Starting phenix.real_space_refine
on Sun Apr  5 15:34:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zrg_14913/04_2026/7zrg_14913.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zrg_14913/04_2026/7zrg_14913.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zrg_14913/04_2026/7zrg_14913.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zrg_14913/04_2026/7zrg_14913.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zrg_14913/04_2026/7zrg_14913.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zrg_14913/04_2026/7zrg_14913.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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
     K       7      8.98       5
     P       8      5.49       5
     S      62      5.16       5
     C    7124      2.51       5
     N    1824      2.21       5
     O    2007      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11032
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4155
          Classifications: {'peptide': 557}
          Link IDs: {'PTRANS': 25, 'TRANS': 531}
    Chain: "C"
      Number of atoms: 1431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1431
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 13, 'TRANS': 176}
    Chain: "D"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 200
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "B"
      Number of atoms: 5008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5008
          Classifications: {'peptide': 674}
          Link IDs: {'PTRANS': 26, 'TRANS': 647}
    Chain: "A"
      Number of atoms: 207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 207
          Unusual residues: {'  K': 7, 'CDL': 2}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.45, per 1000 atoms: 0.22
  Number of scatterers: 11032
  At special positions: 0
  Unit cell: (100.188, 111.32, 148.764, 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)
     K       7     19.00
     S      62     16.00
     P       8     15.00
     O    2007      8.00
     N    1824      7.00
     C    7124      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: 0.92
  Conformation dependent library (CDL) restraints added in 531.1 milliseconds
  

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2634

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 10 sheets defined
      63.0% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 32
      removed outlier: 3.959A  pdb=" N   MET A  17 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      Proline residue:  A  22  - end of helix
    Processing helix  chain 'A' and resid 39 through 51
    Processing helix  chain 'A' and resid 58 through 83
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 125 through 131
    Processing helix  chain 'A' and resid 131 through 157
    Processing helix  chain 'A' and resid 165 through 177
    Processing helix  chain 'A' and resid 177 through 193
      removed outlier: 3.963A  pdb=" N   VAL A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 3.931A  pdb=" N   GLN A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ILE A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 274
      removed outlier: 4.388A  pdb=" N   ILE A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      Proline residue:  A 263  - end of helix
    Processing helix  chain 'A' and resid 276 through 305
      removed outlier: 4.454A  pdb=" N   GLY A 280 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 313
      removed outlier: 4.094A  pdb=" N   ALA A 311 " --> pdb=" O   PRO A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 342
    Processing helix  chain 'A' and resid 355 through 368
      removed outlier: 3.748A  pdb=" N   VAL A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 377 through 399
    Processing helix  chain 'A' and resid 410 through 436
      removed outlier: 4.562A  pdb=" N   THR A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      Proline residue:  A 425  - end of helix
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 449 through 465
      removed outlier: 4.043A  pdb=" N   PHE A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 495
    Processing helix  chain 'A' and resid 496 through 509
      removed outlier: 3.888A  pdb=" N   SER A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 550
      removed outlier: 3.991A  pdb=" N   PHE A 527 " --> pdb=" O   HIS A 523 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   THR A 542 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   PHE A 543 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      Proline residue:  A 545  - end of helix
    Processing helix  chain 'A' and resid 550 through 557
    Processing helix  chain 'C' and resid 3 through 21
      removed outlier: 4.124A  pdb=" N   ALA C   7 " --> pdb=" O   GLY C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 34
    Processing helix  chain 'C' and resid 34 through 39
    Processing helix  chain 'C' and resid 91 through 109
    Processing helix  chain 'C' and resid 117 through 122
      removed outlier: 3.800A  pdb=" N   VAL C 121 " --> pdb=" O   PRO C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 140
    Processing helix  chain 'C' and resid 140 through 149
      removed outlier: 3.646A  pdb=" N   VAL C 144 " --> pdb=" O   GLN C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 162
    Processing helix  chain 'C' and resid 178 through 190
    Processing helix  chain 'D' and resid 2 through 25
    Processing helix  chain 'B' and resid 11 through 24
      removed outlier: 4.748A  pdb=" N   ALA B  17 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLU B  20 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 54
    Processing helix  chain 'B' and resid 61 through 97
      removed outlier: 4.156A  pdb=" N   SER B  65 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 209
    Processing helix  chain 'B' and resid 215 through 238
    Processing helix  chain 'B' and resid 238 through 246
      removed outlier: 4.162A  pdb=" N   TRP B 245 " --> pdb=" O   PRO B 241 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   GLY B 246 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 263
    Processing helix  chain 'B' and resid 264 through 285
      removed outlier: 5.434A  pdb=" N   SER B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   ALA B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 299
      removed outlier: 3.649A  pdb=" N   GLY B 299 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 341
    Processing helix  chain 'B' and resid 346 through 360
    Processing helix  chain 'B' and resid 397 through 406
    Processing helix  chain 'B' and resid 413 through 427
      removed outlier: 4.155A  pdb=" N   ASP B 417 " --> pdb=" O   PRO B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 462
      removed outlier: 3.715A  pdb=" N   LYS B 462 " --> pdb=" O   ALA B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 486
    Processing helix  chain 'B' and resid 495 through 509
      removed outlier: 3.658A  pdb=" N   GLU B 509 " --> pdb=" O   GLN B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 521
      No H-bonds generated for 'chain 'B' and resid 519 through 521'
    Processing helix  chain 'B' and resid 522 through 528
    Processing helix  chain 'B' and resid 539 through 544
    Processing helix  chain 'B' and resid 557 through 595
      removed outlier: 4.123A  pdb=" N   ASP B 583 " --> pdb=" O   SER B 579 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL B 584 " --> pdb=" O   ILE B 580 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ALA B 585 " --> pdb=" O   ALA B 581 " (cutoff:3.500A)
      Proline residue:  B 592  - end of helix
      removed outlier: 3.570A  pdb=" N   PHE B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 606
      removed outlier: 3.751A  pdb=" N   ASN B 603 " --> pdb=" O   PRO B 600 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ALA B 604 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 631
      removed outlier: 4.488A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   VAL B 629 " --> pdb=" O   ALA B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 638
    Processing helix  chain 'B' and resid 645 through 680
      removed outlier: 4.044A  pdb=" N   GLY B 658 " --> pdb=" O   LEU B 654 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   GLY B 661 " --> pdb=" O   TYR B 657 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   LEU B 662 " --> pdb=" O   GLY B 658 " (cutoff:3.500A)
      Proline residue:  B 665  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204
    Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404
      removed outlier: 3.602A  pdb=" N   LYS A 407 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44
      removed outlier: 6.336A  pdb=" N   ILE C  43 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132
    Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 134
      removed outlier: 3.645A  pdb=" N   GLU B 145 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 153
    Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289
    Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304
      removed outlier: 6.549A  pdb=" N   VAL B 303 " --> pdb=" O   ALA B 514 " (cutoff:3.500A)
      removed outlier: 8.971A  pdb=" N   THR B 516 " --> pdb=" O   VAL B 303 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   VAL B 513 " --> pdb=" O   VAL B 531 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   VAL B 533 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET B 515 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 307
      removed outlier: 6.675A  pdb=" N   LEU B 306 " --> pdb=" O   ILE B 470 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   MET B 469 " --> pdb=" O   LEU B 491 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 429 through 431

    648 hydrogen bonds defined for protein.
    1914 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: 2.02

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1946
        1.33 -     1.45: 2647
        1.45 -     1.57: 6503
        1.57 -     1.70: 17
        1.70 -     1.82: 112
  Bond restraints: 11225
  Sorted by residual:
  bond pdb=" OA3 CDL A 609 "
       pdb=" PA1 CDL A 609 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.44e+00
  bond pdb=" OA3 CDL A 608 "
       pdb=" PA1 CDL A 608 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.11e+00
  bond pdb=" OB3 CDL A 608 "
       pdb=" PB2 CDL A 608 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.08e+00
  bond pdb=" OB3 CDL A 609 "
       pdb=" PB2 CDL A 609 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.00e-02 1.00e+04 6.08e+00
  bond pdb=" C11 CDL A 608 "
       pdb=" C12 CDL A 608 "
    ideal  model  delta    sigma   weight residual
    1.523  1.491  0.032 1.50e-02 4.44e+03 4.48e+00
  ... (remaining 11220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 14857
        2.12 -     4.24: 295
        4.24 -     6.36: 59
        6.36 -     8.48: 23
        8.48 -    10.59: 4
  Bond angle restraints: 15238
  Sorted by residual:
  angle pdb=" CA  TYR A 381 "
        pdb=" CB  TYR A 381 "
        pdb=" CG  TYR A 381 "
      ideal   model   delta    sigma   weight residual
     113.90  120.97   -7.07 1.80e+00 3.09e-01 1.54e+01
  angle pdb=" C   ASP B 366 "
        pdb=" N   VAL B 367 "
        pdb=" CA  VAL B 367 "
      ideal   model   delta    sigma   weight residual
     121.97  128.98   -7.01 1.80e+00 3.09e-01 1.52e+01
  angle pdb=" CB  MET B  36 "
        pdb=" CG  MET B  36 "
        pdb=" SD  MET B  36 "
      ideal   model   delta    sigma   weight residual
     112.70  123.29  -10.59 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" CB  MET A 274 "
        pdb=" CG  MET A 274 "
        pdb=" SD  MET A 274 "
      ideal   model   delta    sigma   weight residual
     112.70  123.10  -10.40 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" C   LEU A 178 "
        pdb=" N   VAL A 179 "
        pdb=" CA  VAL A 179 "
      ideal   model   delta    sigma   weight residual
     120.33  123.10   -2.77 8.00e-01 1.56e+00 1.20e+01
  ... (remaining 15233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.78: 5978
       18.78 -    37.56: 589
       37.56 -    56.34: 142
       56.34 -    75.12: 38
       75.12 -    93.90: 14
  Dihedral angle restraints: 6761
    sinusoidal: 2661
      harmonic: 4100
  Sorted by residual:
  dihedral pdb=" CA  ALA A 470 "
           pdb=" C   ALA A 470 "
           pdb=" N   PHE A 471 "
           pdb=" CA  PHE A 471 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.07   18.93     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  GLY B 658 "
           pdb=" C   GLY B 658 "
           pdb=" N   LEU B 659 "
           pdb=" CA  LEU B 659 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.67   18.33     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA5 CDL A 608 "
           pdb=" CA4 CDL A 608 "
           pdb=" OA6 CDL A 608 "
           pdb=" CA6 CDL A 608 "
      ideal   model   delta sinusoidal    sigma   weight residual
     168.24  -97.86  -93.90     1      3.00e+01 1.11e-03 1.14e+01
  ... (remaining 6758 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1405
       0.052 -    0.103: 337
       0.103 -    0.155: 60
       0.155 -    0.206: 5
       0.206 -    0.258: 5
  Chirality restraints: 1812
  Sorted by residual:
  chirality pdb=" CA4 CDL A 608 "
            pdb=" CA3 CDL A 608 "
            pdb=" CA6 CDL A 608 "
            pdb=" OA6 CDL A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.57   -2.32   -0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CB  VAL B 664 "
            pdb=" CA  VAL B 664 "
            pdb=" CG1 VAL B 664 "
            pdb=" CG2 VAL B 664 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CB  ILE B 182 "
            pdb=" CA  ILE B 182 "
            pdb=" CG1 ILE B 182 "
            pdb=" CG2 ILE B 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1809 not shown)

  Planarity restraints: 1908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 105 "   -0.016 2.00e-02 2.50e+03   2.09e-02 7.67e+00
        pdb=" CG  PHE B 105 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 105 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 105 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 105 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 105 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 105 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 381 "    0.017 2.00e-02 2.50e+03   1.43e-02 4.08e+00
        pdb=" CG  TYR A 381 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 381 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 381 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 381 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 381 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 381 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR A 381 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 361 "    0.033 5.00e-02 4.00e+02   4.94e-02 3.90e+00
        pdb=" N   PRO A 362 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 362 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 362 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1905 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.86: 3790
        2.86 -     3.43: 12485
        3.43 -     4.00: 21344
        4.00 -     4.57: 30580
        4.57 -     5.14: 43138
  Nonbonded interactions: 111337
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 541 "
            pdb=" OH  TYR B 587 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG  SER A 325 "
            pdb=" O   ASN C 131 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   SER A 119 "
            pdb=" OG1 THR A 123 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OD1 ASN B 474 "
            pdb=" OG1 THR B 477 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OG  SER A 343 "
            pdb=" O   ASN A 466 "
     model   vdw
     2.304 3.040
  ... (remaining 111332 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.210
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
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   0.044  11225  Z= 0.194
  Angle     :  0.782  10.595  15238  Z= 0.396
  Chirality :  0.046   0.258   1812
  Planarity :  0.005   0.049   1908
  Dihedral  : 16.908  93.902   4127
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.21), residues: 1437
  helix:  0.09 (0.16), residues: 881
  sheet: -1.58 (0.57), residues: 87
  loop : -2.02 (0.26), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 107 
 TYR   0.035   0.002   TYR A 381 
 PHE   0.048   0.002   PHE B 105 
 TRP   0.012   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (11225)
  covalent geometry    : angle       0.78157 (15238)
  hydrogen bonds       : bond        0.08332 (  648)
  hydrogen bonds       : angle       5.02592 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 TYR cc_start: 0.8029 (m-10) cc_final: 0.7828 (m-10)
REVERT: B  515 MET cc_start: 0.7513 (ptm) cc_final: 0.7248 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0934
  time to fit residues: 22.5249
Evaluate side-chains
  136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 540 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.143357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.106855 restraints weight = 15102.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.106162 restraints weight = 16653.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.107303 restraints weight = 13063.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.107673 restraints weight = 9446.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.108074 restraints weight = 8089.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11225  Z= 0.194
  Angle     :  0.612   7.862  15238  Z= 0.306
  Chirality :  0.041   0.166   1812
  Planarity :  0.005   0.067   1908
  Dihedral  : 12.899  88.041   1747
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.55 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.22), residues: 1437
  helix:  0.88 (0.17), residues: 867
  sheet: -1.69 (0.62), residues: 73
  loop : -1.91 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 394 
 TYR   0.029   0.002   TYR A 381 
 PHE   0.021   0.002   PHE B 105 
 TRP   0.008   0.001   TRP B  31 
 HIS   0.005   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (11225)
  covalent geometry    : angle       0.61189 (15238)
  hydrogen bonds       : bond        0.04369 (  648)
  hydrogen bonds       : angle       4.31033 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A  135 VAL cc_start: 0.8799 (m) cc_final: 0.8550 (p)
REVERT: B  125 GLN cc_start: 0.5320 (pm20) cc_final: 0.4664 (tm-30)
  outliers start: 8
  outliers final: 5
  residues processed: 156
  average time/residue: 0.0996
  time to fit residues: 22.5820
Evaluate side-chains
  134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 88 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 122 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 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 = 0.3701 r_free = 0.3701 target = 0.144028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.107740 restraints weight = 15187.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.105997 restraints weight = 14591.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.108180 restraints weight = 11911.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.108251 restraints weight = 8647.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.108395 restraints weight = 7620.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11225  Z= 0.132
  Angle     :  0.548   7.421  15238  Z= 0.273
  Chirality :  0.039   0.173   1812
  Planarity :  0.004   0.039   1908
  Dihedral  : 12.213  87.929   1747
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.96 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.22), residues: 1437
  helix:  1.15 (0.17), residues: 874
  sheet: -1.63 (0.64), residues: 73
  loop : -1.80 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 148 
 TYR   0.026   0.001   TYR A 381 
 PHE   0.015   0.001   PHE B 105 
 TRP   0.006   0.001   TRP B  71 
 HIS   0.002   0.000   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11225)
  covalent geometry    : angle       0.54758 (15238)
  hydrogen bonds       : bond        0.03966 (  648)
  hydrogen bonds       : angle       4.16085 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.381 
Fit side-chains
REVERT: B   13 LEU cc_start: 0.7969 (pt) cc_final: 0.7518 (pp)
REVERT: B  125 GLN cc_start: 0.5307 (pm20) cc_final: 0.4766 (tm-30)
REVERT: B  560 GLU cc_start: 0.7088 (pm20) cc_final: 0.6821 (mp0)
  outliers start: 11
  outliers final: 9
  residues processed: 150
  average time/residue: 0.0892
  time to fit residues: 20.0648
Evaluate side-chains
  139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  664 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 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 = 0.3683 r_free = 0.3683 target = 0.142537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.106034 restraints weight = 15174.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.105189 restraints weight = 16463.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.106803 restraints weight = 12650.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.106970 restraints weight = 9053.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.107530 restraints weight = 7656.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11225  Z= 0.144
  Angle     :  0.552   9.343  15238  Z= 0.274
  Chirality :  0.040   0.202   1812
  Planarity :  0.004   0.045   1908
  Dihedral  : 11.676  88.420   1747
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.43 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.22), residues: 1437
  helix:  1.25 (0.17), residues: 876
  sheet: -1.71 (0.64), residues: 73
  loop : -1.74 (0.25), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 359 
 TYR   0.026   0.001   TYR A 381 
 PHE   0.015   0.001   PHE A 373 
 TRP   0.007   0.001   TRP B  71 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (11225)
  covalent geometry    : angle       0.55201 (15238)
  hydrogen bonds       : bond        0.03996 (  648)
  hydrogen bonds       : angle       4.11128 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A  327 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8591 (m-80)
REVERT: B   13 LEU cc_start: 0.7898 (pt) cc_final: 0.7593 (pp)
REVERT: B  125 GLN cc_start: 0.5262 (pm20) cc_final: 0.4724 (tm-30)
REVERT: B  560 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6859 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 156
  average time/residue: 0.0979
  time to fit residues: 22.3452
Evaluate side-chains
  145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  560 GLU
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  664 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 117 optimal weight:    9.9990
   chunk 116 optimal weight:    0.7980
   chunk 60 optimal weight:    6.9990
   chunk 136 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0030
   chunk 121 optimal weight:   10.0000
   chunk 135 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.1980
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.145285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.109255 restraints weight = 15066.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.108758 restraints weight = 14640.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.109682 restraints weight = 12668.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.110322 restraints weight = 9520.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.110448 restraints weight = 7533.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11225  Z= 0.104
  Angle     :  0.518   9.008  15238  Z= 0.257
  Chirality :  0.038   0.228   1812
  Planarity :  0.003   0.037   1908
  Dihedral  : 11.111  87.200   1747
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.70 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.22), residues: 1437
  helix:  1.46 (0.18), residues: 884
  sheet: -1.72 (0.65), residues: 73
  loop : -1.67 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 148 
 TYR   0.025   0.001   TYR A 381 
 PHE   0.010   0.001   PHE A 260 
 TRP   0.007   0.001   TRP A 176 
 HIS   0.002   0.000   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (11225)
  covalent geometry    : angle       0.51826 (15238)
  hydrogen bonds       : bond        0.03615 (  648)
  hydrogen bonds       : angle       3.98764 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A  235 PHE cc_start: 0.8436 (t80) cc_final: 0.8192 (t80)
REVERT: A  327 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8446 (m-80)
REVERT: B  125 GLN cc_start: 0.5203 (pm20) cc_final: 0.4731 (tm-30)
REVERT: B  558 LEU cc_start: 0.7984 (tt) cc_final: 0.7741 (tp)
REVERT: B  560 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6752 (mp0)
  outliers start: 22
  outliers final: 15
  residues processed: 152
  average time/residue: 0.0954
  time to fit residues: 21.7054
Evaluate side-chains
  147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  560 GLU
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  664 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 106 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 108 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.143103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.106943 restraints weight = 15215.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.105963 restraints weight = 14969.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.107279 restraints weight = 13391.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.107780 restraints weight = 9484.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.107780 restraints weight = 8027.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11225  Z= 0.131
  Angle     :  0.535   7.843  15238  Z= 0.266
  Chirality :  0.039   0.168   1812
  Planarity :  0.004   0.039   1908
  Dihedral  : 10.965  87.045   1747
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.76 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.22), residues: 1437
  helix:  1.45 (0.17), residues: 882
  sheet: -1.69 (0.65), residues: 73
  loop : -1.61 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 394 
 TYR   0.025   0.001   TYR A 381 
 PHE   0.013   0.001   PHE A 373 
 TRP   0.008   0.001   TRP B  71 
 HIS   0.002   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (11225)
  covalent geometry    : angle       0.53548 (15238)
  hydrogen bonds       : bond        0.03810 (  648)
  hydrogen bonds       : angle       4.00488 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  235 PHE cc_start: 0.8520 (t80) cc_final: 0.8275 (t80)
REVERT: A  272 GLU cc_start: 0.7387 (tt0) cc_final: 0.7169 (tt0)
REVERT: A  325 SER cc_start: 0.8858 (p) cc_final: 0.8641 (p)
REVERT: A  327 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8478 (m-80)
REVERT: A  445 MET cc_start: 0.7045 (mmt) cc_final: 0.6788 (mmt)
REVERT: B   13 LEU cc_start: 0.7921 (pt) cc_final: 0.7701 (pp)
REVERT: B  558 LEU cc_start: 0.8297 (tt) cc_final: 0.8076 (tp)
REVERT: B  560 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6862 (mp0)
  outliers start: 21
  outliers final: 18
  residues processed: 154
  average time/residue: 0.0917
  time to fit residues: 21.1515
Evaluate side-chains
  155 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  560 GLU
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  664 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 139 optimal weight:    8.9990
   chunk 75 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 96 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 134 optimal weight:    0.0770
   chunk 67 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
C  80 GLN
B 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.144212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.107106 restraints weight = 15119.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.105818 restraints weight = 10796.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.106337 restraints weight = 9988.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.107074 restraints weight = 8209.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.107315 restraints weight = 6755.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11225  Z= 0.108
  Angle     :  0.518   9.686  15238  Z= 0.257
  Chirality :  0.038   0.155   1812
  Planarity :  0.003   0.037   1908
  Dihedral  : 10.654  89.208   1747
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.64 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.22), residues: 1437
  helix:  1.56 (0.18), residues: 883
  sheet: -1.75 (0.64), residues: 73
  loop : -1.59 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 202 
 TYR   0.024   0.001   TYR A 381 
 PHE   0.011   0.001   PHE A 373 
 TRP   0.007   0.001   TRP A 176 
 HIS   0.002   0.000   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (11225)
  covalent geometry    : angle       0.51808 (15238)
  hydrogen bonds       : bond        0.03611 (  648)
  hydrogen bonds       : angle       3.95046 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8453 (t80) cc_final: 0.8228 (t80)
REVERT: A  325 SER cc_start: 0.8839 (p) cc_final: 0.8637 (p)
REVERT: A  327 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8499 (m-80)
REVERT: B   13 LEU cc_start: 0.7958 (pt) cc_final: 0.7744 (pp)
REVERT: B  125 GLN cc_start: 0.5596 (OUTLIER) cc_final: 0.5347 (tm-30)
REVERT: B  560 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6815 (mp0)
  outliers start: 22
  outliers final: 18
  residues processed: 157
  average time/residue: 0.0973
  time to fit residues: 22.5857
Evaluate side-chains
  154 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  560 GLU
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  664 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0060
   chunk 20 optimal weight:    0.5980
   chunk 106 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0770
   chunk 127 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 104 optimal weight:    0.5980
   chunk 65 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.4154

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 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 = 0.3711 r_free = 0.3711 target = 0.144770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.105356 restraints weight = 15058.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.107543 restraints weight = 9247.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.108505 restraints weight = 6674.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.109620 restraints weight = 5558.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.109736 restraints weight = 4834.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11225  Z= 0.102
  Angle     :  0.527   9.799  15238  Z= 0.258
  Chirality :  0.038   0.144   1812
  Planarity :  0.003   0.036   1908
  Dihedral  : 10.335  88.597   1747
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.90 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.22), residues: 1437
  helix:  1.62 (0.18), residues: 882
  sheet: -1.80 (0.61), residues: 78
  loop : -1.60 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 394 
 TYR   0.024   0.001   TYR A 381 
 PHE   0.009   0.001   PHE A 373 
 TRP   0.007   0.001   TRP A 176 
 HIS   0.003   0.000   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (11225)
  covalent geometry    : angle       0.52691 (15238)
  hydrogen bonds       : bond        0.03521 (  648)
  hydrogen bonds       : angle       3.91616 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8462 (t80) cc_final: 0.8248 (t80)
REVERT: A  325 SER cc_start: 0.8810 (p) cc_final: 0.8597 (p)
REVERT: A  327 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8523 (m-80)
REVERT: B   13 LEU cc_start: 0.7814 (pt) cc_final: 0.7598 (pp)
REVERT: B  560 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6805 (mp0)
  outliers start: 22
  outliers final: 19
  residues processed: 157
  average time/residue: 0.0981
  time to fit residues: 22.7515
Evaluate side-chains
  157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  560 GLU
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  664 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 128 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 119 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0020
   chunk 142 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.107957 restraints weight = 14998.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.107128 restraints weight = 16437.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.108678 restraints weight = 13741.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.108685 restraints weight = 10589.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.108961 restraints weight = 8930.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11225  Z= 0.109
  Angle     :  0.528   9.945  15238  Z= 0.258
  Chirality :  0.038   0.146   1812
  Planarity :  0.003   0.037   1908
  Dihedral  : 10.112  84.671   1747
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.08 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.22), residues: 1437
  helix:  1.62 (0.18), residues: 882
  sheet: -1.78 (0.61), residues: 78
  loop : -1.63 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 202 
 TYR   0.024   0.001   TYR A 381 
 PHE   0.010   0.001   PHE A 373 
 TRP   0.008   0.001   TRP B  71 
 HIS   0.002   0.000   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (11225)
  covalent geometry    : angle       0.52750 (15238)
  hydrogen bonds       : bond        0.03572 (  648)
  hydrogen bonds       : angle       3.91518 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  235 PHE cc_start: 0.8495 (t80) cc_final: 0.8285 (t80)
REVERT: A  299 MET cc_start: 0.8438 (mtt) cc_final: 0.8110 (mtt)
REVERT: A  325 SER cc_start: 0.8750 (p) cc_final: 0.8538 (p)
REVERT: A  327 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8626 (m-80)
  outliers start: 25
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0992
  time to fit residues: 23.2000
Evaluate side-chains
  157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  664 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 139 optimal weight:    2.9990
   chunk 86 optimal weight:   40.0000
   chunk 37 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 134 optimal weight:    0.0970
   chunk 88 optimal weight:    8.9990
   chunk 133 optimal weight:    1.9990
   chunk 71 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.145409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.106138 restraints weight = 15080.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.108435 restraints weight = 9159.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.109638 restraints weight = 6509.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.110137 restraints weight = 5271.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110403 restraints weight = 5002.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11225  Z= 0.109
  Angle     :  0.536   9.430  15238  Z= 0.262
  Chirality :  0.039   0.145   1812
  Planarity :  0.003   0.050   1908
  Dihedral  :  9.972  82.411   1747
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.52 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.22), residues: 1437
  helix:  1.64 (0.18), residues: 880
  sheet: -1.80 (0.61), residues: 78
  loop : -1.60 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 148 
 TYR   0.024   0.001   TYR A 381 
 PHE   0.010   0.001   PHE A 373 
 TRP   0.008   0.001   TRP B  71 
 HIS   0.002   0.000   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (11225)
  covalent geometry    : angle       0.53604 (15238)
  hydrogen bonds       : bond        0.03550 (  648)
  hydrogen bonds       : angle       3.90722 ( 1914)

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

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

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2874 Ramachandran restraints generated.
    1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8471 (t80) cc_final: 0.8270 (t80)
REVERT: A  299 MET cc_start: 0.8453 (mtt) cc_final: 0.8133 (mtt)
REVERT: A  325 SER cc_start: 0.8737 (p) cc_final: 0.8532 (p)
REVERT: A  327 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8640 (m-80)
REVERT: B  212 ARG cc_start: 0.7133 (mmp-170) cc_final: 0.6857 (mmp-170)
  outliers start: 22
  outliers final: 20
  residues processed: 156
  average time/residue: 0.0948
  time to fit residues: 21.9328
Evaluate side-chains
  157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  664 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 122 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 76 optimal weight:   10.0000
   chunk 137 optimal weight:    1.9990
   chunk 96 optimal weight:   20.0000
   chunk 63 optimal weight:    0.6980
   chunk 114 optimal weight:   10.0000
   chunk 116 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 129 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.145071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.105814 restraints weight = 15033.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.107893 restraints weight = 9058.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109141 restraints weight = 6553.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.109998 restraints weight = 5370.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110227 restraints weight = 4750.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11225  Z= 0.111
  Angle     :  0.536   9.452  15238  Z= 0.262
  Chirality :  0.039   0.146   1812
  Planarity :  0.003   0.054   1908
  Dihedral  :  9.830  81.721   1747
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.43 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.22), residues: 1437
  helix:  1.63 (0.18), residues: 880
  sheet: -1.78 (0.61), residues: 78
  loop : -1.60 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 148 
 TYR   0.024   0.001   TYR A 381 
 PHE   0.011   0.001   PHE A 373 
 TRP   0.008   0.001   TRP B  71 
 HIS   0.002   0.000   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (11225)
  covalent geometry    : angle       0.53630 (15238)
  hydrogen bonds       : bond        0.03570 (  648)
  hydrogen bonds       : angle       3.90962 ( 1914)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1716.48 seconds
wall clock time: 30 minutes 27.87 seconds (1827.87 seconds total)