   chunk 0 optimal weight:    0.1980
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.2158

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 154 ASN
** A 374 HIS ** 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 = 0.3524 r_free = 0.3524 target = 0.118766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.101614 restraints weight = 18177.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 3.30
r_work: 0.3113 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6724  Z= 0.159
  Angle     :  0.627  10.296   9154  Z= 0.319
  Chirality :  0.045   0.164    974
  Planarity :  0.005   0.061   1173
  Dihedral  :  4.671  31.313   1010
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 14.92 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.29), residues: 788
  helix:  0.03 (0.28), residues: 381
  sheet:  1.58 (0.81), residues: 43
  loop : -1.58 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 306 
 TYR   0.015   0.001   TYR B 369 
 PHE   0.009   0.001   PHE A 314 
 TRP   0.065   0.002   TRP A 168 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6708)
  covalent geometry    : angle       0.61512 ( 9119)
  SS BOND              : bond        0.00313 (    7)
  SS BOND              : angle       0.80451 (   14)
  hydrogen bonds       : bond        0.05329 (  253)
  hydrogen bonds       : angle       4.63395 (  701)
  metal coordination   : bond        0.00099 (    2)
  link_BETA1-4         : bond        0.00419 (    1)
  link_BETA1-4         : angle       3.84878 (    3)
  link_NAG-ASN         : bond        0.00300 (    6)
  link_NAG-ASN         : angle       2.22801 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 144
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7567 (tp30)
REVERT: A  215 TYR cc_start: 0.8625 (m-80) cc_final: 0.8390 (m-80)
REVERT: A  224 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7524 (mt-10)
REVERT: A  329 GLU cc_start: 0.8184 (pt0) cc_final: 0.7885 (pt0)
REVERT: A  347 THR cc_start: 0.8558 (p) cc_final: 0.8219 (p)
REVERT: A  360 MET cc_start: 0.8591 (ptm) cc_final: 0.8360 (ptm)
REVERT: A  564 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7377 (mm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 145
  average time/residue: 0.0844
  time to fit residues: 16.2944
Evaluate side-chains
  147 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  368 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 56 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0770
   chunk 3 optimal weight:    0.1980
   chunk 40 optimal weight:    0.0570
   chunk 57 optimal weight:    0.0980
   chunk 8 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0980
   chunk 41 optimal weight:    0.5980
   chunk 1 optimal weight:    0.2980
   overall best weight:    0.1056

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** 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 = 0.3546 r_free = 0.3546 target = 0.120165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.104518 restraints weight = 12652.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.64
r_work: 0.3187 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6724  Z= 0.123
  Angle     :  0.614   9.914   9154  Z= 0.312
  Chirality :  0.044   0.160    974
  Planarity :  0.005   0.069   1173
  Dihedral  :  4.489  32.080   1010
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.64 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.30), residues: 788
  helix:  0.18 (0.28), residues: 380
  sheet:  1.54 (0.79), residues: 43
  loop : -1.57 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.012   0.001   TYR B 369 
 PHE   0.007   0.001   PHE A 285 
 TRP   0.069   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6708)
  covalent geometry    : angle       0.60253 ( 9119)
  SS BOND              : bond        0.00199 (    7)
  SS BOND              : angle       0.81895 (   14)
  hydrogen bonds       : bond        0.04650 (  253)
  hydrogen bonds       : angle       4.55304 (  701)
  metal coordination   : bond        0.00094 (    2)
  link_BETA1-4         : bond        0.00462 (    1)
  link_BETA1-4         : angle       3.88689 (    3)
  link_NAG-ASN         : bond        0.00293 (    6)
  link_NAG-ASN         : angle       2.13307 (   18)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 150
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   70 SER cc_start: 0.8103 (p) cc_final: 0.7894 (p)
REVERT: A  189 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7494 (tp30)
REVERT: A  215 TYR cc_start: 0.8578 (m-80) cc_final: 0.8240 (m-80)
REVERT: A  224 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7380 (mt-10)
REVERT: A  329 GLU cc_start: 0.8097 (pt0) cc_final: 0.7808 (pt0)
REVERT: A  347 THR cc_start: 0.8502 (p) cc_final: 0.8148 (p)
REVERT: A  350 ASP cc_start: 0.7560 (t0) cc_final: 0.7200 (p0)
REVERT: A  360 MET cc_start: 0.8559 (ptm) cc_final: 0.8290 (ptm)
REVERT: A  541 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8028 (mtmm)
REVERT: A  560 LEU cc_start: 0.8772 (mp) cc_final: 0.8525 (mp)
REVERT: A  564 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7281 (mm-30)
REVERT: A  580 ASN cc_start: 0.8027 (t0) cc_final: 0.7747 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 151
  average time/residue: 0.0882
  time to fit residues: 17.5503
Evaluate side-chains
  151 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 146
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  368 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 58 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0010
   chunk 72 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0170
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.3824

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 394 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 = 0.3504 r_free = 0.3504 target = 0.117311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.100314 restraints weight = 18141.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 3.25
r_work: 0.3090 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3095
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3095
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6724  Z= 0.235
  Angle     :  0.681  10.740   9154  Z= 0.349
  Chirality :  0.049   0.169    974
  Planarity :  0.005   0.069   1173
  Dihedral  :  4.871  30.464   1010
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 16.36 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.02 (0.29), residues: 788
  helix: -0.12 (0.27), residues: 389
  sheet:  1.53 (0.80), residues: 43
  loop : -1.56 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 306 
 TYR   0.019   0.002   TYR A 183 
 PHE   0.020   0.002   PHE A 308 
 TRP   0.068   0.003   TRP A 168 
 HIS   0.007   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 6708)
  covalent geometry    : angle       0.66794 ( 9119)
  SS BOND              : bond        0.00505 (    7)
  SS BOND              : angle       1.25512 (   14)
  hydrogen bonds       : bond        0.06203 (  253)
  hydrogen bonds       : angle       4.71380 (  701)
  metal coordination   : bond        0.00201 (    2)
  link_BETA1-4         : bond        0.00304 (    1)
  link_BETA1-4         : angle       3.75374 (    3)
  link_NAG-ASN         : bond        0.00405 (    6)
  link_NAG-ASN         : angle       2.46342 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2259.98 seconds
wall clock time: 39 minutes 24.02 seconds (2364.02 seconds total)