Starting phenix.real_space_refine
on Tue Mar  3 20:23:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d9u_30621/03_2026/7d9u_30621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d9u_30621/03_2026/7d9u_30621.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d9u_30621/03_2026/7d9u_30621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d9u_30621/03_2026/7d9u_30621.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d9u_30621/03_2026/7d9u_30621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d9u_30621/03_2026/7d9u_30621.cif"
  }
  resolution = 3.8
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      2      5.21       5
     S      56      5.16       5
     C    5264      2.51       5
     N    1389      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8190
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3742
          Classifications: {'peptide': 506}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 23, 'TRANS': 482}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 261
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 216
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 16, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASP:plan': 7, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 162
    Chain: "B"
      Number of atoms: 4372
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 569, 4368
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 138
      Conformer: "B"
        Number of residues, atoms: 569, 4368
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 138
          bond proxies already assigned to first conformer: 4452
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {' MG': 2, 'G2P': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'Z90': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LEU A 254 " occ=0.92
      ... (3 atoms not shown)
      pdb=" CB  LEU A 254 " occ=0.92
  Time building chain proxies: 2.62, per 1000 atoms: 0.32
  Number of scatterers: 8190
  At special positions: 0
  Unit cell: (99.275, 137.94, 137.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      56     16.00
     P       3     15.00
     Mg      2     11.99
     O    1476      8.00
     N    1389      7.00
     C    5264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 472.3 milliseconds
  

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 11 sheets defined
      49.6% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 83
    Processing helix  chain 'A' and resid 85 through 101
    Processing helix  chain 'A' and resid 115 through 126
    Processing helix  chain 'A' and resid 128 through 146
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.892A  pdb=" N   PHE A 166 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   SER A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   THR A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 226
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 302 through 309
    Processing helix  chain 'A' and resid 334 through 341
    Processing helix  chain 'A' and resid 399 through 403
    Processing helix  chain 'A' and resid 408 through 458
      removed outlier: 3.853A  pdb=" N   VAL A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 468
      removed outlier: 4.240A  pdb=" N   GLN A 468 " --> pdb=" O   GLN A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 497
      removed outlier: 3.637A  pdb=" N   ILE A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 519
      removed outlier: 3.699A  pdb=" N   GLU A 519 " --> pdb=" O   GLN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 561
    Processing helix  chain 'A' and resid 598 through 610
      removed outlier: 3.884A  pdb=" N   THR A 602 " --> pdb=" O   GLY A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 627
    Processing helix  chain 'B' and resid 2 through 29
      removed outlier: 4.084A  pdb=" N   ASN B   6 " --> pdb=" O   TYR B   2 " (cutoff:3.500A)
      Proline residue:  B  19  - end of helix
      removed outlier: 3.820A  pdb=" N   TRP B  22 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 59
      removed outlier: 3.803A  pdb=" N   THR B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 82
      removed outlier: 3.699A  pdb=" N   ILE B  66 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 90
      removed outlier: 3.850A  pdb=" N   LEU B  87 " --> pdb=" O   TYR B  83 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B  90 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 112
      removed outlier: 4.597A  pdb=" N   ASP B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   ALA B 103 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 158
      removed outlier: 3.774A  pdb=" N   ILE B 147 " --> pdb=" O   GLN B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 235 through 240
    Processing helix  chain 'B' and resid 249 through 253
      removed outlier: 3.865A  pdb=" N   VAL B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 253'
    Processing helix  chain 'B' and resid 264 through 271
    Processing helix  chain 'B' and resid 282 through 285
      removed outlier: 4.365A  pdb=" N   LEU B 285 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 282 through 285'
    Processing helix  chain 'B' and resid 329 through 335
      removed outlier: 3.668A  pdb=" N   LEU B 333 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 348 through 398
      removed outlier: 4.393A  pdb=" N   LEU B 354 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 408
      removed outlier: 4.247A  pdb=" N   HIS B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 437
    Processing helix  chain 'B' and resid 443 through 461
    Processing helix  chain 'B' and resid 491 through 507
      removed outlier: 3.848A  pdb=" N   SER B 495 " --> pdb=" O   HIS B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 557
      removed outlier: 3.710A  pdb=" N   ASN B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 574
      removed outlier: 3.917A  pdb=" N   SER B 574 " --> pdb=" O   ARG B 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 234
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300
      removed outlier: 6.405A  pdb=" N   MET A 291 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A 290 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A 292 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY A 368 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525
      removed outlier: 4.296A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR A 481 " --> pdb=" O   GLY A 536 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE A 484 " --> pdb=" O   GLY A 576 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 583 through 585
    Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 124
      removed outlier: 3.617A  pdb=" N   ARG B 121 " --> pdb=" O   HIS B 134 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 164
      removed outlier: 3.941A  pdb=" N   ASP B 163 " --> pdb=" O   GLU B 182 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLU B 182 " --> pdb=" O   ASP B 163 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 231
      removed outlier: 3.658A  pdb=" N   PHE B 223 " --> pdb=" O   ILE B 319 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE B 319 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   VAL B 277 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 415 through 417
      removed outlier: 3.686A  pdb=" N   GLY B 531 " --> pdb=" O   CYS B 541 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   CYS B 541 " --> pdb=" O   GLY B 531 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 478 through 479
      removed outlier: 3.591A  pdb=" N   ILE B 422 " --> pdb=" O   HIS B 524 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   HIS B 524 " --> pdb=" O   ILE B 422 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   ASN B 563 " --> pdb=" O   ILE B 519 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   SER B 565 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ILE B 523 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   MET B 599 " --> pdb=" O   PRO B 589 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL B 601 " --> pdb=" O   ARG B 587 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 469 through 470
    Processing sheet with id=AB2, first strand: chain 'B' and resid 511 through 512

    441 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2635
        1.34 -     1.46: 1766
        1.46 -     1.58: 3858
        1.58 -     1.69: 5
        1.69 -     1.81: 86
  Bond restraints: 8350
  Sorted by residual:
  bond pdb=" O3B G2P A1001 "
       pdb=" PG  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.716  1.606  0.110 2.00e-02 2.50e+03 3.02e+01
  bond pdb=" O1A G2P A1001 "
       pdb=" PA  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.507  1.608 -0.101 2.00e-02 2.50e+03 2.57e+01
  bond pdb=" O1B G2P A1001 "
       pdb=" PB  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.510  1.608 -0.098 2.00e-02 2.50e+03 2.43e+01
  bond pdb=" C4  G2P A1001 "
       pdb=" C5  G2P A1001 "
    ideal  model  delta    sigma   weight residual
    1.384  1.467 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" CBN Z90 B 701 "
       pdb=" CBO Z90 B 701 "
    ideal  model  delta    sigma   weight residual
    1.405  1.480 -0.075 2.00e-02 2.50e+03 1.39e+01
  ... (remaining 8345 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 11226
        2.26 -     4.52: 94
        4.52 -     6.77: 12
        6.77 -     9.03: 7
        9.03 -    11.29: 4
  Bond angle restraints: 11343
  Sorted by residual:
  angle pdb=" C3A G2P A1001 "
        pdb=" PB  G2P A1001 "
        pdb=" O3B G2P A1001 "
      ideal   model   delta    sigma   weight residual
      99.71  111.00  -11.29 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" PA  G2P A1001 "
        pdb=" C3A G2P A1001 "
        pdb=" PB  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     120.83  110.32   10.51 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" C3A G2P A1001 "
        pdb=" PA  G2P A1001 "
        pdb=" O5' G2P A1001 "
      ideal   model   delta    sigma   weight residual
      99.14  109.41  -10.27 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" C5  G2P A1001 "
        pdb=" C4  G2P A1001 "
        pdb=" N3  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     128.08  118.68    9.40 3.00e+00 1.11e-01 9.81e+00
  angle pdb=" N3  G2P A1001 "
        pdb=" C4  G2P A1001 "
        pdb=" N9  G2P A1001 "
      ideal   model   delta    sigma   weight residual
     126.73  134.95   -8.22 3.00e+00 1.11e-01 7.51e+00
  ... (remaining 11338 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.93: 4833
       24.93 -    49.86: 153
       49.86 -    74.80: 11
       74.80 -    99.73: 2
       99.73 -   124.66: 2
  Dihedral angle restraints: 5001
    sinusoidal: 1878
      harmonic: 3123
  Sorted by residual:
  dihedral pdb=" CAX Z90 B 701 "
           pdb=" CAV Z90 B 701 "
           pdb=" CAW Z90 B 701 "
           pdb=" CBB Z90 B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.41  -55.93 -124.66     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" CAW Z90 B 701 "
           pdb=" CBB Z90 B 701 "
           pdb=" NBP Z90 B 701 "
           pdb=" CBC Z90 B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -158.43  -36.24 -122.19     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" CA  LEU B 338 "
           pdb=" C   LEU B 338 "
           pdb=" N   TYR B 339 "
           pdb=" CA  TYR B 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.21   15.79     0      5.00e+00 4.00e-02 9.97e+00
  ... (remaining 4998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 875
       0.032 -    0.063: 316
       0.063 -    0.095: 101
       0.095 -    0.127: 46
       0.127 -    0.158: 4
  Chirality restraints: 1342
  Sorted by residual:
  chirality pdb=" C1' G2P A1001 "
            pdb=" C2' G2P A1001 "
            pdb=" N9  G2P A1001 "
            pdb=" O4' G2P A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.52   -0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  PRO B 210 "
            pdb=" N   PRO B 210 "
            pdb=" C   PRO B 210 "
            pdb=" CB  PRO B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" C2' G2P A1001 "
            pdb=" C1' G2P A1001 "
            pdb=" C3' G2P A1001 "
            pdb=" O2' G2P A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.62    0.14 2.00e-01 2.50e+01 5.01e-01
  ... (remaining 1339 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 565 "   -0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO A 566 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 566 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 566 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 485 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.19e+00
        pdb=" C   SER A 485 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   SER A 485 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ASP A 486 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 642 "    0.018 5.00e-02 4.00e+02   2.72e-02 1.19e+00
        pdb=" N   PRO A 643 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 643 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 643 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 499
        2.73 -     3.27: 8569
        3.27 -     3.81: 13433
        3.81 -     4.36: 15179
        4.36 -     4.90: 26681
  Nonbonded interactions: 64361
  Sorted by model distance:
  nonbonded pdb=" O1A G2P A1001 "
            pdb=" O3B G2P A1001 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OG  SER B 280 "
            pdb=" O   CYS B 303 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   LEU A 520 "
            pdb=" NE2 GLN A 548 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OD1 ASN B   6 "
            pdb=" OG1 THR B  48 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OD1 ASP A 486 "
            pdb="MG    MG A1003 "
     model   vdw
     2.245 2.170
  ... (remaining 64356 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=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.490
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
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   0.110   8350  Z= 0.203
  Angle     :  0.592  11.289  11343  Z= 0.292
  Chirality :  0.040   0.158   1342
  Planarity :  0.003   0.034   1431
  Dihedral  : 12.325 124.661   2975
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.43 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.72 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.11 (0.24), residues: 1049
  helix: -0.18 (0.21), residues: 476
  sheet: -2.02 (0.35), residues: 189
  loop : -2.55 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  88 
 TYR   0.011   0.001   TYR B   2 
 PHE   0.012   0.001   PHE A 607 
 TRP   0.003   0.001   TRP B  22 
 HIS   0.002   0.001   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 8350)
  covalent geometry    : angle       0.59189 (11343)
  hydrogen bonds       : bond        0.15541 (  441)
  hydrogen bonds       : angle       6.11334 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8286 (pp20) cc_final: 0.7546 (pp20)
REVERT: A  255 TYR cc_start: 0.7250 (m-80) cc_final: 0.6734 (m-10)
REVERT: A  399 TYR cc_start: 0.8432 (m-80) cc_final: 0.7619 (m-10)
REVERT: A  443 LEU cc_start: 0.8824 (tp) cc_final: 0.8605 (tp)
REVERT: A  444 GLU cc_start: 0.8808 (tp30) cc_final: 0.8363 (tm-30)
REVERT: A  452 ASP cc_start: 0.8567 (t0) cc_final: 0.8353 (t0)
REVERT: A  583 PHE cc_start: 0.8735 (m-80) cc_final: 0.8223 (m-80)
REVERT: A  591 MET cc_start: 0.8850 (tpp) cc_final: 0.8368 (tpt)
REVERT: A  597 PHE cc_start: 0.8246 (m-80) cc_final: 0.8021 (m-80)
REVERT: B   73 MET cc_start: 0.8435 (tpp) cc_final: 0.8040 (tpt)
REVERT: B  284 LEU cc_start: 0.9155 (mt) cc_final: 0.8890 (mp)
REVERT: B  479 TYR cc_start: 0.8549 (t80) cc_final: 0.8179 (t80)
REVERT: B  480 MET cc_start: 0.8763 (ttt) cc_final: 0.8563 (ttt)
REVERT: B  563 ASN cc_start: 0.7915 (p0) cc_final: 0.7706 (p0)
REVERT: B  569 TYR cc_start: 0.8868 (t80) cc_final: 0.8572 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0813
  time to fit residues: 16.5910
Evaluate side-chains
  97 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0970
   overall best weight:    0.5756

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A 300 GLN
A 303 ASN
A 422 GLN
B 242 GLN
B 266 HIS
B 408 HIS
B 437 HIS
B 451 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.084420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.069142 restraints weight = 28940.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.071627 restraints weight = 14381.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.073279 restraints weight = 8960.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.074395 restraints weight = 6442.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.075082 restraints weight = 5099.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3134
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3129
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8350  Z= 0.120
  Angle     :  0.558   8.421  11343  Z= 0.284
  Chirality :  0.042   0.146   1342
  Planarity :  0.004   0.040   1431
  Dihedral  :  8.758 134.456   1189
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 12.40 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -1.08 (0.26), residues: 1049
  helix:  0.75 (0.23), residues: 486
  sheet: -1.72 (0.36), residues: 186
  loop : -2.08 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 381 
 TYR   0.009   0.001   TYR B 479 
 PHE   0.019   0.001   PHE A 458 
 TRP   0.035   0.005   TRP B 602 
 HIS   0.011   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8350)
  covalent geometry    : angle       0.55760 (11343)
  hydrogen bonds       : bond        0.04238 (  441)
  hydrogen bonds       : angle       4.78833 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8346 (pp20) cc_final: 0.7668 (pp20)
REVERT: A  255 TYR cc_start: 0.7346 (m-80) cc_final: 0.7118 (m-10)
REVERT: A  399 TYR cc_start: 0.8451 (m-80) cc_final: 0.7810 (m-10)
REVERT: A  423 ASP cc_start: 0.8936 (t70) cc_final: 0.8470 (t0)
REVERT: A  444 GLU cc_start: 0.8507 (tp30) cc_final: 0.8237 (tm-30)
REVERT: A  591 MET cc_start: 0.8762 (tpp) cc_final: 0.8275 (tpt)
REVERT: B  106 ASP cc_start: 0.8783 (t0) cc_final: 0.8129 (t0)
REVERT: B  284 LEU cc_start: 0.8924 (mt) cc_final: 0.8590 (mp)
REVERT: B  569 TYR cc_start: 0.8592 (t80) cc_final: 0.8150 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 115
  average time/residue: 0.0518
  time to fit residues: 9.5958
Evaluate side-chains
  108 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue  303 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0670
   chunk 75 optimal weight:    3.9990
   chunk 104 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.1722

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

Flipped N/Q/H residues before XYZ refinement:
A 300 GLN
** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.083201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.067315 restraints weight = 33225.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.069886 restraints weight = 15915.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.071647 restraints weight = 9730.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.072818 restraints weight = 6878.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.073625 restraints weight = 5402.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8350  Z= 0.147
  Angle     :  0.574   8.122  11343  Z= 0.288
  Chirality :  0.042   0.184   1342
  Planarity :  0.004   0.041   1431
  Dihedral  :  8.876 141.465   1189
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.29 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.72 (0.26), residues: 1049
  helix:  1.01 (0.23), residues: 487
  sheet: -1.44 (0.37), residues: 185
  loop : -1.92 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 139 
 TYR   0.009   0.001   TYR B 136 
 PHE   0.019   0.002   PHE A 458 
 TRP   0.023   0.003   TRP B 602 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8350)
  covalent geometry    : angle       0.57408 (11343)
  hydrogen bonds       : bond        0.04110 (  441)
  hydrogen bonds       : angle       4.54266 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8367 (pp20) cc_final: 0.7702 (pp20)
REVERT: A  151 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8697 (mp)
REVERT: A  399 TYR cc_start: 0.8473 (m-80) cc_final: 0.7841 (m-10)
REVERT: A  423 ASP cc_start: 0.8962 (t70) cc_final: 0.8494 (t0)
REVERT: A  591 MET cc_start: 0.8673 (tpp) cc_final: 0.8209 (tpt)
REVERT: B   73 MET cc_start: 0.8209 (tpt) cc_final: 0.8009 (tpt)
REVERT: B  284 LEU cc_start: 0.8956 (mt) cc_final: 0.8684 (mp)
  outliers start: 23
  outliers final: 15
  residues processed: 114
  average time/residue: 0.0513
  time to fit residues: 9.4755
Evaluate side-chains
  109 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  505 MET
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 90 optimal weight:    0.3980
   chunk 95 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    0.4980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B 419 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.083669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.067237 restraints weight = 42999.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.070821 restraints weight = 18921.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.072745 restraints weight = 9158.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.073163 restraints weight = 6874.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.073269 restraints weight = 5676.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8350  Z= 0.129
  Angle     :  0.561   8.819  11343  Z= 0.284
  Chirality :  0.042   0.157   1342
  Planarity :  0.004   0.042   1431
  Dihedral  :  8.969 142.641   1189
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.88 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.49 (0.26), residues: 1049
  helix:  1.17 (0.23), residues: 487
  sheet: -1.29 (0.38), residues: 186
  loop : -1.78 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 381 
 TYR   0.040   0.001   TYR B 569 
 PHE   0.028   0.001   PHE B 433 
 TRP   0.021   0.003   TRP B 602 
 HIS   0.003   0.001   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8350)
  covalent geometry    : angle       0.56117 (11343)
  hydrogen bonds       : bond        0.03987 (  441)
  hydrogen bonds       : angle       4.38338 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8414 (pp20) cc_final: 0.7776 (pp20)
REVERT: A  151 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8724 (mp)
REVERT: A  339 MET cc_start: 0.8642 (mmp) cc_final: 0.8391 (mmm)
REVERT: A  423 ASP cc_start: 0.8960 (t70) cc_final: 0.8699 (t0)
REVERT: A  591 MET cc_start: 0.8671 (tpp) cc_final: 0.8217 (tpt)
REVERT: B   73 MET cc_start: 0.8146 (tpt) cc_final: 0.7932 (tpt)
REVERT: B  164 MET cc_start: 0.8082 (mtm) cc_final: 0.7854 (mtm)
REVERT: B  284 LEU cc_start: 0.8975 (mt) cc_final: 0.8682 (mp)
REVERT: B  569 TYR cc_start: 0.8658 (t80) cc_final: 0.7861 (t80)
  outliers start: 22
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0519
  time to fit residues: 9.4052
Evaluate side-chains
  108 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  505 MET
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 4 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 94 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    0.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.082464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.065587 restraints weight = 43760.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.068444 restraints weight = 18503.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.070387 restraints weight = 10594.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.071697 restraints weight = 7246.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.072512 restraints weight = 5560.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8350  Z= 0.132
  Angle     :  0.555   8.099  11343  Z= 0.280
  Chirality :  0.042   0.139   1342
  Planarity :  0.004   0.041   1431
  Dihedral  :  9.024 143.039   1189
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.88 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.30 (0.26), residues: 1049
  helix:  1.29 (0.23), residues: 487
  sheet: -1.12 (0.38), residues: 186
  loop : -1.67 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 139 
 TYR   0.029   0.001   TYR B 569 
 PHE   0.034   0.001   PHE A 458 
 TRP   0.014   0.002   TRP B 602 
 HIS   0.003   0.001   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8350)
  covalent geometry    : angle       0.55522 (11343)
  hydrogen bonds       : bond        0.03942 (  441)
  hydrogen bonds       : angle       4.25344 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8418 (pp20) cc_final: 0.7714 (pp20)
REVERT: A  151 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8699 (mp)
REVERT: A  296 MET cc_start: 0.8435 (mmt) cc_final: 0.8084 (mmp)
REVERT: A  339 MET cc_start: 0.8644 (mmp) cc_final: 0.8359 (mmm)
REVERT: A  423 ASP cc_start: 0.8978 (t70) cc_final: 0.8729 (t0)
REVERT: A  591 MET cc_start: 0.8703 (tpp) cc_final: 0.8262 (tpt)
REVERT: B   73 MET cc_start: 0.8245 (tpt) cc_final: 0.7987 (tpt)
REVERT: B  284 LEU cc_start: 0.8988 (mt) cc_final: 0.8731 (mp)
REVERT: B  564 VAL cc_start: 0.9272 (t) cc_final: 0.8936 (p)
REVERT: B  569 TYR cc_start: 0.8662 (t80) cc_final: 0.8390 (t80)
  outliers start: 23
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0534
  time to fit residues: 9.4799
Evaluate side-chains
  107 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 49 optimal weight:    0.2980
   chunk 3 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 102 optimal weight:    0.7980
   chunk 63 optimal weight:    0.1980
   chunk 89 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.083446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.067643 restraints weight = 32926.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.070250 restraints weight = 15316.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.071993 restraints weight = 9199.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.073155 restraints weight = 6501.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.073793 restraints weight = 5102.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8350  Z= 0.109
  Angle     :  0.543   9.979  11343  Z= 0.271
  Chirality :  0.041   0.139   1342
  Planarity :  0.003   0.041   1431
  Dihedral  :  9.006 143.351   1189
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.06 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.14 (0.26), residues: 1049
  helix:  1.35 (0.23), residues: 488
  sheet: -0.95 (0.38), residues: 186
  loop : -1.55 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 360 
 TYR   0.026   0.001   TYR B 569 
 PHE   0.030   0.001   PHE A 458 
 TRP   0.015   0.002   TRP B 602 
 HIS   0.003   0.001   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8350)
  covalent geometry    : angle       0.54252 (11343)
  hydrogen bonds       : bond        0.03793 (  441)
  hydrogen bonds       : angle       4.12204 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8451 (pp20) cc_final: 0.7813 (pp20)
REVERT: A  148 ASP cc_start: 0.7937 (p0) cc_final: 0.7736 (p0)
REVERT: A  151 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8667 (mp)
REVERT: A  296 MET cc_start: 0.8381 (mmt) cc_final: 0.8033 (mmp)
REVERT: A  339 MET cc_start: 0.8671 (mmp) cc_final: 0.8456 (mmm)
REVERT: A  423 ASP cc_start: 0.8958 (t70) cc_final: 0.8697 (t0)
REVERT: A  591 MET cc_start: 0.8680 (tpp) cc_final: 0.8225 (tpt)
REVERT: B   73 MET cc_start: 0.8229 (tpt) cc_final: 0.7988 (tpt)
REVERT: B  164 MET cc_start: 0.8205 (mtm) cc_final: 0.7982 (mtm)
REVERT: B  284 LEU cc_start: 0.8963 (mt) cc_final: 0.8664 (mp)
REVERT: B  564 VAL cc_start: 0.9236 (t) cc_final: 0.8922 (p)
REVERT: B  569 TYR cc_start: 0.8569 (t80) cc_final: 0.8280 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 116
  average time/residue: 0.0557
  time to fit residues: 10.5626
Evaluate side-chains
  106 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 6 optimal weight:    0.1980
   chunk 34 optimal weight:   10.0000
   chunk 70 optimal weight:    0.7980
   chunk 61 optimal weight:    0.3980
   chunk 24 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.6582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.083477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.068037 restraints weight = 28454.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.070475 restraints weight = 14125.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.072132 restraints weight = 8798.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.073228 restraints weight = 6342.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.073939 restraints weight = 5058.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8350  Z= 0.114
  Angle     :  0.551   9.058  11343  Z= 0.274
  Chirality :  0.041   0.167   1342
  Planarity :  0.004   0.040   1431
  Dihedral  :  9.012 143.100   1189
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.36 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.05 (0.26), residues: 1049
  helix:  1.40 (0.24), residues: 489
  sheet: -0.85 (0.39), residues: 186
  loop : -1.50 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 381 
 TYR   0.022   0.001   TYR B 569 
 PHE   0.041   0.002   PHE B 433 
 TRP   0.012   0.002   TRP B 602 
 HIS   0.002   0.001   HIS B 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8350)
  covalent geometry    : angle       0.55054 (11343)
  hydrogen bonds       : bond        0.03759 (  441)
  hydrogen bonds       : angle       4.10542 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8452 (pp20) cc_final: 0.7810 (pp20)
REVERT: A  296 MET cc_start: 0.8367 (mmt) cc_final: 0.8050 (mmp)
REVERT: A  339 MET cc_start: 0.8676 (mmp) cc_final: 0.8465 (mmm)
REVERT: A  341 MET cc_start: 0.8071 (mtt) cc_final: 0.7868 (mtt)
REVERT: A  423 ASP cc_start: 0.8969 (t70) cc_final: 0.8713 (t0)
REVERT: A  591 MET cc_start: 0.8683 (tpp) cc_final: 0.8249 (tpt)
REVERT: B   73 MET cc_start: 0.8180 (tpt) cc_final: 0.7949 (tpt)
REVERT: B  284 LEU cc_start: 0.8952 (mt) cc_final: 0.8647 (mp)
REVERT: B  564 VAL cc_start: 0.9236 (t) cc_final: 0.8930 (p)
REVERT: B  569 TYR cc_start: 0.8556 (t80) cc_final: 0.8262 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 105
  average time/residue: 0.0540
  time to fit residues: 9.3117
Evaluate side-chains
  109 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0970
   chunk 68 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0980
   chunk 74 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0270
   chunk 53 optimal weight:    0.1980
   chunk 98 optimal weight:    0.9990
   chunk 79 optimal weight:    0.3980
   overall best weight:    0.1636

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 271 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.085238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.070478 restraints weight = 23709.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.072807 restraints weight = 12437.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.074330 restraints weight = 7944.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.075368 restraints weight = 5849.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.075925 restraints weight = 4718.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8350  Z= 0.099
  Angle     :  0.552   9.086  11343  Z= 0.272
  Chirality :  0.041   0.163   1342
  Planarity :  0.003   0.040   1431
  Dihedral  :  8.931 143.978   1189
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.65 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.04 (0.26), residues: 1049
  helix:  1.43 (0.23), residues: 488
  sheet: -0.70 (0.39), residues: 186
  loop : -1.45 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 552 
 TYR   0.022   0.001   TYR B 569 
 PHE   0.032   0.001   PHE A 458 
 TRP   0.012   0.002   TRP B 602 
 HIS   0.002   0.001   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 8350)
  covalent geometry    : angle       0.55193 (11343)
  hydrogen bonds       : bond        0.03588 (  441)
  hydrogen bonds       : angle       4.02839 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8410 (pp20) cc_final: 0.7770 (pp20)
REVERT: A  296 MET cc_start: 0.8243 (mmt) cc_final: 0.7934 (mmp)
REVERT: A  339 MET cc_start: 0.8699 (mmp) cc_final: 0.8354 (mmm)
REVERT: A  423 ASP cc_start: 0.8913 (t70) cc_final: 0.8664 (t0)
REVERT: A  591 MET cc_start: 0.8636 (tpp) cc_final: 0.8231 (tpt)
REVERT: B   73 MET cc_start: 0.8137 (tpt) cc_final: 0.7934 (tpt)
REVERT: B  106 ASP cc_start: 0.8751 (t0) cc_final: 0.8143 (t0)
REVERT: B  284 LEU cc_start: 0.8925 (mt) cc_final: 0.8601 (mp)
REVERT: B  564 VAL cc_start: 0.9189 (t) cc_final: 0.8894 (p)
REVERT: B  569 TYR cc_start: 0.8492 (t80) cc_final: 0.8228 (t80)
  outliers start: 14
  outliers final: 13
  residues processed: 115
  average time/residue: 0.0591
  time to fit residues: 10.6891
Evaluate side-chains
  111 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0570
   chunk 86 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
B 105 HIS
** B 168 GLN ** 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 = 0.3322 r_free = 0.3322 target = 0.084479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.069014 restraints weight = 28487.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.071500 restraints weight = 14224.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.073165 restraints weight = 8814.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.074271 restraints weight = 6337.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.075015 restraints weight = 5043.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8350  Z= 0.112
  Angle     :  0.552   8.483  11343  Z= 0.275
  Chirality :  0.041   0.157   1342
  Planarity :  0.003   0.040   1431
  Dihedral  :  9.071 148.270   1189
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.89 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.17 (0.27), residues: 1049
  helix:  1.51 (0.24), residues: 488
  sheet: -0.58 (0.40), residues: 186
  loop : -1.36 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 552 
 TYR   0.021   0.001   TYR B 569 
 PHE   0.043   0.001   PHE A 458 
 TRP   0.010   0.002   TRP B 602 
 HIS   0.002   0.001   HIS B 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8350)
  covalent geometry    : angle       0.55229 (11343)
  hydrogen bonds       : bond        0.03646 (  441)
  hydrogen bonds       : angle       4.00814 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8430 (pp20) cc_final: 0.7789 (pp20)
REVERT: A  296 MET cc_start: 0.8292 (mmt) cc_final: 0.7983 (mmp)
REVERT: A  339 MET cc_start: 0.8658 (mmp) cc_final: 0.8288 (mmm)
REVERT: A  423 ASP cc_start: 0.8938 (t70) cc_final: 0.8682 (t0)
REVERT: A  591 MET cc_start: 0.8652 (tpp) cc_final: 0.8262 (tpt)
REVERT: B   73 MET cc_start: 0.8154 (tpt) cc_final: 0.7951 (tpt)
REVERT: B  106 ASP cc_start: 0.8719 (t0) cc_final: 0.8173 (t0)
REVERT: B  284 LEU cc_start: 0.8950 (mt) cc_final: 0.8651 (mp)
REVERT: B  564 VAL cc_start: 0.9202 (t) cc_final: 0.8854 (p)
REVERT: B  569 TYR cc_start: 0.8507 (t80) cc_final: 0.8226 (t80)
  outliers start: 14
  outliers final: 13
  residues processed: 108
  average time/residue: 0.0554
  time to fit residues: 9.7624
Evaluate side-chains
  109 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0870
   chunk 77 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** 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 = 0.3320 r_free = 0.3320 target = 0.084371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.067351 restraints weight = 43200.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.070278 restraints weight = 18265.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.072258 restraints weight = 10463.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.073583 restraints weight = 7135.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.074421 restraints weight = 5449.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8350  Z= 0.113
  Angle     :  0.553   8.408  11343  Z= 0.276
  Chirality :  0.041   0.161   1342
  Planarity :  0.003   0.040   1431
  Dihedral  :  8.977 143.487   1189
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 18.89 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.21 (0.27), residues: 1049
  helix:  1.55 (0.24), residues: 487
  sheet: -0.59 (0.40), residues: 186
  loop : -1.34 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 552 
 TYR   0.020   0.001   TYR B 569 
 PHE   0.041   0.001   PHE A 458 
 TRP   0.010   0.002   TRP B 602 
 HIS   0.002   0.001   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8350)
  covalent geometry    : angle       0.55287 (11343)
  hydrogen bonds       : bond        0.03662 (  441)
  hydrogen bonds       : angle       4.02849 ( 1260)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8434 (pp20) cc_final: 0.7796 (pp20)
REVERT: A  205 PHE cc_start: 0.6266 (m-80) cc_final: 0.6055 (m-80)
REVERT: A  296 MET cc_start: 0.8309 (mmt) cc_final: 0.7987 (mmp)
REVERT: A  339 MET cc_start: 0.8729 (mmp) cc_final: 0.8484 (mmm)
REVERT: A  423 ASP cc_start: 0.8950 (t70) cc_final: 0.8699 (t0)
REVERT: A  591 MET cc_start: 0.8661 (tpp) cc_final: 0.8283 (tpt)
REVERT: B   73 MET cc_start: 0.8196 (tpt) cc_final: 0.7988 (tpt)
REVERT: B  284 LEU cc_start: 0.8956 (mt) cc_final: 0.8655 (mp)
REVERT: B  564 VAL cc_start: 0.9168 (t) cc_final: 0.8825 (p)
REVERT: B  569 TYR cc_start: 0.8511 (t80) cc_final: 0.8225 (t80)
  outliers start: 13
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0568
  time to fit residues: 9.7147
Evaluate side-chains
  107 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  303 CYS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  474 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** 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 = 0.3302 r_free = 0.3302 target = 0.083450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.067283 restraints weight = 33970.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.069873 restraints weight = 15958.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.071669 restraints weight = 9650.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.072843 restraints weight = 6805.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.073537 restraints weight = 5347.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8350  Z= 0.135
  Angle     :  0.565   7.666  11343  Z= 0.284
  Chirality :  0.042   0.152   1342
  Planarity :  0.003   0.040   1431
  Dihedral  :  9.029 142.698   1189
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 19.24 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.23 (0.27), residues: 1049
  helix:  1.53 (0.24), residues: 487
  sheet: -0.58 (0.39), residues: 186
  loop : -1.25 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 139 
 TYR   0.019   0.001   TYR B 569 
 PHE   0.041   0.001   PHE A 458 
 TRP   0.010   0.002   TRP B 602 
 HIS   0.002   0.001   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8350)
  covalent geometry    : angle       0.56500 (11343)
  hydrogen bonds       : bond        0.03749 (  441)
  hydrogen bonds       : angle       4.08183 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1391.18 seconds
wall clock time: 24 minutes 43.76 seconds (1483.76 seconds total)