Starting phenix.real_space_refine
on Tue Jul 29 18:19:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zrg_14913/07_2025/7zrg_14913.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zrg_14913/07_2025/7zrg_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_14913/07_2025/7zrg_14913.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2025/7zrg_14913.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2025/7zrg_14913.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zrg_14913/07_2025/7zrg_14913.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.93, per 1000 atoms: 0.63
  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: 3.28
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 0.98
  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: 3.43

  Time building geometry restraints manager: 3.69 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:             1.210
  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:             0.000
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.420
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.270
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.012   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.048   0.002   PHE B 105 
 TYR   0.035   0.002   TYR A 381 
 ARG   0.008   0.000   ARG B 107 

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

*********************** 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  : 1.239 
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: 0.2366
  time to fit residues: 56.7749
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  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 112 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 129 optimal weight:    0.0970
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.148850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.112545 restraints weight = 14906.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.113159 restraints weight = 8964.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.112316 restraints weight = 6901.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.0938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11225  Z= 0.119
  Angle     :  0.549   7.347  15238  Z= 0.272
  Chirality :  0.039   0.152   1812
  Planarity :  0.004   0.051   1908
  Dihedral  : 12.850  88.448   1747
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  6.61 %
    Favored  : 92.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.22), residues: 1437
  helix:  1.04 (0.17), residues: 873
  sheet: -1.67 (0.62), residues: 73
  loop : -1.81 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  59 
 HIS   0.004   0.001   HIS A 451 
 PHE   0.019   0.001   PHE B 105 
 TYR   0.026   0.001   TYR A 381 
 ARG   0.003   0.000   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  648)
  hydrogen bonds       : angle       4.18790 ( 1914)
  covalent geometry    : bond        0.00260 (11225)
  covalent geometry    : angle       0.54883 (15238)

*********************** 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
  170 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 163
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
REVERT: B  125 GLN cc_start: 0.5573 (pm20) cc_final: 0.4854 (tm-30)
REVERT: B  515 MET cc_start: 0.7603 (ptm) cc_final: 0.7276 (ppp)
  outliers start: 7
  outliers final: 4
  residues processed: 165
  average time/residue: 0.3053
  time to fit residues: 72.3078
Evaluate side-chains
  141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
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  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 79 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 108 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0060
   chunk 138 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.7198

-------------------------------------------------------------------------------
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 = 0.3748 r_free = 0.3748 target = 0.147728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.111660 restraints weight = 15192.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111611 restraints weight = 9213.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.111733 restraints weight = 7129.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1207

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= 0.113
  Angle     :  0.535   9.108  15238  Z= 0.263
  Chirality :  0.039   0.171   1812
  Planarity :  0.004   0.039   1908
  Dihedral  : 12.000  84.823   1747
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.14 %
    Favored  : 89.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.22), residues: 1437
  helix:  1.31 (0.18), residues: 878
  sheet: -1.63 (0.64), residues: 73
  loop : -1.78 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  71 
 HIS   0.004   0.001   HIS A 451 
 PHE   0.014   0.001   PHE B 105 
 TYR   0.025   0.001   TYR A 381 
 ARG   0.003   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03658 (  648)
  hydrogen bonds       : angle       4.04839 ( 1914)
  covalent geometry    : bond        0.00245 (11225)
  covalent geometry    : angle       0.53532 (15238)

*********************** 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
  154 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 2.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 TYR cc_start: 0.8098 (m-10) cc_final: 0.7895 (m-10)
REVERT: B  125 GLN cc_start: 0.5439 (pm20) cc_final: 0.4866 (tm-30)
REVERT: B  448 ILE cc_start: 0.6634 (tp) cc_final: 0.6333 (tt)
  outliers start: 8
  outliers final: 7
  residues processed: 150
  average time/residue: 0.3763
  time to fit residues: 85.1515
Evaluate side-chains
  141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 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  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 97 optimal weight:    0.9990
   chunk 136 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 125 optimal weight:   10.0000
   chunk 89 optimal weight:   20.0000
   chunk 76 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 108 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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**
B 194 ASN
B 540 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.141721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.105686 restraints weight = 15094.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.103670 restraints weight = 14314.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.104271 restraints weight = 13668.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11225  Z= 0.171
  Angle     :  0.578   8.147  15238  Z= 0.288
  Chirality :  0.041   0.205   1812
  Planarity :  0.004   0.065   1908
  Dihedral  : 11.518  83.092   1747
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.73 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.22), residues: 1437
  helix:  1.21 (0.17), residues: 877
  sheet: -1.61 (0.65), residues: 73
  loop : -1.76 (0.25), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  71 
 HIS   0.004   0.001   HIS A 451 
 PHE   0.016   0.002   PHE A 471 
 TYR   0.026   0.002   TYR A 381 
 ARG   0.003   0.000   ARG C 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  648)
  hydrogen bonds       : angle       4.15421 ( 1914)
  covalent geometry    : bond        0.00401 (11225)
  covalent geometry    : angle       0.57757 (15238)

*********************** 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
  154 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 1.761 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8545 (m-80)
REVERT: C  186 ASP cc_start: 0.7220 (m-30) cc_final: 0.6959 (m-30)
REVERT: B  125 GLN cc_start: 0.5259 (pm20) cc_final: 0.4589 (tm-30)
REVERT: B  560 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6696 (mp0)
  outliers start: 15
  outliers final: 9
  residues processed: 146
  average time/residue: 0.3719
  time to fit residues: 79.5406
Evaluate side-chains
  139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 2.938 
-------------------------------------------------------------------------------
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  544 ILE
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  560 GLU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0170
   chunk 122 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 125 optimal weight:    5.9990
   chunk 90 optimal weight:    9.9990
   overall best weight:    2.5624

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.135984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.097251 restraints weight = 15327.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.096960 restraints weight = 15341.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.098133 restraints weight = 11746.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  11225  Z= 0.218
  Angle     :  0.623   7.482  15238  Z= 0.311
  Chirality :  0.043   0.298   1812
  Planarity :  0.004   0.081   1908
  Dihedral  : 11.659  87.752   1747
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.40 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.22), residues: 1437
  helix:  1.06 (0.17), residues: 870
  sheet: -1.68 (0.65), residues: 73
  loop : -1.76 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  71 
 HIS   0.003   0.001   HIS A 451 
 PHE   0.020   0.002   PHE A 471 
 TYR   0.026   0.002   TYR A 381 
 ARG   0.003   0.000   ARG A 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04508 (  648)
  hydrogen bonds       : angle       4.32397 ( 1914)
  covalent geometry    : bond        0.00522 (11225)
  covalent geometry    : angle       0.62260 (15238)

*********************** 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
  157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 1.792 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 MET cc_start: 0.8514 (mtt) cc_final: 0.8246 (mtt)
REVERT: A  327 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8528 (m-80)
REVERT: A  471 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.6567 (m-10)
REVERT: C  186 ASP cc_start: 0.7194 (m-30) cc_final: 0.6934 (m-30)
REVERT: B  125 GLN cc_start: 0.5375 (pm20) cc_final: 0.4703 (tm-30)
REVERT: B  560 GLU cc_start: 0.7135 (pm20) cc_final: 0.6849 (mp0)
  outliers start: 18
  outliers final: 14
  residues processed: 153
  average time/residue: 0.3450
  time to fit residues: 78.0361
Evaluate side-chains
  148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 2.545 
-------------------------------------------------------------------------------
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  376 VAL
Chi-restraints excluded: chain A residue  471 PHE
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  535 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 95 optimal weight:    5.9990
   chunk 134 optimal weight:    0.0980
   chunk 90 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 85 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 60 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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**
D  25 ASN
B 316 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.138777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.100908 restraints weight = 15327.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.099550 restraints weight = 9676.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.100171 restraints weight = 8006.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11225  Z= 0.161
  Angle     :  0.569   8.083  15238  Z= 0.284
  Chirality :  0.041   0.207   1812
  Planarity :  0.004   0.050   1908
  Dihedral  : 11.358  89.688   1747
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.46 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.22), residues: 1437
  helix:  1.18 (0.17), residues: 872
  sheet: -1.69 (0.65), residues: 73
  loop : -1.70 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A 451 
 PHE   0.016   0.001   PHE A 373 
 TYR   0.025   0.002   TYR A 381 
 ARG   0.002   0.000   ARG B 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04185 (  648)
  hydrogen bonds       : angle       4.22969 ( 1914)
  covalent geometry    : bond        0.00379 (11225)
  covalent geometry    : angle       0.56942 (15238)

*********************** 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: 23
    poor density    : 138
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8511 (m-80)
REVERT: C  186 ASP cc_start: 0.7241 (m-30) cc_final: 0.6913 (m-30)
REVERT: B   13 LEU cc_start: 0.7761 (pt) cc_final: 0.7373 (pp)
REVERT: B  383 MET cc_start: 0.2383 (tpt) cc_final: 0.2154 (tpt)
REVERT: B  463 MET cc_start: 0.5015 (mtt) cc_final: 0.4650 (mtm)
REVERT: B  560 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6827 (mp0)
  outliers start: 23
  outliers final: 17
  residues processed: 154
  average time/residue: 0.2213
  time to fit residues: 50.3769
Evaluate side-chains
  150 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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 B residue   45 LEU
Chi-restraints excluded: chain B residue   69 SER
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  535 MET
Chi-restraints excluded: chain B residue  560 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 102 optimal weight:    0.8980
   chunk 115 optimal weight:    7.9990
   chunk 99 optimal weight:    0.3980
   chunk 133 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 63 optimal weight:    0.4980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN
A 252 ASN
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.142983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.106869 restraints weight = 15175.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.105736 restraints weight = 14848.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.106221 restraints weight = 13631.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2093

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= 0.111
  Angle     :  0.528   7.240  15238  Z= 0.263
  Chirality :  0.039   0.158   1812
  Planarity :  0.003   0.039   1908
  Dihedral  : 10.803  86.611   1747
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.99 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.22), residues: 1437
  helix:  1.43 (0.18), residues: 871
  sheet: -1.82 (0.62), residues: 78
  loop : -1.55 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 176 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.012   0.001   PHE A 373 
 TYR   0.025   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 (  648)
  hydrogen bonds       : angle       4.09229 ( 1914)
  covalent geometry    : bond        0.00247 (11225)
  covalent geometry    : angle       0.52811 (15238)

*********************** 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
  168 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8506 (t80) cc_final: 0.8296 (t80)
REVERT: A  325 SER cc_start: 0.8868 (p) cc_final: 0.8598 (p)
REVERT: C  186 ASP cc_start: 0.7281 (m-30) cc_final: 0.6933 (m-30)
REVERT: B   13 LEU cc_start: 0.7698 (pt) cc_final: 0.7290 (pp)
REVERT: B  202 ARG cc_start: 0.7042 (ttm110) cc_final: 0.6780 (ttt90)
REVERT: B  206 MET cc_start: 0.7095 (ppp) cc_final: 0.6841 (ppp)
REVERT: B  560 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6860 (mp0)
  outliers start: 21
  outliers final: 16
  residues processed: 160
  average time/residue: 0.2261
  time to fit residues: 52.2643
Evaluate side-chains
  157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 VAL
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 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  283 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  535 MET
Chi-restraints excluded: chain B residue  560 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 127 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 122 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0170
   chunk 17 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.3622

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.140745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.103585 restraints weight = 15141.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.102049 restraints weight = 10936.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.102304 restraints weight = 10700.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11225  Z= 0.144
  Angle     :  0.567   9.972  15238  Z= 0.280
  Chirality :  0.040   0.166   1812
  Planarity :  0.004   0.044   1908
  Dihedral  : 10.587  84.057   1747
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.22), residues: 1437
  helix:  1.41 (0.18), residues: 869
  sheet: -1.83 (0.61), residues: 78
  loop : -1.57 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  71 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.014   0.001   PHE A 373 
 TYR   0.025   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  648)
  hydrogen bonds       : angle       4.12150 ( 1914)
  covalent geometry    : bond        0.00335 (11225)
  covalent geometry    : angle       0.56654 (15238)

*********************** 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
  160 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.8588 (t80) cc_final: 0.8346 (t80)
REVERT: A  325 SER cc_start: 0.8877 (p) cc_final: 0.8611 (p)
REVERT: C  186 ASP cc_start: 0.7264 (m-30) cc_final: 0.6950 (m-30)
REVERT: B   13 LEU cc_start: 0.7798 (pt) cc_final: 0.7531 (pp)
REVERT: B  213 ARG cc_start: 0.7520 (tpm170) cc_final: 0.7150 (tpm170)
REVERT: B  560 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6821 (mp0)
  outliers start: 22
  outliers final: 18
  residues processed: 153
  average time/residue: 0.2236
  time to fit residues: 50.7057
Evaluate side-chains
  152 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  207 VAL
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 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  283 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  535 MET
Chi-restraints excluded: chain B residue  560 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 112 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0040
   chunk 53 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0060
   chunk 114 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 130 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.3810

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.144500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.104693 restraints weight = 15120.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.106953 restraints weight = 9361.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.108053 restraints weight = 6692.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11225  Z= 0.102
  Angle     :  0.528   9.159  15238  Z= 0.260
  Chirality :  0.038   0.143   1812
  Planarity :  0.003   0.038   1908
  Dihedral  : 10.127  83.693   1747
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.23 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.23), residues: 1437
  helix:  1.58 (0.18), residues: 873
  sheet: -1.88 (0.61), residues: 78
  loop : -1.54 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 176 
 HIS   0.003   0.000   HIS B 404 
 PHE   0.011   0.001   PHE A 373 
 TYR   0.024   0.001   TYR A 381 
 ARG   0.002   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  648)
  hydrogen bonds       : angle       4.02988 ( 1914)
  covalent geometry    : bond        0.00220 (11225)
  covalent geometry    : angle       0.52802 (15238)

*********************** 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
  167 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ILE cc_start: 0.9177 (mm) cc_final: 0.8939 (mt)
REVERT: A  235 PHE cc_start: 0.8462 (t80) cc_final: 0.8233 (t80)
REVERT: A  325 SER cc_start: 0.8731 (p) cc_final: 0.8502 (p)
REVERT: C  186 ASP cc_start: 0.7271 (m-30) cc_final: 0.6929 (m-30)
REVERT: B   13 LEU cc_start: 0.7715 (pt) cc_final: 0.7371 (pp)
REVERT: B  125 GLN cc_start: 0.5315 (pm20) cc_final: 0.4788 (tm-30)
REVERT: B  202 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6896 (ttt90)
  outliers start: 20
  outliers final: 16
  residues processed: 158
  average time/residue: 0.2246
  time to fit residues: 51.7868
Evaluate side-chains
  156 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  207 VAL
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 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  283 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  535 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 86 optimal weight:   30.0000
   chunk 95 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 141 optimal weight:    4.9990
   chunk 122 optimal weight:    0.4980
   chunk 43 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.138702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.100335 restraints weight = 15273.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.099297 restraints weight = 14195.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.099551 restraints weight = 12120.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11225  Z= 0.150
  Angle     :  0.559   9.439  15238  Z= 0.276
  Chirality :  0.040   0.154   1812
  Planarity :  0.004   0.043   1908
  Dihedral  : 10.095  82.372   1747
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.14 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.22), residues: 1437
  helix:  1.46 (0.18), residues: 875
  sheet: -1.81 (0.61), residues: 78
  loop : -1.62 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  71 
 HIS   0.003   0.001   HIS B 404 
 PHE   0.013   0.001   PHE A 373 
 TYR   0.025   0.001   TYR A 381 
 ARG   0.003   0.000   ARG B 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  648)
  hydrogen bonds       : angle       4.10157 ( 1914)
  covalent geometry    : bond        0.00356 (11225)
  covalent geometry    : angle       0.55944 (15238)

********************** 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
  158 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 1.203 
Fit side-chains
REVERT: A  190 ILE cc_start: 0.9205 (mm) cc_final: 0.8997 (mt)
REVERT: A  235 PHE cc_start: 0.8587 (t80) cc_final: 0.8330 (t80)
REVERT: A  325 SER cc_start: 0.8766 (p) cc_final: 0.8561 (p)
REVERT: A  327 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8762 (m-80)
REVERT: A  389 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7808 (mp)
REVERT: C  186 ASP cc_start: 0.7284 (m-30) cc_final: 0.6964 (m-30)
REVERT: B   13 LEU cc_start: 0.7768 (pt) cc_final: 0.7517 (pp)
REVERT: B  125 GLN cc_start: 0.5187 (pm20) cc_final: 0.4697 (tm-30)
  outliers start: 22
  outliers final: 19
  residues processed: 152
  average time/residue: 0.2192
  time to fit residues: 48.9330
Evaluate side-chains
  155 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  389 LEU
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain C residue   34 PHE
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  283 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  535 MET
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 41 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 123 optimal weight:    6.9990
   chunk 141 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 118 optimal weight:    8.9990
   chunk 86 optimal weight:   40.0000
   chunk 15 optimal weight:    0.0050
   overall best weight:    0.7998

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.143026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.106028 restraints weight = 15012.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.105230 restraints weight = 9880.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.105799 restraints weight = 8656.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11225  Z= 0.116
  Angle     :  0.542   9.812  15238  Z= 0.267
  Chirality :  0.039   0.150   1812
  Planarity :  0.003   0.038   1908
  Dihedral  :  9.941  82.260   1747
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.31 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.22), residues: 1437
  helix:  1.52 (0.18), residues: 875
  sheet: -1.84 (0.60), residues: 78
  loop : -1.60 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 176 
 HIS   0.005   0.001   HIS B 404 
 PHE   0.013   0.001   PHE A 373 
 TYR   0.025   0.001   TYR A 381 
 ARG   0.002   0.000   ARG A 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  648)
  hydrogen bonds       : angle       4.05371 ( 1914)
  covalent geometry    : bond        0.00261 (11225)
  covalent geometry    : angle       0.54168 (15238)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4130.60 seconds
wall clock time: 79 minutes 21.13 seconds (4761.13 seconds total)