Starting phenix.real_space_refine
on Thu Mar 13 15:29:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dx4_30895/03_2025/7dx4_30895_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dx4_30895/03_2025/7dx4_30895.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dx4_30895/03_2025/7dx4_30895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dx4_30895/03_2025/7dx4_30895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dx4_30895/03_2025/7dx4_30895_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dx4_30895/03_2025/7dx4_30895_neut.cif"
  }
  resolution = 3.6
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 805 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    5241      2.51       5
     N    1364      2.21       5
     O    1586      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8234
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "E"
      Number of atoms: 1542
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
      Conformer: "B"
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
          bond proxies already assigned to first conformer: 1572
    Chain: "H"
      Number of atoms: 939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 939
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 806
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 7, 'TRANS': 104}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 9.06, per 1000 atoms: 1.10
  Number of scatterers: 8234
  At special positions: 0
  Unit cell: (144.56, 91.52, 78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1586      8.00
     N    1364      7.00
     C    5241      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  97 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 322 "
      " NAG A 704 " - " ASN A  53 "
      " NAG E 601 " - " ASN E 343 "
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1902

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 12 sheets defined
      43.9% alpha, 12.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.988A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.534A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS A  74 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   THR A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.631A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
      removed outlier: 4.132A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.936A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.510A  pdb=" N   ARG A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 171
      removed outlier: 3.613A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 193
      removed outlier: 3.572A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.627A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 220 through 231
      removed outlier: 3.715A  pdb=" N   HIS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE A 230 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.817A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.558A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.917A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 3.709A  pdb=" N   ALA A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA A 384 " --> pdb=" O   GLN A 380 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 411
      removed outlier: 3.859A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
      removed outlier: 3.966A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 4.392A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.664A  pdb=" N   TRP A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 515
    Processing helix  chain 'A' and resid 516 through 531
      removed outlier: 3.760A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.800A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.682A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.645A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS A 596 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASP A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'E' and resid 338 through 343
    Processing helix  chain 'E' and resid 365 through 370
      removed outlier: 3.606A  pdb=" N   TYR E 369 " --> pdb=" O   TYR E 365 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASN E 370 " --> pdb=" O   SER E 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 365 through 370'
    Processing helix  chain 'E' and resid 385 through 390
      removed outlier: 3.554A  pdb=" N   ASN E 388 " --> pdb=" O   THR E 385 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU E 390 " --> pdb=" O   LEU E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 404 through 408
      removed outlier: 3.788A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 438 through 443
    Processing helix  chain 'E' and resid 502 through 506
      removed outlier: 3.653A  pdb=" N   GLN E 506 " --> pdb=" O   VAL E 503 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 81 through 85
      removed outlier: 3.760A  pdb=" N   GLU L  85 " --> pdb=" O   ALA L  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.635A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.817A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE E 402 " --> pdb=" O   TYR E 508 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   CYS E 432 " --> pdb=" O   LEU E 513 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362
      removed outlier: 6.917A  pdb=" N   CYS E 361 " --> pdb=" O   CYS E 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7
      removed outlier: 4.157A  pdb=" N   VAL H  21 " --> pdb=" O   MET H  82 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR H  79 " --> pdb=" O   ASP H  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 13
      removed outlier: 3.568A  pdb=" N   VAL H  38 " --> pdb=" O   TYR H  96 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE H  35 " --> pdb=" O   GLY H  51 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   GLY H  51 " --> pdb=" O   ILE H  35 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   TRP H  37 " --> pdb=" O   MET H  49 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12
    Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12
      removed outlier: 3.794A  pdb=" N   GLY L  99 " --> pdb=" O   ASP L  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 17 through 21
      removed outlier: 3.612A  pdb=" N   SER L  74 " --> pdb=" O   SER L  67 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    866 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: 2.43

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2374
        1.33 -     1.45: 1789
        1.45 -     1.58: 4226
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 8455
  Sorted by residual:
  bond pdb=" C   GLY A 319 "
       pdb=" N   LEU A 320 "
    ideal  model  delta    sigma   weight residual
    1.330  1.362 -0.032 1.37e-02 5.33e+03 5.36e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.64e+00
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.36e+00
  bond pdb=" CB  MET A 579 "
       pdb=" CG  MET A 579 "
    ideal  model  delta    sigma   weight residual
    1.520  1.467  0.053 3.00e-02 1.11e+03 3.13e+00
  bond pdb=" C1  NAG A 704 "
       pdb=" O5  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.13e+00
  ... (remaining 8450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 11077
        2.29 -     4.57: 355
        4.57 -     6.86: 40
        6.86 -     9.15: 15
        9.15 -    11.43: 4
  Bond angle restraints: 11491
  Sorted by residual:
  angle pdb=" N   ASP H 113 "
        pdb=" CA  ASP H 113 "
        pdb=" C   ASP H 113 "
      ideal   model   delta    sigma   weight residual
     114.16  102.73   11.43 1.48e+00 4.57e-01 5.97e+01
  angle pdb=" C   PHE H 112 "
        pdb=" N   ASP H 113 "
        pdb=" CA  ASP H 113 "
      ideal   model   delta    sigma   weight residual
     120.70  131.47  -10.77 1.63e+00 3.76e-01 4.36e+01
  angle pdb=" N   ASN E 440 "
        pdb=" CA  ASN E 440 "
        pdb=" CB  ASN E 440 "
      ideal   model   delta    sigma   weight residual
     110.13  102.65    7.48 1.48e+00 4.57e-01 2.56e+01
  angle pdb=" C   GLY L  52 "
        pdb=" N   ASN L  53 "
        pdb=" CA  ASN L  53 "
      ideal   model   delta    sigma   weight residual
     121.54  130.87   -9.33 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" C   ILE L  50 "
        pdb=" N   TYR L  51 "
        pdb=" CA  TYR L  51 "
      ideal   model   delta    sigma   weight residual
     120.94  128.52   -7.58 1.57e+00 4.06e-01 2.33e+01
  ... (remaining 11486 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.43: 4892
       20.43 -    40.85: 119
       40.85 -    61.28: 23
       61.28 -    81.71: 4
       81.71 -   102.13: 8
  Dihedral angle restraints: 5046
    sinusoidal: 2058
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" CA  PHE H 112 "
           pdb=" C   PHE H 112 "
           pdb=" N   ASP H 113 "
           pdb=" CA  ASP H 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.40   52.60     0      5.00e+00 4.00e-02 1.11e+02
  dihedral pdb=" CA  LEU L  48 "
           pdb=" C   LEU L  48 "
           pdb=" N   LEU L  49 "
           pdb=" CA  LEU L  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.43   29.57     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  ALA H 108 "
           pdb=" C   ALA H 108 "
           pdb=" N   ALA H 109 "
           pdb=" CA  ALA H 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.19  -27.81     0      5.00e+00 4.00e-02 3.09e+01
  ... (remaining 5043 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1030
       0.073 -    0.145: 173
       0.145 -    0.218: 16
       0.218 -    0.291: 4
       0.291 -    0.363: 2
  Chirality restraints: 1225
  Sorted by residual:
  chirality pdb=" CG  LEU A 558 "
            pdb=" CB  LEU A 558 "
            pdb=" CD1 LEU A 558 "
            pdb=" CD2 LEU A 558 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.23   -0.36 2.00e-01 2.50e+01 3.30e+00
  chirality pdb=" CB  ILE H  35 "
            pdb=" CA  ILE H  35 "
            pdb=" CG1 ILE H  35 "
            pdb=" CG2 ILE H  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CG  LEU A 333 "
            pdb=" CB  LEU A 333 "
            pdb=" CD1 LEU A 333 "
            pdb=" CD2 LEU A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1222 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN E 440 "    0.018 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" CG  ASN E 440 "   -0.064 2.00e-02 2.50e+03
        pdb=" OD1 ASN E 440 "    0.024 2.00e-02 2.50e+03
        pdb=" ND2 ASN E 440 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 497 "    0.019 2.00e-02 2.50e+03   2.14e-02 8.02e+00
        pdb=" CG  PHE E 497 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 497 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 497 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 497 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 497 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 497 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "    0.046 5.00e-02 4.00e+02   6.88e-02 7.57e+00
        pdb=" N   PRO A 583 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        0.77 -     1.59: 5
        1.59 -     2.42: 43
        2.42 -     3.25: 8163
        3.25 -     4.07: 21544
        4.07 -     4.90: 39724
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 69479
  Sorted by model distance:
  nonbonded pdb=" C   LEU H   4 "
            pdb=" OG  SER H  26 "
     model   vdw
     0.766 3.270
  nonbonded pdb=" N   LEU H   5 "
            pdb=" OG  SER H  26 "
     model   vdw
     0.943 3.120
  nonbonded pdb=" CA  LEU H   5 "
            pdb=" CB  SER H  26 "
     model   vdw
     1.145 3.870
  nonbonded pdb=" O   LEU H   4 "
            pdb=" OG  SER H  26 "
     model   vdw
     1.387 3.040
  nonbonded pdb=" O   THR H  29 "
            pdb=" NH2 ARG H  99 "
     model   vdw
     1.521 3.120
  ... (remaining 69474 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             2.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.090
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.060
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
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      :  0.007   0.062   8455  Z= 0.430
  Angle     :  1.002  11.433  11491  Z= 0.575
  Chirality :  0.057   0.363   1225
  Planarity :  0.007   0.069   1484
  Dihedral  : 11.251 102.133   3117
  Min Nonbonded Distance : 0.766

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.99 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.25 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -4.20 (0.21), residues: 1021
  helix: -3.94 (0.14), residues: 368
  sheet: -2.19 (0.43), residues: 137
  loop : -1.95 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.004   TRP A 302 
 HIS   0.014   0.002   HIS A 401 
 PHE   0.049   0.004   PHE E 497 
 TYR   0.037   0.004   TYR E 495 
 ARG   0.019   0.002   ARG A 169 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7292 (mtp180)
REVERT: A  255 TYR cc_start: 0.7745 (m-80) cc_final: 0.7154 (m-10)
REVERT: E  385 THR cc_start: 0.8294 (p) cc_final: 0.8018 (t)
REVERT: E  444 LYS cc_start: 0.8917 (pttt) cc_final: 0.8090 (mttm)
REVERT: E  445 VAL cc_start: 0.8876 (t) cc_final: 0.8674 (p)
REVERT: E  470 THR cc_start: 0.8507 (p) cc_final: 0.8304 (p)
REVERT: H   48 TRP cc_start: 0.8687 (t60) cc_final: 0.8091 (t60)
REVERT: L  108 LEU cc_start: 0.8540 (tt) cc_final: 0.7894 (tp)
REVERT: L  109 THR cc_start: 0.8894 (p) cc_final: 0.8677 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.2173
  time to fit residues: 65.7578
Evaluate side-chains
  132 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0050
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN
A 239 HIS
A 305 GLN
A 540 HIS
A 599 ASN
E 498 GLN
E 501 ASN
H  40 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.121303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.099146 restraints weight = 28521.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.104858 restraints weight = 11433.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.108099 restraints weight = 5434.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3798 r_free = 0.3798    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8455  Z= 0.214
  Angle     :  0.707   9.123  11491  Z= 0.373
  Chirality :  0.046   0.189   1225
  Planarity :  0.006   0.062   1484
  Dihedral  :  8.364  63.762   1226
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.95 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.56 (0.24), residues: 1021
  helix: -2.13 (0.21), residues: 392
  sheet: -1.54 (0.42), residues: 142
  loop : -1.20 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 302 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.031   0.002   PHE A 603 
 TYR   0.024   0.002   TYR E 495 
 ARG   0.007   0.001   ARG E 454 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.7685 (m-80) cc_final: 0.7079 (m-10)
REVERT: A  366 MET cc_start: 0.8136 (tpp) cc_final: 0.7790 (tpp)
REVERT: A  375 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7977 (mm-30)
REVERT: A  484 ILE cc_start: 0.8006 (mm) cc_final: 0.7670 (mm)
REVERT: E  385 THR cc_start: 0.8524 (p) cc_final: 0.8242 (t)
REVERT: E  444 LYS cc_start: 0.9100 (pttt) cc_final: 0.8115 (mttm)
REVERT: E  498 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8126 (mt0)
REVERT: E  506 GLN cc_start: 0.7666 (mt0) cc_final: 0.7317 (mt0)
REVERT: E  507 PRO cc_start: 0.8751 (Cg_exo) cc_final: 0.8551 (Cg_endo)
REVERT: H   48 TRP cc_start: 0.8633 (t60) cc_final: 0.7899 (t60)
REVERT: L   34 ASP cc_start: 0.7492 (m-30) cc_final: 0.7182 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 177
  average time/residue: 0.1842
  time to fit residues: 45.7976
Evaluate side-chains
  130 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain E residue  498 GLN
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:    0.0470
   chunk 83 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.2084

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

Flipped N/Q/H residues before XYZ refinement:
A 540 HIS
A 599 ASN
E 498 GLN
H   7 GLN
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.110795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.087415 restraints weight = 28701.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.092458 restraints weight = 11949.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.096263 restraints weight = 5789.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   8455  Z= 0.366
  Angle     :  0.759   9.421  11491  Z= 0.391
  Chirality :  0.052   0.616   1225
  Planarity :  0.005   0.061   1484
  Dihedral  :  7.280  55.927   1226
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  9.31 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.88 (0.25), residues: 1021
  helix: -1.19 (0.23), residues: 395
  sheet: -1.58 (0.41), residues: 142
  loop : -1.03 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 436 
 HIS   0.005   0.001   HIS L  36 
 PHE   0.032   0.003   PHE H 112 
 TYR   0.029   0.002   TYR E 453 
 ARG   0.007   0.001   ARG E 454 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.7801 (m-80) cc_final: 0.7175 (m-10)
REVERT: A  323 MET cc_start: 0.8027 (tpp) cc_final: 0.7089 (mpp)
REVERT: A  366 MET cc_start: 0.8355 (tpp) cc_final: 0.7764 (tpp)
REVERT: E  385 THR cc_start: 0.8714 (p) cc_final: 0.8459 (t)
REVERT: E  430 THR cc_start: 0.8312 (p) cc_final: 0.8108 (t)
REVERT: E  444 LYS cc_start: 0.9177 (pttt) cc_final: 0.7996 (mttm)
REVERT: E  470 THR cc_start: 0.8641 (p) cc_final: 0.8401 (p)
  outliers start: 19
  outliers final: 17
  residues processed: 151
  average time/residue: 0.2161
  time to fit residues: 47.2646
Evaluate side-chains
  136 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  498 GLN
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 91 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 12 optimal weight:   40.0000
   chunk 59 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 58 optimal weight:    8.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 HIS
** L  91 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 = 0.3933 r_free = 0.3933 target = 0.114519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.092382 restraints weight = 19049.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.096320 restraints weight = 8714.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.098925 restraints weight = 5258.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8455  Z= 0.223
  Angle     :  0.681   9.451  11491  Z= 0.348
  Chirality :  0.045   0.213   1225
  Planarity :  0.004   0.043   1484
  Dihedral  :  7.475  74.424   1226
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.44 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.29 (0.26), residues: 1021
  helix: -0.53 (0.25), residues: 398
  sheet: -1.37 (0.42), residues: 148
  loop : -0.81 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 302 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.035   0.002   PHE H 112 
 TYR   0.028   0.002   TYR A 521 
 ARG   0.006   0.001   ARG E 454 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 LEU cc_start: 0.8642 (tp) cc_final: 0.8423 (tp)
REVERT: A  255 TYR cc_start: 0.7677 (m-80) cc_final: 0.7067 (m-10)
REVERT: A  323 MET cc_start: 0.7878 (tpp) cc_final: 0.7122 (mpp)
REVERT: A  366 MET cc_start: 0.8306 (tpp) cc_final: 0.7674 (tpp)
REVERT: E  385 THR cc_start: 0.8554 (p) cc_final: 0.8327 (t)
REVERT: E  444 LYS cc_start: 0.9148 (pttt) cc_final: 0.7917 (mttm)
REVERT: E  470 THR cc_start: 0.8347 (p) cc_final: 0.8041 (p)
REVERT: E  506 GLN cc_start: 0.7724 (mt0) cc_final: 0.7268 (mt0)
REVERT: L   34 ASP cc_start: 0.7369 (m-30) cc_final: 0.6996 (m-30)
REVERT: L   80 LEU cc_start: 0.9485 (mt) cc_final: 0.9185 (mt)
REVERT: L   81 GLN cc_start: 0.8612 (mt0) cc_final: 0.8260 (mp10)
  outliers start: 17
  outliers final: 13
  residues processed: 150
  average time/residue: 0.1661
  time to fit residues: 36.6012
Evaluate side-chains
  132 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 74 optimal weight:    0.5980
   chunk 80 optimal weight:   30.0000
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 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 = 0.4008 r_free = 0.4008 target = 0.119861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.098572 restraints weight = 29593.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.103089 restraints weight = 12523.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.104759 restraints weight = 7004.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3751 r_free = 0.3751    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3751 r_free = 0.3751    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8455  Z= 0.237
  Angle     :  0.685  11.838  11491  Z= 0.346
  Chirality :  0.045   0.195   1225
  Planarity :  0.004   0.043   1484
  Dihedral  :  7.590  84.131   1226
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.35 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.03 (0.27), residues: 1021
  helix: -0.24 (0.26), residues: 399
  sheet: -1.20 (0.41), residues: 158
  loop : -0.74 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.035   0.002   PHE H 112 
 TYR   0.026   0.002   TYR A 521 
 ARG   0.005   0.001   ARG E 454 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8284 (tt)
REVERT: A  127 TYR cc_start: 0.8277 (t80) cc_final: 0.7987 (t80)
REVERT: A  222 LEU cc_start: 0.8762 (tp) cc_final: 0.8554 (tp)
REVERT: A  255 TYR cc_start: 0.7661 (m-80) cc_final: 0.7080 (m-10)
REVERT: A  323 MET cc_start: 0.7758 (tpp) cc_final: 0.7138 (mpp)
REVERT: A  558 LEU cc_start: 0.8656 (mt) cc_final: 0.8429 (mt)
REVERT: E  385 THR cc_start: 0.8624 (p) cc_final: 0.8372 (t)
REVERT: E  444 LYS cc_start: 0.9184 (pttt) cc_final: 0.8029 (mttm)
REVERT: E  470 THR cc_start: 0.8408 (p) cc_final: 0.8162 (p)
REVERT: E  472 ILE cc_start: 0.8601 (mm) cc_final: 0.8389 (mt)
REVERT: H   82 MET cc_start: 0.8537 (tmm) cc_final: 0.8250 (tmm)
REVERT: L   81 GLN cc_start: 0.8539 (mt0) cc_final: 0.8282 (mp10)
  outliers start: 21
  outliers final: 14
  residues processed: 147
  average time/residue: 0.1788
  time to fit residues: 38.2367
Evaluate side-chains
  137 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 40 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   chunk 64 optimal weight:    0.2980
   chunk 71 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   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  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 506 GLN
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.121116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.098139 restraints weight = 35030.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.103420 restraints weight = 13370.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.105266 restraints weight = 6818.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3788 r_free = 0.3788    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3788 r_free = 0.3788    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8455  Z= 0.183
  Angle     :  0.656  10.633  11491  Z= 0.329
  Chirality :  0.044   0.216   1225
  Planarity :  0.004   0.040   1484
  Dihedral  :  7.551  86.617   1226
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.46 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.76 (0.27), residues: 1021
  helix:  0.06 (0.26), residues: 399
  sheet: -1.02 (0.41), residues: 160
  loop : -0.66 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.031   0.002   PHE H 112 
 TYR   0.020   0.001   TYR A 521 
 ARG   0.004   0.001   ARG E 454 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8225 (t80) cc_final: 0.8013 (t80)
REVERT: A  255 TYR cc_start: 0.7678 (m-80) cc_final: 0.7052 (m-10)
REVERT: A  366 MET cc_start: 0.8646 (tpp) cc_final: 0.7997 (tpp)
REVERT: E  385 THR cc_start: 0.8667 (p) cc_final: 0.8420 (t)
REVERT: E  432 CYS cc_start: 0.4996 (m) cc_final: 0.4714 (m)
REVERT: E  444 LYS cc_start: 0.9162 (pttt) cc_final: 0.7962 (mttm)
REVERT: E  472 ILE cc_start: 0.8630 (mm) cc_final: 0.8360 (mt)
REVERT: L   34 ASP cc_start: 0.7429 (m-30) cc_final: 0.7072 (m-30)
REVERT: L   81 GLN cc_start: 0.8569 (mt0) cc_final: 0.8309 (mp10)
REVERT: L   93 TYR cc_start: 0.8144 (t80) cc_final: 0.7666 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 147
  average time/residue: 0.2316
  time to fit residues: 49.8703
Evaluate side-chains
  135 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   41 LEU
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.120263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.096775 restraints weight = 28533.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.101791 restraints weight = 12219.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.106025 restraints weight = 6418.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3805 r_free = 0.3805    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3805 r_free = 0.3805    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8455  Z= 0.194
  Angle     :  0.657  10.339  11491  Z= 0.328
  Chirality :  0.044   0.224   1225
  Planarity :  0.004   0.038   1484
  Dihedral  :  7.586  89.007   1226
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.37 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.55 (0.27), residues: 1021
  helix:  0.19 (0.26), residues: 399
  sheet: -0.79 (0.41), residues: 160
  loop : -0.55 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.039   0.002   PHE H 112 
 TYR   0.019   0.001   TYR A 521 
 ARG   0.006   0.001   ARG H 101 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8219 (tt)
REVERT: A  255 TYR cc_start: 0.7643 (m-80) cc_final: 0.7034 (m-10)
REVERT: A  375 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8042 (mm-30)
REVERT: E  385 THR cc_start: 0.8585 (p) cc_final: 0.8336 (t)
REVERT: E  432 CYS cc_start: 0.5005 (m) cc_final: 0.4708 (m)
REVERT: E  444 LYS cc_start: 0.9176 (pttt) cc_final: 0.7973 (mttm)
REVERT: E  472 ILE cc_start: 0.8586 (mm) cc_final: 0.8371 (mt)
REVERT: E  508 TYR cc_start: 0.8468 (m-80) cc_final: 0.8252 (m-80)
REVERT: L   34 ASP cc_start: 0.7377 (m-30) cc_final: 0.7063 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 151
  average time/residue: 0.1668
  time to fit residues: 36.8793
Evaluate side-chains
  143 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  340 GLU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 26 optimal weight:    0.4980
   chunk 0 optimal weight:    8.9990
   chunk 37 optimal weight:    0.6980
   chunk 73 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0970
   chunk 76 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.120906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.097849 restraints weight = 32584.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.102959 restraints weight = 12909.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.106725 restraints weight = 6618.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3808 r_free = 0.3808    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3808 r_free = 0.3808    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8455  Z= 0.202
  Angle     :  0.679  10.121  11491  Z= 0.337
  Chirality :  0.044   0.225   1225
  Planarity :  0.004   0.037   1484
  Dihedral  :  7.619  90.313   1226
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.26 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.36 (0.27), residues: 1021
  helix:  0.33 (0.27), residues: 399
  sheet: -0.68 (0.41), residues: 162
  loop : -0.43 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.035   0.002   PHE H 112 
 TYR   0.021   0.002   TYR A 521 
 ARG   0.006   0.001   ARG L  56 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8244 (tt)
REVERT: A  255 TYR cc_start: 0.7698 (m-80) cc_final: 0.7091 (m-10)
REVERT: A  375 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8115 (mm-30)
REVERT: E  385 THR cc_start: 0.8634 (p) cc_final: 0.8395 (t)
REVERT: E  432 CYS cc_start: 0.5064 (m) cc_final: 0.4768 (m)
REVERT: E  444 LYS cc_start: 0.9190 (pttt) cc_final: 0.8001 (mttm)
REVERT: E  466 ARG cc_start: 0.8352 (ttm110) cc_final: 0.7650 (ptm160)
REVERT: E  508 TYR cc_start: 0.8460 (m-80) cc_final: 0.8243 (m-80)
REVERT: H   81 TYR cc_start: 0.7804 (m-80) cc_final: 0.7543 (m-80)
REVERT: L   34 ASP cc_start: 0.7423 (m-30) cc_final: 0.7126 (m-30)
  outliers start: 18
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1775
  time to fit residues: 38.9706
Evaluate side-chains
  142 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  340 GLU
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.118191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.095054 restraints weight = 30077.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.099625 restraints weight = 12615.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.103581 restraints weight = 6861.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3768 r_free = 0.3768    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3768 r_free = 0.3768    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.4640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8455  Z= 0.270
  Angle     :  0.710   9.966  11491  Z= 0.356
  Chirality :  0.046   0.233   1225
  Planarity :  0.004   0.043   1484
  Dihedral  :  7.799  92.399   1226
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.05 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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 (0.27), residues: 1021
  helix:  0.29 (0.26), residues: 399
  sheet: -0.86 (0.41), residues: 164
  loop : -0.37 (0.32), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 436 
 HIS   0.003   0.001   HIS L  36 
 PHE   0.031   0.002   PHE A 603 
 TYR   0.023   0.002   TYR A 521 
 ARG   0.008   0.001   ARG L  56 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8314 (tt)
REVERT: A  127 TYR cc_start: 0.8020 (t80) cc_final: 0.7599 (t80)
REVERT: A  255 TYR cc_start: 0.7706 (m-80) cc_final: 0.7135 (m-10)
REVERT: A  375 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7990 (mm-30)
REVERT: E  385 THR cc_start: 0.8644 (p) cc_final: 0.8424 (t)
REVERT: E  432 CYS cc_start: 0.5185 (m) cc_final: 0.4864 (m)
REVERT: E  444 LYS cc_start: 0.9168 (pttt) cc_final: 0.7995 (mttm)
REVERT: E  484 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7835 (mm-30)
REVERT: E  508 TYR cc_start: 0.8492 (m-80) cc_final: 0.8260 (m-80)
  outliers start: 19
  outliers final: 16
  residues processed: 138
  average time/residue: 0.1772
  time to fit residues: 35.7455
Evaluate side-chains
  140 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  340 GLU
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    0.0270
   chunk 63 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 59 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.3642

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.118241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.094559 restraints weight = 27300.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.100153 restraints weight = 11597.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.103827 restraints weight = 5639.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3775
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3775 r_free = 0.3775    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3774 r_free = 0.3774    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8455  Z= 0.258
  Angle     :  0.718  12.581  11491  Z= 0.358
  Chirality :  0.046   0.228   1225
  Planarity :  0.004   0.048   1484
  Dihedral  :  7.793  92.029   1226
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.94 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.38 (0.28), residues: 1021
  helix:  0.30 (0.26), residues: 400
  sheet: -0.89 (0.41), residues: 164
  loop : -0.34 (0.32), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 436 
 HIS   0.003   0.001   HIS L  36 
 PHE   0.039   0.002   PHE H 112 
 TYR   0.024   0.002   TYR A 521 
 ARG   0.007   0.001   ARG H  99 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8302 (tt)
REVERT: A  127 TYR cc_start: 0.8032 (t80) cc_final: 0.7613 (t80)
REVERT: A  375 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8092 (mm-30)
REVERT: E  385 THR cc_start: 0.8619 (p) cc_final: 0.8404 (t)
REVERT: E  432 CYS cc_start: 0.5180 (m) cc_final: 0.4854 (m)
REVERT: E  444 LYS cc_start: 0.9154 (pttt) cc_final: 0.7977 (mttm)
REVERT: E  486 PHE cc_start: 0.7656 (t80) cc_final: 0.7317 (t80)
REVERT: E  508 TYR cc_start: 0.8483 (m-80) cc_final: 0.8225 (m-80)
  outliers start: 19
  outliers final: 17
  residues processed: 136
  average time/residue: 0.1641
  time to fit residues: 32.8728
Evaluate side-chains
  139 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  340 GLU
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  399 SER
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain H residue   19 VAL
Chi-restraints excluded: chain H residue   35 ILE
Chi-restraints excluded: chain H residue   94 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 26 optimal weight:    0.2980
   chunk 89 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0370
   chunk 51 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.121503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.098272 restraints weight = 31288.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.103825 restraints weight = 12289.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.107551 restraints weight = 5911.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3826 r_free = 0.3826    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3826 r_free = 0.3826    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.4857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8455  Z= 0.197
  Angle     :  0.703  12.288  11491  Z= 0.349
  Chirality :  0.045   0.215   1225
  Planarity :  0.004   0.039   1484
  Dihedral  :  7.585  90.101   1226
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.62 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.27 (0.28), residues: 1021
  helix:  0.33 (0.27), residues: 396
  sheet: -0.63 (0.42), residues: 162
  loop : -0.30 (0.32), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 478 
 HIS   0.003   0.001   HIS L  36 
 PHE   0.037   0.002   PHE H 112 
 TYR   0.023   0.001   TYR A 521 
 ARG   0.005   0.001   ARG H 101 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3788.94 seconds
wall clock time: 67 minutes 34.60 seconds (4054.60 seconds total)